# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to # command:# Making conformation for sequence T0339 numbered 1 through 416 Created new target T0339 from T0339.a2m # command:CPU_time= 6.255 sec, elapsed time= 6.274 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t3iA/T0339-1t3iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t3iA expands to /projects/compbio/data/pdb/1t3i.pdb.gz 1t3iA:# T0339 read from 1t3iA/T0339-1t3iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t3iA read from 1t3iA/T0339-1t3iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1t3iA to template set # found chain 1t3iA in template set Warning: unaligning (T0339)P33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1t3iA)G62 Warning: unaligning (T0339)P36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t3iA)G62 Warning: unaligning (T0339)E414 because last residue in template chain is (1t3iA)S414 T0339 2 :RKVYMDYNATTPLEPEVIQAMTKAMWEAWGN 1t3iA 28 :PLVYLDNAATSQKPRAVLEKLMHYYENDNAN # choosing archetypes in rotamer library T0339 37 :YSAGRKAKDIINAARESLAKMIGGK 1t3iA 64 :HQLSVRATDAYEAVRNKVAKFINAR T0339 62 :PQDIIFTSGGTESNNLVIHSVVKHF 1t3iA 90 :PREIVYTRNATEAINLVAYSWGMNN T0339 91 :TSKGH 1t3iA 115 :LKAGD T0339 109 :HFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSK 1t3iA 120 :EIITTVMEHHSNLVPWQMVAAKTGAVLKFVQLDE T0339 144 :SGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1t3iA 154 :QESFDLEHFKTLLSEKTKLVTVVHISNTLGCVNPAEEIAQ T0339 188 :LNQER 1t3iA 194 :LAHQA T0339 199 :PILVHTDAAQALGKQRVDVEDLGVDFLTIVGHK 1t3iA 199 :GAKVLVDACQSAPHYPLDVQLIDCDWLVASGHK T0339 232 :FYGPRIGALYIR 1t3iA 233 :CAPTGIGFLYGK T0339 244 :GLGEF 1t3iA 246 :EILEA T0339 251 :LYPMLFGGG 1t3iA 251 :MPPFFGGGE T0339 260 :QERNFRPGTENTPMIAGLGKAAELVTQ 1t3iA 274 :LPHKFEAGTPAIAEAIALGAAVDYLTD T0339 287 :NCEAYEAHMRDVRDYLEERLEA 1t3iA 302 :GMENIHNYEVELTHYLWQGLGQ T0339 312 :QKRIHLNSQFPGTQRLPNTCNFSIRG 1t3iA 324 :IPQLRLYGPNPKHGDRAALASFNVAG T0339 340 :LQGHVVLAQCRV 1t3iA 350 :LHASDVATMVDQ T0339 352 :LMASVGAACH 1t3iA 364 :IAIRSGHHCT T0339 362 :SDH 1t3iA 380 :FDA T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQAVAQL 1t3iA 383 :SGSARASLYFYNTKEEIDLFLQSLQATIRFF Number of specific fragments extracted= 18 number of extra gaps= 0 total=18 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t3iA/T0339-1t3iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1t3iA/T0339-1t3iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t3iA read from 1t3iA/T0339-1t3iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t3iA in template set Warning: unaligning (T0339)S35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t3iA)G62 Warning: unaligning (T0339)E414 because last residue in template chain is (1t3iA)S414 T0339 2 :RKVYMDYNATTPLEPEVIQAMTKAMWEAWGN 1t3iA 28 :PLVYLDNAATSQKPRAVLEKLMHYYENDNAN T0339 36 :PYSAGRKAKDIINAARESLAKMIGG 1t3iA 63 :AHQLSVRATDAYEAVRNKVAKFINA T0339 61 :KPQDIIFTSGGTESNNLVIHSVVKHFH 1t3iA 89 :SPREIVYTRNATEAINLVAYSWGMNNL T0339 105 :GAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSK 1t3iA 116 :KAGDEIITTVMEHHSNLVPWQMVAAKTGAVLKFVQLDE T0339 144 :SGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKALN 1t3iA 154 :QESFDLEHFKTLLSEKTKLVTVVHISNTLGCVNPAEEIAQLAHQAG T0339 200 :ILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFYGP 1t3iA 200 :AKVLVDACQSAPHYPLDVQLIDCDWLVASGHKMCAP T0339 236 :RIGALYIRG 1t3iA 237 :GIGFLYGKE T0339 246 :GEFTPLYPMLFGGGQ 1t3iA 246 :EILEAMPPFFGGGEM T0339 261 :ERNFRPGTENTPMIAGLGKAAELVTQ 1t3iA 275 :PHKFEAGTPAIAEAIALGAAVDYLTD T0339 287 :NCEAYEAHMRDVRDYLEERLEAEFG 1t3iA 302 :GMENIHNYEVELTHYLWQGLGQIPQ T0339 315 :IHLNSQFPGTQRLPNTCNFSIRG 1t3iA 327 :LRLYGPNPKHGDRAALASFNVAG T0339 340 :LQGHVVLAQCRV 1t3iA 350 :LHASDVATMVDQ T0339 352 :LMASVGAACH 1t3iA 364 :IAIRSGHHCT T0339 369 :SPVLLSYGVP 1t3iA 374 :QPLHRLFDAS T0339 384 :NALRLSVGRSTTRAEVDLVVQDLKQAVAQL 1t3iA 384 :GSARASLYFYNTKEEIDLFLQSLQATIRFF Number of specific fragments extracted= 15 number of extra gaps= 0 total=33 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t3iA/T0339-1t3iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1t3iA/T0339-1t3iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t3iA read from 1t3iA/T0339-1t3iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t3iA in template set Warning: unaligning (T0339)P33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1t3iA)G62 Warning: unaligning (T0339)S35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t3iA)G62 Warning: unaligning (T0339)E414 because last residue in template chain is (1t3iA)S414 T0339 3 :KVYMDYNATTPLEPEVIQAMTKAMWEAWGN 1t3iA 29 :LVYLDNAATSQKPRAVLEKLMHYYENDNAN T0339 36 :PYSAGRKAKDIINAARESLAKMIGG 1t3iA 63 :AHQLSVRATDAYEAVRNKVAKFINA T0339 61 :KPQDIIFTSGGTESNNLVIHSV 1t3iA 89 :SPREIVYTRNATEAINLVAYSW T0339 100 :HSPVKGAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVS 1t3iA 111 :GMNNLKAGDEIITTVMEHHSNLVPWQMVAAKTGAVLKFVQLD T0339 143 :VSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKA 1t3iA 153 :EQESFDLEHFKTLLSEKTKLVTVVHISNTLGCVNPAEEIAQLAHQ T0339 198 :PPILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFYGPR 1t3iA 198 :AGAKVLVDACQSAPHYPLDVQLIDCDWLVASGHKMCAPT T0339 237 :IGALYIRGLGEFTPLYPMLFGGGQ 1t3iA 238 :IGFLYGKEEILEAMPPFFGGGEMI T0339 261 :ERNFRPGTENTPMIAGLGKAAELVT 1t3iA 275 :PHKFEAGTPAIAEAIALGAAVDYLT T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1t3iA 301 :LGMENIHNYEVELTHYLWQGLGQIPQLRLYG T0339 320 :QFPGTQRLPNTCNFSIRGPRLQGHVVLAQCRVLMASVGAACHSDHG 1t3iA 332 :PNPKHGDRAALASFNVAGLHASDVATMVDQDGIAIRSGHHCTQPLH T0339 378 :PFDVARNALRLSVGRSTTRAEVDLVVQDLKQAVAQL 1t3iA 378 :RLFDASGSARASLYFYNTKEEIDLFLQSLQATIRFF Number of specific fragments extracted= 11 number of extra gaps= 0 total=44 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jf9A/T0339-1jf9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jf9A expands to /projects/compbio/data/pdb/1jf9.pdb.gz 1jf9A:# T0339 read from 1jf9A/T0339-1jf9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jf9A read from 1jf9A/T0339-1jf9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jf9A to template set # found chain 1jf9A in template set Warning: unaligning (T0339)P33 because of BadResidue code BAD_PEPTIDE in next template residue (1jf9A)H55 Warning: unaligning (T0339)S34 because of BadResidue code BAD_PEPTIDE at template residue (1jf9A)H55 Warning: unaligning (T0339)Q260 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1jf9A)P271 Warning: unaligning (T0339)E261 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1jf9A)P271 T0339 2 :RKVYMDYNATTPLEPEVIQAMTKAMWEAWGN 1jf9A 23 :PLAYLDSAASAQKPSQVIDAEAEFYRHGYAA T0339 35 :SP 1jf9A 56 :RG T0339 37 :YSAGRKAKDIINAARESLAKMIGGK 1jf9A 59 :HTLSAQATEKMENVRKRASLFINAR T0339 62 :PQDIIFTSGGTESNNLVIHSVVKHF 1jf9A 85 :AEELVFVRGTTEGINLVANSWGNSN T0339 91 :TSKGH 1jf9A 110 :VRAGD T0339 109 :HFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSK 1jf9A 115 :NIIISQMEHHANIVPWQMLCARVGAELRVIPLNP T0339 144 :SGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1jf9A 149 :DGTLQLETLPTLFDEKTRLLAITHVSNVLGTENPLAEMIT T0339 188 :LNQER 1jf9A 189 :LAHQH T0339 199 :PILVHTDAAQALGKQRVDVEDLGVDFLTIVGHK 1jf9A 194 :GAKVLVDGAQAVMHHPVDVQALDCDFYVFSGHK T0339 232 :FYGPRIGALYIR 1jf9A 228 :YGPTGIGILYVK T0339 244 :GLGEFTP 1jf9A 241 :ALLQEMP T0339 253 :PMLFGGG 1jf9A 248 :PWEGGGS T0339 262 :RNFRPGTENTPMIAGLGKAAELVTQ 1jf9A 272 :WRFEAGTPNTGGIIGLGAALEYVSA T0339 287 :NCEAYEAHMRDVRDYLEERLEA 1jf9A 298 :GLNNIAEYEQNLMHYALSQLES T0339 312 :QKRIHLNSQ 1jf9A 320 :VPDLTLYGP T0339 322 :PGT 1jf9A 329 :QNR T0339 328 :PNTCNFSIRG 1jf9A 332 :LGVIAFNLGK T0339 340 :LQGHVVLAQCRV 1jf9A 342 :HHAYDVGSFLDN T0339 352 :LMASVGAACH 1jf9A 356 :IAVRTGHHCA T0339 362 :SDH 1jf9A 372 :YNV T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQAVAQL 1jf9A 375 :PAMCRASLAMYNTHEEVDRLVTGLQRIHRLL Number of specific fragments extracted= 21 number of extra gaps= 2 total=65 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jf9A/T0339-1jf9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1jf9A/T0339-1jf9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jf9A read from 1jf9A/T0339-1jf9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jf9A in template set Warning: unaligning (T0339)P33 because of BadResidue code BAD_PEPTIDE at template residue (1jf9A)H55 Warning: unaligning (T0339)E261 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1jf9A)P271 T0339 2 :RKVYMDYNATTPLEPEVIQAMTKAMWEAWGN 1jf9A 23 :PLAYLDSAASAQKPSQVIDAEAEFYRHGYAA T0339 34 :SSPYSAGRKAKDIINAARESLAKMIGG 1jf9A 56 :RGIHTLSAQATEKMENVRKRASLFINA T0339 61 :KPQDIIFTSGGTESNNLVIHSVVKHFH 1jf9A 84 :SAEELVFVRGTTEGINLVANSWGNSNV T0339 105 :GAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSK 1jf9A 111 :RAGDNIIISQMEHHANIVPWQMLCARVGAELRVIPLNP T0339 144 :SGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKALN 1jf9A 149 :DGTLQLETLPTLFDEKTRLLAITHVSNVLGTENPLAEMITLAHQHG T0339 200 :ILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFYGP 1jf9A 195 :AKVLVDGAQAVMHHPVDVQALDCDFYVFSGHKLYGP T0339 236 :RIGALYIRG 1jf9A 232 :GIGILYVKE T0339 246 :GEFTPLYPMLFGGGQ 1jf9A 241 :ALLQEMPPWEGGGSM T0339 262 :RNFRPGTENTPMIAGLGKAAELVTQ 1jf9A 272 :WRFEAGTPNTGGIIGLGAALEYVSA T0339 287 :NCEAYEAHMRDVRDYLEERLEAEFG 1jf9A 298 :GLNNIAEYEQNLMHYALSQLESVPD T0339 315 :IHLNSQ 1jf9A 323 :LTLYGP T0339 324 :TQRLP 1jf9A 329 :QNRLG T0339 330 :TCNFSIRG 1jf9A 334 :VIAFNLGK T0339 340 :LQGHVVLAQCRV 1jf9A 342 :HHAYDVGSFLDN T0339 352 :LMASVGAACH 1jf9A 356 :IAVRTGHHCA T0339 369 :SPVLLSYGVPF 1jf9A 366 :MPLMAYYNVPA T0339 385 :ALRLSVGRSTTRAEVDLVVQDLKQAVAQL 1jf9A 377 :MCRASLAMYNTHEEVDRLVTGLQRIHRLL Number of specific fragments extracted= 17 number of extra gaps= 2 total=82 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jf9A/T0339-1jf9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1jf9A/T0339-1jf9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jf9A read from 1jf9A/T0339-1jf9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jf9A in template set Warning: unaligning (T0339)P33 because of BadResidue code BAD_PEPTIDE in next template residue (1jf9A)H55 Warning: unaligning (T0339)S34 because of BadResidue code BAD_PEPTIDE at template residue (1jf9A)H55 Warning: unaligning (T0339)E261 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1jf9A)P271 T0339 3 :KVYMDYNATTPLEPEVIQAMTKAMWEAWGN 1jf9A 24 :LAYLDSAASAQKPSQVIDAEAEFYRHGYAA T0339 35 :SPYSAGRKAKDIINAARESLAKMIGG 1jf9A 57 :GIHTLSAQATEKMENVRKRASLFINA T0339 61 :KPQDIIFTSGGTESNNLVIHSV 1jf9A 84 :SAEELVFVRGTTEGINLVANSW T0339 100 :HSPVKGAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVS 1jf9A 106 :GNSNVRAGDNIIISQMEHHANIVPWQMLCARVGAELRVIPLN T0339 143 :VSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKA 1jf9A 148 :PDGTLQLETLPTLFDEKTRLLAITHVSNVLGTENPLAEMITLAHQ T0339 198 :PPILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFYGPR 1jf9A 193 :HGAKVLVDGAQAVMHHPVDVQALDCDFYVFSGHKLYGPT T0339 237 :IGALYIRGLGEFTPLYPMLFGGGQ 1jf9A 233 :IGILYVKEALLQEMPPWEGGGSMI T0339 262 :RNFRPGTENTPMIAGLGKAAELVT 1jf9A 272 :WRFEAGTPNTGGIIGLGAALEYVS T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1jf9A 297 :LGLNNIAEYEQNLMHYALSQLESVPDLTLYG T0339 324 :TQRLPNTCNFSIRGPRLQGHVVLAQCRVLMASVGAACHSDHG 1jf9A 328 :PQNRLGVIAFNLGKHHAYDVGSFLDNYGIAVRTGHHCAMPLM T0339 378 :PFDVARNALRLSVGRSTTRAEVDLVVQDLKQAVAQL 1jf9A 370 :AYYNVPAMCRASLAMYNTHEEVDRLVTGLQRIHRLL Number of specific fragments extracted= 11 number of extra gaps= 2 total=93 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eg5A/T0339-1eg5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1eg5A expands to /projects/compbio/data/pdb/1eg5.pdb.gz 1eg5A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0339 read from 1eg5A/T0339-1eg5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eg5A read from 1eg5A/T0339-1eg5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1eg5A to template set # found chain 1eg5A in template set Warning: unaligning (T0339)V356 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1eg5A)H333 Warning: unaligning (T0339)P370 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1eg5A)H333 Warning: unaligning (T0339)L413 because last residue in template chain is (1eg5A)L376 T0339 3 :KVYMDYNATTPLEPEVIQAMTKAMWEAWGNPSSPYSAGRKAKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSVVKHFHAN 1eg5A 2 :RVYFDNNATTRVDDRVLEEMIVFYREKYGNPNSAHGMGIEANLHMEKAREKVAKVLGVSPSEIFFTSCATESINWILKTVAETFEKR T0339 94 :GH 1eg5A 89 :KR T0339 109 :HFITSSVEHDSIRLPLEHL 1eg5A 91 :TIITTPIEHKAVLETMKYL T0339 129 :EEQVAAVTFVPVSK 1eg5A 110 :SMKGFKVKYVPVDS T0339 144 :SGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1eg5A 124 :RGVVKLEELEKLVDEDTFLVSIMAANNEVGTIQPVEDVTR T0339 188 :LNQER 1eg5A 164 :IVKKK T0339 197 :LPPILVHTDAAQALGKQRVDVEDLGVDFLTIVGHK 1eg5A 169 :NKETLVHVDAVQTIGKIPFSLEKLEVDYASFSAHK T0339 232 :FYGPRIGALYIR 1eg5A 205 :HGPKGVGITYIR T0339 247 :EFTPLYPMLFGGGQERNFRPGTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEERLEAE 1eg5A 217 :KGVPIRPLIHGGGQERGLRSGTQNVPGIVGAARAMEIAVEELSEAAKHMEKLRSKLVSGLMNL T0339 314 :RIHLNSQFP 1eg5A 280 :GAHIITPLE T0339 325 :QRLPNTCNFSIRG 1eg5A 289 :ISLPNTLSVSFPN T0339 340 :LQGHVVLAQCRV 1eg5A 302 :IRGSTLQNLLSG T0339 352 :LMAS 1eg5A 316 :IYVS T0339 371 :VLLSYGVPFDVARNALRLSVGRSTTRAEVDLVVQDLKQAVAQ 1eg5A 334 :VLDAMGVDRRIAQGAIRISLCKYNTEEEVDYFLKKIEEILSF Number of specific fragments extracted= 14 number of extra gaps= 0 total=107 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eg5A/T0339-1eg5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1eg5A/T0339-1eg5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eg5A read from 1eg5A/T0339-1eg5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eg5A in template set Warning: unaligning (T0339)V356 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1eg5A)H333 Warning: unaligning (T0339)P370 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1eg5A)H333 Warning: unaligning (T0339)L413 because last residue in template chain is (1eg5A)L376 T0339 3 :KVYMDYNATTPLEPEVIQAMTKAMWEAWGNPSSPYSAGRKAKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSVVKHFH 1eg5A 2 :RVYFDNNATTRVDDRVLEEMIVFYREKYGNPNSAHGMGIEANLHMEKAREKVAKVLGVSPSEIFFTSCATESINWILKTVAETFE T0339 105 :GAKPHFITSSVEHDSIRLPLEHL 1eg5A 87 :KRKRTIITTPIEHKAVLETMKYL T0339 129 :EEQVAAVTFVPVSK 1eg5A 110 :SMKGFKVKYVPVDS T0339 144 :SGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKALN 1eg5A 124 :RGVVKLEELEKLVDEDTFLVSIMAANNEVGTIQPVEDVTRIVKKKN T0339 198 :PPILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFYGP 1eg5A 170 :KETLVHVDAVQTIGKIPFSLEKLEVDYASFSAHKFHGP T0339 236 :RIGALYIRG 1eg5A 209 :GVGITYIRK T0339 246 :G 1eg5A 218 :G T0339 249 :TPLYPMLFGGGQERNFRPGTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEERLEAE 1eg5A 219 :VPIRPLIHGGGQERGLRSGTQNVPGIVGAARAMEIAVEELSEAAKHMEKLRSKLVSGLMNL T0339 311 :G 1eg5A 280 :G T0339 315 :IHLNSQ 1eg5A 281 :AHIITP T0339 323 :GTQRLPNTCNFSIRG 1eg5A 287 :LEISLPNTLSVSFPN T0339 340 :LQGHVVLAQCRV 1eg5A 302 :IRGSTLQNLLSG T0339 352 :LMAS 1eg5A 316 :IYVS T0339 371 :VLLSYGVPFDVARNALRLSVGRSTTRAEVDLVVQDLKQAVAQ 1eg5A 334 :VLDAMGVDRRIAQGAIRISLCKYNTEEEVDYFLKKIEEILSF Number of specific fragments extracted= 14 number of extra gaps= 0 total=121 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eg5A/T0339-1eg5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1eg5A/T0339-1eg5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eg5A read from 1eg5A/T0339-1eg5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eg5A in template set Warning: unaligning (T0339)V356 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1eg5A)H333 Warning: unaligning (T0339)P370 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1eg5A)H333 Warning: unaligning (T0339)L413 because last residue in template chain is (1eg5A)L376 T0339 4 :VYMDYNATTPLEPEVIQAMTKAMWEAWGNPSSPYSAGRKAKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSV 1eg5A 3 :VYFDNNATTRVDDRVLEEMIVFYREKYGNPNSAHGMGIEANLHMEKAREKVAKVLGVSPSEIFFTSCATESINWILKTV T0339 100 :HSPVKGAKPHFITSSVEHDSIRLPLEHL 1eg5A 82 :AETFEKRKRTIITTPIEHKAVLETMKYL T0339 129 :EEQVAAVTFVPVS 1eg5A 110 :SMKGFKVKYVPVD T0339 143 :VSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKA 1eg5A 123 :SRGVVKLEELEKLVDEDTFLVSIMAANNEVGTIQPVEDVTRIVKK T0339 196 :GLPPILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFYGPR 1eg5A 168 :KNKETLVHVDAVQTIGKIPFSLEKLEVDYASFSAHKFHGPK T0339 237 :IGALYIRGLGEFT 1eg5A 210 :VGITYIRKGVPIR T0339 253 :PMLFGGGQERNFRPGTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1eg5A 223 :PLIHGGGQERGLRSGTQNVPGIVGAARAMEIAVEELSEAAKHMEKLRSKLVSGLMNLGAHIITP T0339 323 :GTQRLPNTCNFSIRGPRLQGHVVLAQCRVLMAS 1eg5A 287 :LEISLPNTLSVSFPNIRGSTLQNLLSGYGIYVS T0339 371 :VLLSYGVPFDVARNALRLSVGRSTTRAEVDLVVQDLKQAVAQ 1eg5A 334 :VLDAMGVDRRIAQGAIRISLCKYNTEEEVDYFLKKIEEILSF Number of specific fragments extracted= 9 number of extra gaps= 0 total=130 Will force an alignment to be made, even if fragment is small Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eluA/T0339-1eluA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1eluA expands to /projects/compbio/data/pdb/1elu.pdb.gz 1eluA:# T0339 read from 1eluA/T0339-1eluA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eluA read from 1eluA/T0339-1eluA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1eluA to template set # found chain 1eluA in template set T0339 2 :RKVYMDYNATTPLEPEVIQAMTKAMWEAWGNPSSPYSAGRKAKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSV 1eluA 19 :NKTYFNFGGQGILPTVALEAITAMYGYLQENGPFSIAANQHIQQLIAQLRQALAETFNVDPNTITITDNVTTGCDIVLWGL T0339 90 :QTSKGH 1eluA 100 :DWHQGD T0339 109 :HFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSKV 1eluA 106 :EILLTDCEHPGIIAIVQAIAARFGITYRFFPVAAT T0339 144 :SGQ 1eluA 142 :NQG T0339 148 :E 1eluA 145 :D T0339 149 :VDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1eluA 147 :AAVLANHLGPKTRLVILSHLLWNTGQVLPLAEIMA T0339 188 :LNQER 1eluA 182 :VCRRH T0339 196 :GLP 1eluA 187 :QGN T0339 199 :PILVHTDAAQALGKQRVDVEDLGVDFLTIVGHK 1eluA 191 :PVRVLVDGAQSAGSLPLDFSRLEVDYYAFTGHK T0339 232 :FY 1eluA 225 :FA T0339 234 :GPRIGALYIR 1eluA 228 :PAGVGGLYIH T0339 244 :GLGEFTP 1eluA 239 :DCLGEIN T0339 258 :GG 1eluA 251 :WR T0339 260 :QERNFRPGTENTPMIAGLGKAAELVTQ 1eluA 268 :GGKRFEVATSAYPQYAGLLAALQLHQR T0339 287 :NCEAYEAHMRDVRDYLEERLEA 1eluA 297 :TAEERYQAICQRSEFLWRGLNQ T0339 312 :QKRIHLNSQFPGT 1eluA 319 :LPHVHCLATSAPQ T0339 328 :PNTCNFSIR 1eluA 332 :AGLVSFTVD T0339 337 :G 1eluA 342 :P T0339 340 :LQGHVVLAQCRV 1eluA 343 :LGHRAIVQKLEE T0339 352 :LMASVGAA 1eluA 357 :IYLRTIAD T0339 383 :RNALRLSVGRSTTRAEVDLVVQDL 1eluA 365 :PDCIRACCHYITDEEEINHLLARL Number of specific fragments extracted= 21 number of extra gaps= 0 total=151 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eluA/T0339-1eluA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1eluA/T0339-1eluA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eluA read from 1eluA/T0339-1eluA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eluA in template set T0339 3 :KVYMDYNATTPLEPEVIQAMTKAMWEAWGN 1eluA 20 :KTYFNFGGQGILPTVALEAITAMYGYLQEN T0339 33 :PSS 1eluA 51 :PFS T0339 37 :YSAGRKAKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSV 1eluA 54 :IAANQHIQQLIAQLRQALAETFNVDPNTITITDNVTTGCDIVLWGL T0339 105 :GAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSKVSGQTE 1eluA 102 :HQGDEILLTDCEHPGIIAIVQAIAARFGITYRFFPVAATLNQGD T0339 149 :VDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKALN 1eluA 147 :AAVLANHLGPKTRLVILSHLLWNTGQVLPLAEIMAVCRRHQ T0339 196 :GLPPILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFY 1eluA 188 :GNYPVRVLVDGAQSAGSLPLDFSRLEVDYYAFTGHKWF T0339 234 :GP 1eluA 227 :GP T0339 236 :RIGALYIRG 1eluA 230 :GVGGLYIHG T0339 246 :GEFTPLYPMLFGGGQ 1eluA 239 :DCLGEINPTYVGWRS T0339 261 :ERNFRPGTENTPMIAGLGKAAELVTQ 1eluA 269 :GKRFEVATSAYPQYAGLLAALQLHQR T0339 287 :NCEAYEAHMRDVRDYLEERLEAEFG 1eluA 297 :TAEERYQAICQRSEFLWRGLNQLPH T0339 315 :IHLNSQ 1eluA 322 :VHCLAT T0339 323 :GTQRLP 1eluA 328 :SAPQAG T0339 330 :TCNFSIRGP 1eluA 334 :LVSFTVDSP T0339 340 :LQGHVVLAQCRV 1eluA 343 :LGHRAIVQKLEE T0339 352 :LMASV 1eluA 357 :IYLRT T0339 377 :VPF 1eluA 362 :IAD T0339 383 :RNALRLSVGRSTTRAEVDLVVQDL 1eluA 365 :PDCIRACCHYITDEEEINHLLARL Number of specific fragments extracted= 18 number of extra gaps= 0 total=169 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eluA/T0339-1eluA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1eluA/T0339-1eluA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eluA read from 1eluA/T0339-1eluA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eluA in template set T0339 3 :KVYMDYNATTPLEPEVIQAMTKAMWEAWGNPSSPYSAGRKAKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSV 1eluA 20 :KTYFNFGGQGILPTVALEAITAMYGYLQENGPFSIAANQHIQQLIAQLRQALAETFNVDPNTITITDNVTTGCDIVLWGL T0339 103 :VKGAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSKVSGQTE 1eluA 100 :DWHQGDEILLTDCEHPGIIAIVQAIAARFGITYRFFPVAATLNQGD T0339 149 :VDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKA 1eluA 147 :AAVLANHLGPKTRLVILSHLLWNTGQVLPLAEIMAVCRR T0339 197 :LPPILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFYGPR 1eluA 189 :NYPVRVLVDGAQSAGSLPLDFSRLEVDYYAFTGHKWFAGP T0339 237 :IGALYIRGLGEFTPLYPMLFGGGQ 1eluA 231 :VGGLYIHGDCLGEINPTYVGWRSI T0339 261 :ERNFRPGTENTPMIAGLGKAAELVT 1eluA 269 :GKRFEVATSAYPQYAGLLAALQLHQ T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1eluA 296 :GTAEERYQAICQRSEFLWRGLNQLPHVHCLA T0339 323 :GTQRLPNTCNFSIRG 1eluA 327 :TSAPQAGLVSFTVDS T0339 338 :PRLQGHVVLAQCRVLMASV 1eluA 343 :LGHRAIVQKLEEQRIYLRT T0339 380 :DVARNALRLSVGRSTTRAEVDLVVQDL 1eluA 362 :IADPDCIRACCHYITDEEEINHLLARL Number of specific fragments extracted= 10 number of extra gaps= 0 total=179 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p3wA/T0339-1p3wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1p3wA expands to /projects/compbio/data/pdb/1p3w.pdb.gz 1p3wA:# T0339 read from 1p3wA/T0339-1p3wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p3wA read from 1p3wA/T0339-1p3wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1p3wA to template set # found chain 1p3wA in template set Warning: unaligning (T0339)A359 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p3wA)E334 Warning: unaligning (T0339)Q367 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1p3wA)E334 T0339 1 :ERKVYMDYNATTPLEPEVIQAMT 1p3wA 2 :KLPIYLDYSATTPVDPRVAEKMM T0339 28 :EAW 1p3wA 25 :QFM T0339 31 :GNPSSP 1p3wA 34 :GNPASR T0339 37 :YSAGRKAKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSVVKHF 1p3wA 41 :HRFGWQAEEAVDIARNQIADLVGADPREIVFTSGATESDNLAIKGAANFY T0339 91 :TSKGH 1p3wA 91 :QKKGK T0339 109 :HFITSSVEHDSIRLPLEHL 1p3wA 96 :HIITSKTEHKAVLDTCRQL T0339 129 :EEQVAAVTFVPVSK 1p3wA 115 :EREGFEVTYLAPQR T0339 144 :SGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1p3wA 129 :NGIIDLKELEAAMRDDTILVSIMHVNNEIGVVQDIAAIGE T0339 188 :LNQER 1p3wA 169 :MCRAR T0339 199 :PILVHTDAAQALGKQRVDVEDLGVDFLTIVGHK 1p3wA 174 :GIIYHVDATQSVGKLPIDLSQLKVDLMSFSGHK T0339 232 :FYGPRIGALYIR 1p3wA 208 :YGPKGIGALYVR T0339 244 :G 1p3wA 221 :K T0339 247 :EFTPLYPMLFGGGQERNFRPGTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEERLEA 1p3wA 222 :PRVRIEAQMHGGGHERGMRSGTLPVHQIVGMGEAYRIAKEEMATEMERLRGLRNRLWNGIKD T0339 312 :QKRIHLNSQFP 1p3wA 284 :IEEVYLNGDLE T0339 325 :QRLPNTCNFSIRG 1p3wA 295 :HGAPNILNVSFNY T0339 340 :LQGHVVLAQCRVLMASVGA 1p3wA 308 :VEGESLIMALKDLAVSSGS T0339 368 :PSPVLLSYGVPFDVARNALRLSVGRSTTRAEVDLVVQDLKQAVAQLED 1p3wA 335 :PSYVLRALGLNDELAHSSIRFSLGRFTTEEEIDYTIELVRKSIGRLRD Number of specific fragments extracted= 17 number of extra gaps= 0 total=196 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p3wA/T0339-1p3wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1p3wA/T0339-1p3wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p3wA read from 1p3wA/T0339-1p3wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p3wA in template set Warning: unaligning (T0339)A359 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p3wA)E334 Warning: unaligning (T0339)Q367 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1p3wA)E334 T0339 1 :ERKVYMDYNATTPLEPEVIQAMTKAMW 1p3wA 2 :KLPIYLDYSATTPVDPRVAEKMMQFMT T0339 28 :EAWGNPSSP 1p3wA 31 :GTFGNPASR T0339 37 :YSAGRKAKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSVVKHFH 1p3wA 41 :HRFGWQAEEAVDIARNQIADLVGADPREIVFTSGATESDNLAIKGAANFYQ T0339 105 :GAKPHFITSSVEHDSIRLPLEHL 1p3wA 92 :KKGKHIITSKTEHKAVLDTCRQL T0339 129 :EEQVAAVTFVPVSK 1p3wA 115 :EREGFEVTYLAPQR T0339 144 :SGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKALN 1p3wA 129 :NGIIDLKELEAAMRDDTILVSIMHVNNEIGVVQDIAAIGEMCRARG T0339 200 :ILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFYGP 1p3wA 175 :IIYHVDATQSVGKLPIDLSQLKVDLMSFSGHKIYGP T0339 236 :RIGALYIRG 1p3wA 212 :GIGALYVRR T0339 246 :GEFTPLYPMLFGGGQERNFRPGTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEERLEAEFG 1p3wA 221 :KPRVRIEAQMHGGGHERGMRSGTLPVHQIVGMGEAYRIAKEEMATEMERLRGLRNRLWNGIKDIEE T0339 315 :IHLNSQ 1p3wA 287 :VYLNGD T0339 323 :GTQRLPNTCNFSIRG 1p3wA 293 :LEHGAPNILNVSFNY T0339 340 :LQGHVVLAQCRVLMASVGA 1p3wA 308 :VEGESLIMALKDLAVSSGS T0339 368 :PSPVLLSYGVPFDVARNALRLSVGRSTTRAEVDLVVQDLKQAVAQLEDQ 1p3wA 335 :PSYVLRALGLNDELAHSSIRFSLGRFTTEEEIDYTIELVRKSIGRLRDL Number of specific fragments extracted= 13 number of extra gaps= 0 total=209 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p3wA/T0339-1p3wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1p3wA/T0339-1p3wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p3wA read from 1p3wA/T0339-1p3wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p3wA in template set Warning: unaligning (T0339)A359 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p3wA)E334 Warning: unaligning (T0339)Q367 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1p3wA)E334 T0339 1 :ERKVYMDYNATTPLEPEVIQAMTKAMW 1p3wA 2 :KLPIYLDYSATTPVDPRVAEKMMQFMT T0339 28 :EAWGNPS 1p3wA 31 :GTFGNPA T0339 35 :SPYSAGRKAKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSV 1p3wA 39 :RSHRFGWQAEEAVDIARNQIADLVGADPREIVFTSGATESDNLAIKGA T0339 100 :HSPVKGAKPHFITSSVEHDSIRLPLEHL 1p3wA 87 :ANFYQKKGKHIITSKTEHKAVLDTCRQL T0339 129 :EEQVAAVTFVPVS 1p3wA 115 :EREGFEVTYLAPQ T0339 143 :VSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKA 1p3wA 128 :RNGIIDLKELEAAMRDDTILVSIMHVNNEIGVVQDIAAIGEMCRA T0339 198 :PPILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFYGPR 1p3wA 173 :RGIIYHVDATQSVGKLPIDLSQLKVDLMSFSGHKIYGPK T0339 237 :IGALYIRGLGEFT 1p3wA 213 :IGALYVRRKPRVR T0339 251 :LYPMLFGGGQERNFRPGTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1p3wA 226 :IEAQMHGGGHERGMRSGTLPVHQIVGMGEAYRIAKEEMATEMERLRGLRNRLWNGIKDIEEVYLNG T0339 322 :PGTQRLPNTCNFSIRGPRLQGHVVLAQ 1p3wA 292 :DLEHGAPNILNVSFNYVEGESLIMALK T0339 351 :VLMASVGA 1p3wA 319 :DLAVSSGS T0339 368 :PSPVLLSYGVPFDVARNALRLSVGRSTTRAEVDLVVQDLKQAVAQLED 1p3wA 335 :PSYVLRALGLNDELAHSSIRFSLGRFTTEEEIDYTIELVRKSIGRLRD Number of specific fragments extracted= 12 number of extra gaps= 0 total=221 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qz9A/T0339-1qz9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qz9A expands to /projects/compbio/data/pdb/1qz9.pdb.gz 1qz9A:Skipped atom 19, because occupancy 0.25 <= existing 0.750 in 1qz9A Skipped atom 21, because occupancy 0.250 <= existing 0.750 in 1qz9A Skipped atom 23, because occupancy 0.250 <= existing 0.750 in 1qz9A Skipped atom 770, because occupancy 0.500 <= existing 0.500 in 1qz9A Skipped atom 772, because occupancy 0.500 <= existing 0.500 in 1qz9A Skipped atom 774, because occupancy 0.500 <= existing 0.500 in 1qz9A Skipped atom 776, because occupancy 0.500 <= existing 0.500 in 1qz9A Skipped atom 1084, because occupancy 0.200 <= existing 0.800 in 1qz9A Skipped atom 1086, because occupancy 0.200 <= existing 0.800 in 1qz9A Skipped atom 1088, because occupancy 0.200 <= existing 0.800 in 1qz9A Skipped atom 1090, because occupancy 0.200 <= existing 0.800 in 1qz9A Skipped atom 1092, because occupancy 0.200 <= existing 0.800 in 1qz9A Skipped atom 3613, because occupancy 0.200 <= existing 0.800 in 1qz9A Skipped atom 3882, because occupancy 0.250 <= existing 0.750 in 1qz9A Skipped atom 5300, because occupancy 0.500 <= existing 0.500 in 1qz9A Skipped atom 5302, because occupancy 0.500 <= existing 0.500 in 1qz9A Skipped atom 5304, because occupancy 0.500 <= existing 0.500 in 1qz9A Skipped atom 5306, because occupancy 0.500 <= existing 0.500 in 1qz9A Skipped atom 5391, because occupancy 0.300 <= existing 0.700 in 1qz9A Skipped atom 5393, because occupancy 0.300 <= existing 0.700 in 1qz9A Skipped atom 5395, because occupancy 0.300 <= existing 0.700 in 1qz9A Skipped atom 5397, because occupancy 0.300 <= existing 0.700 in 1qz9A Skipped atom 5399, because occupancy 0.300 <= existing 0.700 in 1qz9A Skipped atom 5475, because occupancy 0.500 <= existing 0.500 in 1qz9A Skipped atom 5477, because occupancy 0.500 <= existing 0.500 in 1qz9A Skipped atom 5479, because occupancy 0.500 <= existing 0.500 in 1qz9A Skipped atom 5481, because occupancy 0.500 <= existing 0.500 in 1qz9A Skipped atom 5483, because occupancy 0.500 <= existing 0.500 in 1qz9A # T0339 read from 1qz9A/T0339-1qz9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qz9A read from 1qz9A/T0339-1qz9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qz9A to template set # found chain 1qz9A in template set Warning: unaligning (T0339)V132 because of BadResidue code BAD_PEPTIDE at template residue (1qz9A)G146 T0339 1 :ERKVYMDYNATTPLEPEVIQAMTKAMWEAWGNPSSPYSAGRKAKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSVVKHFHAN 1qz9A 27 :EGVIYLDGNSLGARPVAALARAQAVIAEEWGNGLIRSWNSAGWRDLSERLGNRLATLIGARDGEVVVTDTTSINLFKVLSAALRVQATR T0339 91 :TSKGH 1qz9A 116 :SPERR T0339 109 :HFITSSVEHDSIRLPLEHLVEEQ 1qz9A 121 :VIVTETSNFPTDLYIAEGLADML T0339 133 :AAVTFVP 1qz9A 147 :YTLRLVD T0339 148 :EVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1qz9A 154 :SPEELPQAIDQDTAVVMLTHVNYKTGYMHDMQALTA T0339 188 :LNQER 1qz9A 190 :LSHEC T0339 199 :PILVHTDAAQALGKQRVDVEDLGVDFLTIVGHK 1qz9A 195 :GALAIWDLAHSAGAVPVDLHQAGADYAIGCTYK T0339 232 :FY 1qz9A 229 :LN T0339 234 :GPR 1qz9A 232 :GPG T0339 237 :IGALYIR 1qz9A 236 :QAFVWVS T0339 244 :GLGEFT 1qz9A 244 :QLCDLV T0339 250 :PLYPMLFGGG 1qz9A 251 :QPLSGWFGHS T0339 260 :QERNFRPGTENTPMIAGLGKAAELVTQ 1qz9A 274 :GIARYLCGTQPITSLAMVECGLDVFAQ T0339 287 :NCEAYEAHMRDVRDYLEERLEAEFGQKRIHLNSQFPGTQR 1qz9A 302 :DMASLRRKSLALTDLFIELVEQRCAAHELTLVTPREHAKR T0339 328 :PNTCNFSIRG 1qz9A 342 :GSHVSFEHPE T0339 342 :GHVVLAQCRV 1qz9A 352 :GYAVIQALID T0339 352 :LMASVGA 1qz9A 364 :VIGDYRE T0339 383 :RNALRLSV 1qz9A 371 :PRIMRFGF T0339 391 :GRSTTRAEVDLVVQDLKQAVAQ 1qz9A 380 :PLYTTFTEVWDAVQILGEILDR Number of specific fragments extracted= 19 number of extra gaps= 1 total=240 Will force an alignment to be made, even if fragment is small Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qz9A/T0339-1qz9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1qz9A/T0339-1qz9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qz9A read from 1qz9A/T0339-1qz9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qz9A in template set Warning: unaligning (T0339)V132 because of BadResidue code BAD_PEPTIDE at template residue (1qz9A)G146 T0339 2 :RKVYMDYNATTPLEPEVIQAMTKAMWEAWGN 1qz9A 28 :GVIYLDGNSLGARPVAALARAQAVIAEEWGN T0339 33 :PSSPYSAG 1qz9A 61 :IRSWNSAG T0339 43 :AKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSVVKHFHANQ 1qz9A 69 :WRDLSERLGNRLATLIGARDGEVVVTDTTSINLFKVLSAALRVQATRS T0339 105 :GAKPHFITSSVEHDSIRLPLEHLVEEQ 1qz9A 117 :PERRVIVTETSNFPTDLYIAEGLADML T0339 133 :AAVTFVP 1qz9A 147 :YTLRLVD T0339 148 :EVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKALN 1qz9A 154 :SPEELPQAIDQDTAVVMLTHVNYKTGYMHDMQALTALSHECG T0339 200 :ILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFY 1qz9A 196 :ALAIWDLAHSAGAVPVDLHQAGADYAIGCTYKYL T0339 234 :GPRI 1qz9A 232 :GPGS T0339 238 :GALYIRG 1qz9A 237 :AFVWVSP T0339 246 :GEFTPLY 1qz9A 244 :QLCDLVP T0339 253 :PMLFGGGQ 1qz9A 252 :PLSGWFGH T0339 261 :ERNFRPGTENTPMIAGLGKAAELVTQ 1qz9A 275 :IARYLCGTQPITSLAMVECGLDVFAQ T0339 287 :NCEAYEAHMRDVRDYLEERLEAEFGQKRIHLNSQFPGTQR 1qz9A 302 :DMASLRRKSLALTDLFIELVEQRCAAHELTLVTPREHAKR T0339 328 :PNTCNFSIRG 1qz9A 342 :GSHVSFEHPE T0339 342 :GHVVLAQCRV 1qz9A 352 :GYAVIQALID T0339 379 :FDVA 1qz9A 362 :RGVI T0339 383 :RNALRLSV 1qz9A 371 :PRIMRFGF T0339 391 :GRSTTRAEVDLVVQDLKQAVAQ 1qz9A 380 :PLYTTFTEVWDAVQILGEILDR Number of specific fragments extracted= 18 number of extra gaps= 1 total=258 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qz9A/T0339-1qz9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1qz9A/T0339-1qz9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qz9A read from 1qz9A/T0339-1qz9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qz9A in template set Warning: unaligning (T0339)V132 because of BadResidue code BAD_PEPTIDE in next template residue (1qz9A)Q145 Warning: unaligning (T0339)A133 because of BadResidue code BAD_PEPTIDE at template residue (1qz9A)Q145 Warning: unaligning (T0339)A134 because of BadResidue code BAD_PEPTIDE at template residue (1qz9A)G146 T0339 3 :KVYMDYNATTPLEPEVIQAMTKAMWEAWGNPSSPYSAGRKAKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSVVKHFHAN 1qz9A 29 :VIYLDGNSLGARPVAALARAQAVIAEEWGNGLIRSWNSAGWRDLSERLGNRLATLIGARDGEVVVTDTTSINLFKVLSAALRVQATR T0339 104 :KGAKPHFITSSVEHDSIRLPLEHLVEEQ 1qz9A 116 :SPERRVIVTETSNFPTDLYIAEGLADML T0339 135 :VTFVPVS 1qz9A 147 :YTLRLVD T0339 148 :EVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKA 1qz9A 154 :SPEELPQAIDQDTAVVMLTHVNYKTGYMHDMQALTALSHE T0339 198 :PPILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFYGPR 1qz9A 194 :CGALAIWDLAHSAGAVPVDLHQAGADYAIGCTYKYLNGG T0339 237 :IGALYIRGLGEFTPLYPMLFGGGQ 1qz9A 236 :QAFVWVSPQLCDLVPQPLSGWFGH T0339 261 :ERNFRPGTENTPMIAGLGKAAELVT 1qz9A 275 :IARYLCGTQPITSLAMVECGLDVFA T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFG 1qz9A 301 :TDMASLRRKSLALTDLFIELVEQRCA T0339 312 :QKRIH 1qz9A 330 :LTLVT T0339 321 :FPGTQRLPNTCNFSIRG 1qz9A 335 :PREHAKRGSHVSFEHPE T0339 340 :LQGHVVLAQCRVLMASV 1qz9A 352 :GYAVIQALIDRGVIGDY T0339 381 :VARNALRLSVG 1qz9A 369 :REPRIMRFGFT T0339 392 :RSTTRAEVDLVVQDLKQAVAQ 1qz9A 381 :LYTTFTEVWDAVQILGEILDR Number of specific fragments extracted= 13 number of extra gaps= 1 total=271 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gc0A/T0339-1gc0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gc0A expands to /projects/compbio/data/pdb/1gc0.pdb.gz 1gc0A:Bad short name: N1 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: C2' for alphabet: pdb_atoms Bad short name: C3 for alphabet: pdb_atoms Bad short name: O3 for alphabet: pdb_atoms Bad short name: C4 for alphabet: pdb_atoms Bad short name: C4' for alphabet: pdb_atoms Bad short name: C5 for alphabet: pdb_atoms Bad short name: C6 for alphabet: pdb_atoms Bad short name: C5' for alphabet: pdb_atoms Bad short name: OP4 for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms # T0339 read from 1gc0A/T0339-1gc0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gc0A read from 1gc0A/T0339-1gc0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gc0A to template set # found chain 1gc0A in template set Warning: unaligning (T0339)A43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gc0A)S63 Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gc0A)Y212 Warning: unaligning (T0339)R326 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gc0A)Q309 T0339 44 :KDIINAARESLAKMIGG 1gc0A 64 :NPTLNLLEARMASLEGG T0339 63 :QDIIFTSGGTESNNLVIHSV 1gc0A 81 :EAGLALASGMGAITSTLWTL T0339 91 :TSKGH 1gc0A 101 :LRPGD T0339 109 :HFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVS 1gc0A 106 :EVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMA T0339 148 :EVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1gc0A 139 :DLQALEAAMTPATRVIYFESPANPNMHMADIAGVAK T0339 188 :LNQER 1gc0A 175 :IARKH T0339 199 :PILVHTDAAQALGKQRVDVED 1gc0A 180 :GATVVVDNTYCTPYLQRPLEL T0339 221 :GVDFLTIVG 1gc0A 201 :GADLVVHSA T0339 232 :FYGPR 1gc0A 213 :LSGHG T0339 237 :IGALYIR 1gc0A 221 :AGIVVGS T0339 244 :GLGEFT 1gc0A 229 :ALVDRI T0339 250 :PLYPMLFG 1gc0A 237 :QGLKDMTG T0339 267 :GTENTPMIAG 1gc0A 245 :AVLSPHDAAL T0339 280 :AAELVTQ 1gc0A 255 :LMRGIKT T0339 288 :CEAYEAHMRDVRDYLEERLEA 1gc0A 262 :LNLRMDRHCANAQVLAEFLAR T0339 312 :QKRIHLNS 1gc0A 283 :QPQVELIH T0339 327 :LPNTCNFSIRGPRLQGHVVLAQCRV 1gc0A 310 :PGGMIAFELKGGIGAGRRFMNALQL T0339 352 :LMASVGAACH 1gc0A 337 :RAVSLGDAES T0339 362 :SDHGDQPSPVLLSYGVPFDVARNALRLSVGR 1gc0A 350 :HPASMTHSSYTPEERAHYGISEGLVRLSVGL T0339 394 :TTR 1gc0A 381 :EDI T0339 400 :DLVVQDLKQAVAQL 1gc0A 384 :DDLLADVQQALKAS Number of specific fragments extracted= 21 number of extra gaps= 0 total=292 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gc0A/T0339-1gc0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1gc0A/T0339-1gc0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gc0A read from 1gc0A/T0339-1gc0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gc0A in template set Warning: unaligning (T0339)A43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gc0A)S63 Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gc0A)Y212 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gc0A)Y212 Warning: unaligning (T0339)R326 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gc0A)Q309 T0339 44 :KDIINAARESLAKMIGGKP 1gc0A 64 :NPTLNLLEARMASLEGGEA T0339 65 :IIFTSGGTESNNLVIHSVV 1gc0A 83 :GLALASGMGAITSTLWTLL T0339 105 :GAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVS 1gc0A 102 :RPGDEVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMA T0339 148 :EVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKALN 1gc0A 139 :DLQALEAAMTPATRVIYFESPANPNMHMADIAGVAKIARKHG T0339 200 :ILVHTDAAQALGKQRVDV 1gc0A 181 :ATVVVDNTYCTPYLQRPL T0339 219 :DLGVDFLTIVG 1gc0A 199 :ELGADLVVHSA T0339 233 :Y 1gc0A 213 :L T0339 234 :GP 1gc0A 215 :GH T0339 236 :RI 1gc0A 218 :DI T0339 238 :GALYIRGLGEFTPL 1gc0A 221 :AGIVVGSQALVDRI T0339 252 :YPMLFGGGQERNFRPGTENTPMIAGLGKAAELVTQ 1gc0A 237 :QGLKDMTGAVLSPHDAALLMRGIKTLNLRMDRHCA T0339 294 :HMRDVRDYLEE 1gc0A 272 :NAQVLAEFLAR T0339 327 :LPNTCNFSIRGPRLQGHVVLAQCRV 1gc0A 310 :PGGMIAFELKGGIGAGRRFMNALQL T0339 352 :LMASVG 1gc0A 337 :RAVSLG T0339 358 :AACHSDHGDQPSPVLLSYGVPFDVARNALRLSVGR 1gc0A 346 :SLAQHPASMTHSSYTPEERAHYGISEGLVRLSVGL T0339 397 :AEVDLVVQDLKQAVAQL 1gc0A 381 :EDIDDLLADVQQALKAS Number of specific fragments extracted= 16 number of extra gaps= 0 total=308 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gc0A/T0339-1gc0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1gc0A/T0339-1gc0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gc0A read from 1gc0A/T0339-1gc0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gc0A in template set Warning: unaligning (T0339)A43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gc0A)S63 Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gc0A)Y212 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gc0A)Y212 Warning: unaligning (T0339)R326 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gc0A)Q309 T0339 44 :KDIINAARESLAKMIGG 1gc0A 64 :NPTLNLLEARMASLEGG T0339 64 :DIIFTSGGTESNNLVIHSV 1gc0A 82 :AGLALASGMGAITSTLWTL T0339 104 :KGAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVS 1gc0A 101 :LRPGDEVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMA T0339 148 :EVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKA 1gc0A 139 :DLQALEAAMTPATRVIYFESPANPNMHMADIAGVAKIARK T0339 198 :PPILVHTDAAQALGKQRVDVE 1gc0A 179 :HGATVVVDNTYCTPYLQRPLE T0339 220 :LGVDFLTIVG 1gc0A 200 :LGADLVVHSA T0339 233 :YGPR 1gc0A 213 :LSGH T0339 237 :IGALYIRGLGEFTPL 1gc0A 221 :AGIVVGSQALVDRIR T0339 264 :FRPGTENTPMIAGLGKAA 1gc0A 242 :MTGAVLSPHDAALLMRGI T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIHL 1gc0A 260 :KTLNLRMDRHCANAQVLAEFLARQPQVELIHY T0339 327 :LPNTCNFSIRG 1gc0A 310 :PGGMIAFELKG T0339 340 :LQGHVVLAQC 1gc0A 322 :IGAGRRFMNA T0339 350 :RVLMASVGAACHSDHG 1gc0A 344 :AESLAQHPASMTHSSY T0339 368 :PSPVLLSYGV 1gc0A 360 :TPEERAHYGI T0339 382 :ARNALRLSVGRSTTR 1gc0A 370 :SEGLVRLSVGLEDID T0339 401 :LVVQDLKQAVAQ 1gc0A 385 :DLLADVQQALKA Number of specific fragments extracted= 16 number of extra gaps= 0 total=324 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjoA/T0339-1vjoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vjoA expands to /projects/compbio/data/pdb/1vjo.pdb.gz 1vjoA:Skipped atom 208, because occupancy 0.500 <= existing 0.500 in 1vjoA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 483, because occupancy 0.500 <= existing 0.500 in 1vjoA Skipped atom 485, because occupancy 0.500 <= existing 0.500 in 1vjoA Skipped atom 487, because occupancy 0.500 <= existing 0.500 in 1vjoA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 919, because occupancy 0.500 <= existing 0.500 in 1vjoA Skipped atom 921, because occupancy 0.500 <= existing 0.500 in 1vjoA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1640, because occupancy 0.350 <= existing 0.650 in 1vjoA Skipped atom 1642, because occupancy 0.350 <= existing 0.650 in 1vjoA Skipped atom 1709, because occupancy 0.350 <= existing 0.650 in 1vjoA Skipped atom 1711, because occupancy 0.350 <= existing 0.650 in 1vjoA Skipped atom 1713, because occupancy 0.350 <= existing 0.650 in 1vjoA Skipped atom 1715, because occupancy 0.350 <= existing 0.650 in 1vjoA Skipped atom 1717, because occupancy 0.350 <= existing 0.650 in 1vjoA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1893, because occupancy 0.350 <= existing 0.650 in 1vjoA Skipped atom 1895, because occupancy 0.350 <= existing 0.650 in 1vjoA Skipped atom 2148, because occupancy 0.500 <= existing 0.500 in 1vjoA Skipped atom 2150, because occupancy 0.500 <= existing 0.500 in 1vjoA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0339 read from 1vjoA/T0339-1vjoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjoA read from 1vjoA/T0339-1vjoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vjoA to template set # found chain 1vjoA in template set Warning: unaligning (T0339)A385 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vjoA)W355 Warning: unaligning (T0339)L386 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjoA)W355 T0339 2 :RKVYMDYNATTPLEPEVIQAM 1vjoA 21 :PSRLLLGPGPSNAHPSVLQAM T0339 32 :NPSSPYSAGRKAKDIINAARESLAKMIGGKPQDIIFTSG 1vjoA 42 :NVSPVGHLDPAFLALMDEIQSLLRYVWQTENPLTIAVSG T0339 71 :GTESNNLVIHSV 1vjoA 82 :GTAAMEATIANA T0339 91 :TSKGH 1vjoA 94 :VEPGD T0339 109 :HFITSSVEHDS 1vjoA 99 :VVLIGVAGYFG T0339 121 :RLPLEHL 1vjoA 110 :NRLVDMA T0339 129 :EEQVAAVTFVPVSK 1vjoA 117 :GRYGADVRTISKPW T0339 144 :SGQTEVDDILAAVR 1vjoA 131 :GEVFSLEELRTALE T0339 158 :PTTRLVTIMLANNETGIVMPVPEISQ 1vjoA 146 :HRPAILALVHAETSTGARQPLEGVGE T0339 188 :LNQER 1vjoA 172 :LCREF T0339 199 :PILVHTDAAQALGKQRVDVEDLGVDFLTIVGHK 1vjoA 177 :GTLLLVDTVTSLGGVPIFLDAWGVDLAYSCSQK T0339 232 :FY 1vjoA 211 :LG T0339 234 :GPRIGALYIR 1vjoA 214 :SPGASPFTMS T0339 244 :GLGEFT 1vjoA 225 :RAIEKL T0339 250 :PLYPMLFGGG 1vjoA 232 :RRRTKVANWY T0339 260 :QERNFRPGTENTPMIAGLGKAAELVTQ 1vjoA 252 :GSERVYHHTAPINLYYALREALRLIAQ T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1vjoA 280 :GLANCWQRHQKNVEYLWERLEDI T0339 314 :RIHLNS 1vjoA 303 :GLSLHV T0339 322 :PGTQRLPNTCNFSIRGP 1vjoA 309 :EKEYRLPTLTTVCIPDG T0339 340 :LQGHVVLAQCRV 1vjoA 326 :VDGKAVARRLLN T0339 352 :LMASVGAACHSDH 1vjoA 339 :HNIEVGGGLGELA T0339 383 :RN 1vjoA 352 :GK T0339 387 :RLSV 1vjoA 356 :RVGL T0339 391 :GRSTTRAEVDLVVQDLKQAV 1vjoA 361 :GFNSRKESVDQLIPALEQVL Number of specific fragments extracted= 24 number of extra gaps= 1 total=348 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjoA/T0339-1vjoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1vjoA/T0339-1vjoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjoA read from 1vjoA/T0339-1vjoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vjoA in template set Warning: unaligning (T0339)A385 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vjoA)W355 Warning: unaligning (T0339)L386 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjoA)W355 T0339 1 :ERKVY 1vjoA 21 :PSRLL T0339 7 :DYNATTPLEPEVIQAM 1vjoA 26 :LGPGPSNAHPSVLQAM T0339 32 :NPSSPYSAGRKAKDIINAARESLAKMIGGKPQDIIFTSG 1vjoA 42 :NVSPVGHLDPAFLALMDEIQSLLRYVWQTENPLTIAVSG T0339 71 :GTESNNLVIHSVV 1vjoA 82 :GTAAMEATIANAV T0339 105 :GAKPHFITSSVEH 1vjoA 95 :EPGDVVLIGVAGY T0339 120 :IRLPLEHLVEEQVAAVTFVPVS 1vjoA 108 :FGNRLVDMAGRYGADVRTISKP T0339 143 :VSGQTEVDDILAAV 1vjoA 130 :WGEVFSLEELRTAL T0339 159 :TTRLVTIMLANNETGIVMPVPEISQRIKALN 1vjoA 147 :RPAILALVHAETSTGARQPLEGVGELCREFG T0339 200 :ILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFYG 1vjoA 178 :TLLLVDTVTSLGGVPIFLDAWGVDLAYSCSQKGLG T0339 235 :PRIGALYIR 1vjoA 215 :PGASPFTMS T0339 246 :GEFTPLYPM 1vjoA 232 :RRRTKVANW T0339 257 :GGGQ 1vjoA 241 :YLDM T0339 261 :ERNFRPGTENTPMIAGLGKAAELVTQ 1vjoA 253 :SERVYHHTAPINLYYALREALRLIAQ T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1vjoA 280 :GLANCWQRHQKNVEYLWERLEDI T0339 311 :G 1vjoA 303 :G T0339 315 :IHLNSQ 1vjoA 304 :LSLHVE T0339 323 :GTQRLPNTCNFSIRGP 1vjoA 310 :KEYRLPTLTTVCIPDG T0339 340 :LQGHVVLAQCRV 1vjoA 326 :VDGKAVARRLLN T0339 352 :LMASVG 1vjoA 339 :HNIEVG T0339 377 :VPFDVARN 1vjoA 346 :GLGELAGK T0339 387 :RLSV 1vjoA 356 :RVGL T0339 391 :GRSTTRAEVDLVVQDLKQAV 1vjoA 361 :GFNSRKESVDQLIPALEQVL Number of specific fragments extracted= 22 number of extra gaps= 1 total=370 Will force an alignment to be made, even if fragment is small Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjoA/T0339-1vjoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1vjoA/T0339-1vjoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjoA read from 1vjoA/T0339-1vjoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vjoA in template set Warning: unaligning (T0339)A385 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vjoA)W355 Warning: unaligning (T0339)L386 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjoA)W355 T0339 5 :YMDYNATTPLEPEVIQAM 1vjoA 24 :LLLGPGPSNAHPSVLQAM T0339 32 :NPSSPYSAGRKAKDIINAARESLAKMIGGKPQDIIFTSG 1vjoA 42 :NVSPVGHLDPAFLALMDEIQSLLRYVWQTENPLTIAVSG T0339 71 :GTESNNLVIHSV 1vjoA 82 :GTAAMEATIANA T0339 104 :KGAKPHFITSSVEH 1vjoA 94 :VEPGDVVLIGVAGY T0339 120 :IRLPLEHLVEEQVAAVTFVPVS 1vjoA 108 :FGNRLVDMAGRYGADVRTISKP T0339 143 :VSGQTEVDDILAAV 1vjoA 130 :WGEVFSLEELRTAL T0339 159 :TTRLVTIMLANNETGIVMPVPEISQRIKA 1vjoA 147 :RPAILALVHAETSTGARQPLEGVGELCRE T0339 198 :PPILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFYGPR 1vjoA 176 :FGTLLLVDTVTSLGGVPIFLDAWGVDLAYSCSQKGLGCS T0339 237 :IGALYIRGLGEFTPLYPMLFGGGQ 1vjoA 217 :ASPFTMSSRAIEKLQRRRTKVANW T0339 261 :ERNFRPGTENTPMIAGLGKAAELVT 1vjoA 253 :SERVYHHTAPINLYYALREALRLIA T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1vjoA 279 :EGLANCWQRHQKNVEYLWERLEDIGLSLHVE T0339 323 :GTQRLPNTCNFSIRG 1vjoA 310 :KEYRLPTLTTVCIPD T0339 338 :PRLQGHVVLAQ 1vjoA 326 :VDGKAVARRLL T0339 349 :CRVLMASVG 1vjoA 338 :EHNIEVGGG T0339 378 :PFDVARN 1vjoA 347 :LGELAGK T0339 387 :RLSVG 1vjoA 356 :RVGLM T0339 392 :RSTTRAEVDLVVQDLKQAV 1vjoA 362 :FNSRKESVDQLIPALEQVL Number of specific fragments extracted= 17 number of extra gaps= 1 total=387 Will force an alignment to be made, even if fragment is small Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cs1A/T0339-1cs1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cs1A expands to /projects/compbio/data/pdb/1cs1.pdb.gz 1cs1A:Bad short name: N1 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: C2' for alphabet: pdb_atoms Bad short name: C3 for alphabet: pdb_atoms Bad short name: O3 for alphabet: pdb_atoms Bad short name: C4 for alphabet: pdb_atoms Bad short name: C4' for alphabet: pdb_atoms Bad short name: C5 for alphabet: pdb_atoms Bad short name: C6 for alphabet: pdb_atoms Bad short name: C5' for alphabet: pdb_atoms Bad short name: OP4 for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms # T0339 read from 1cs1A/T0339-1cs1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cs1A read from 1cs1A/T0339-1cs1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cs1A to template set # found chain 1cs1A in template set Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cs1A)Y199 T0339 33 :PSSPYSAGRKAKDIINAARESLAKMIGG 1cs1A 40 :EPRAHDYSRRGNPTRDVVQRALAELEGG T0339 63 :QDIIFTSGGTESNNLVIHSV 1cs1A 68 :AGAVLTNTGMSAIHLVTTVF T0339 91 :TSKGH 1cs1A 88 :LKPGD T0339 109 :HFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVS 1cs1A 93 :LLVAPHDCYGGSYRLFDSLAKRGCYRVLFVDQG T0339 148 :EVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1cs1A 126 :DEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICH T0339 188 :LNQER 1cs1A 162 :LAREV T0339 199 :PILVHTDAAQALGKQRVDV 1cs1A 167 :GAVSVVDNTFLSPALQNPL T0339 219 :DLGVDFLTIVG 1cs1A 186 :ALGADLVLHSC T0339 232 :FYGPR 1cs1A 200 :LNGHS T0339 237 :IGALYIR 1cs1A 208 :AGVVIAK T0339 244 :G 1cs1A 216 :P T0339 245 :LGEFTPLYPMLFG 1cs1A 218 :VVTELAWWANNIG T0339 267 :GTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRD 1cs1A 231 :VTGGAFDSYLLLRGLRTLVPRMELAQRNAQAIVK T0339 305 :RLEA 1cs1A 265 :YLQT T0339 312 :QKRI 1cs1A 269 :QPLV T0339 316 :HLNSQFPGT 1cs1A 274 :KLYHPSLPE T0339 325 :QRLPNTCNFSIRGPRLQGHVVLAQCRV 1cs1A 294 :KGFGAMLSFELDGDEQTLRRFLGGLSL T0339 352 :LMASVGAACH 1cs1A 323 :LAESLGGVES T0339 362 :SDHGDQPSPVLLSYGVPFDVARNALRLSVGR 1cs1A 336 :HAATMTHAGMAPEARAAAGISETLLRISTGI T0339 394 :TTRA 1cs1A 367 :EDGE T0339 401 :LVVQDLKQAVAQLEDQ 1cs1A 371 :DLIADLENGFRAANKG Number of specific fragments extracted= 21 number of extra gaps= 0 total=408 Will force an alignment to be made, even if fragment is small Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cs1A/T0339-1cs1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1cs1A/T0339-1cs1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cs1A read from 1cs1A/T0339-1cs1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cs1A in template set Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cs1A)Y199 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cs1A)Y199 T0339 37 :YSAGRKAKDIINAARESLAKMIGGK 1cs1A 44 :HDYSRRGNPTRDVVQRALAELEGGA T0339 64 :DIIFTSGGTESNNLVIHSVV 1cs1A 69 :GAVLTNTGMSAIHLVTTVFL T0339 105 :GAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVS 1cs1A 89 :KPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFVDQG T0339 148 :EVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKALN 1cs1A 126 :DEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVG T0339 200 :ILVHTDAAQALGKQRVDV 1cs1A 168 :AVSVVDNTFLSPALQNPL T0339 219 :DLGVDFLTIVG 1cs1A 186 :ALGADLVLHSC T0339 233 :Y 1cs1A 200 :L T0339 234 :GP 1cs1A 202 :GH T0339 236 :RI 1cs1A 205 :DV T0339 238 :GALYIRGLGEFTPLYPMLFGGGQERNFRP 1cs1A 209 :GVVIAKDPDVVTELAWWANNIGVTGGAFD T0339 277 :LGKAAELVTQ 1cs1A 238 :SYLLLRGLRT T0339 287 :NCEAYEAHMRDVR 1cs1A 251 :RMELAQRNAQAIV T0339 304 :ERLEAEFG 1cs1A 264 :KYLQTQPL T0339 315 :IHLNSQFP 1cs1A 272 :VKKLYHPS T0339 323 :GT 1cs1A 281 :PE T0339 326 :RLPNTCNFSIRGPRLQGHVVLAQCRV 1cs1A 295 :GFGAMLSFELDGDEQTLRRFLGGLSL T0339 352 :LMASVG 1cs1A 323 :LAESLG T0339 358 :AACHSDHGDQPSPVLLSYGVPFDVARNALRLSVGRSTTR 1cs1A 332 :SLISHAATMTHAGMAPEARAAAGISETLLRISTGIEDGE T0339 401 :LVVQDLKQAVAQLEDQ 1cs1A 371 :DLIADLENGFRAANKG Number of specific fragments extracted= 19 number of extra gaps= 0 total=427 Will force an alignment to be made, even if fragment is small Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cs1A/T0339-1cs1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1cs1A/T0339-1cs1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cs1A read from 1cs1A/T0339-1cs1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cs1A in template set Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cs1A)Y199 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cs1A)Y199 T0339 45 :DIINAARESLAKMIGG 1cs1A 52 :PTRDVVQRALAELEGG T0339 64 :DIIFTSGGTESNNLVIHSV 1cs1A 69 :GAVLTNTGMSAIHLVTTVF T0339 104 :KGAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVS 1cs1A 88 :LKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFVDQG T0339 148 :EVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKA 1cs1A 126 :DEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLARE T0339 198 :PPILVHTDAAQALGKQ 1cs1A 166 :VGAVSVVDNTFLSPAL T0339 215 :VDVEDLGVDFLTIVG 1cs1A 182 :QNPLALGADLVLHSC T0339 233 :YGPR 1cs1A 200 :LNGH T0339 237 :IGALYIRGLGEFTP 1cs1A 208 :AGVVIAKDPDVVTE T0339 261 :ERNF 1cs1A 228 :NIGV T0339 268 :TENTPM 1cs1A 232 :TGGAFD T0339 277 :LGKAAELVT 1cs1A 238 :SYLLLRGLR T0339 286 :QNCEAYEAHMR 1cs1A 250 :PRMELAQRNAQ T0339 301 :YLEERLEAEFGQKRIHLNSQFPGT 1cs1A 261 :AIVKYLQTQPLVKKLYHPSLPENQ T0339 327 :LPNTCNFSIRG 1cs1A 296 :FGAMLSFELDG T0339 339 :RLQGHVVLAQ 1cs1A 307 :DEQTLRRFLG T0339 351 :V 1cs1A 317 :G T0339 352 :LMASVGAACHSDHG 1cs1A 332 :SLISHAATMTHAGM T0339 367 :QPSPVLLS 1cs1A 346 :APEARAAA T0339 380 :DVARNALRLSVGRSTTRA 1cs1A 354 :GISETLLRISTGIEDGED T0339 402 :VVQDLKQAVAQLE 1cs1A 372 :LIADLENGFRAAN Number of specific fragments extracted= 20 number of extra gaps= 0 total=447 Will force an alignment to be made, even if fragment is small Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v2dA/T0339-1v2dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v2dA expands to /projects/compbio/data/pdb/1v2d.pdb.gz 1v2dA:# T0339 read from 1v2dA/T0339-1v2dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v2dA read from 1v2dA/T0339-1v2dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v2dA to template set # found chain 1v2dA in template set T0339 2 :RKVYMDYNATT 1v2dA 26 :GAVNLGQGFPS T0339 13 :PLEPEVIQAMTKAMWE 1v2dA 38 :PPPPFLLEAVRRALGR T0339 32 :NPSSP 1v2dA 54 :QDQYA T0339 37 :YSAGR 1v2dA 60 :PAGLP T0339 49 :AARESLAKMIGGKPQDIIFTSGGTESNNLVIHSV 1v2dA 65 :ALREALAEEFAVEPESVVVTSGATEALYVLLQSL T0339 91 :TSKGH 1v2dA 99 :VGPGD T0339 109 :HFITSSVEHDSIRLPLEHL 1v2dA 104 :EVVVLEPFFDVYLPDAFLA T0339 132 :VAAVTFVPV 1v2dA 123 :GAKARLVRL T0339 141 :SKVSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1v2dA 134 :TPEGFRLDLSALEKALTPRTRALLLNTPMNPTGLVFGERELEA T0339 185 :IKALNQER 1v2dA 177 :IARLARAH T0339 199 :PILVHTDAAQALGKQR 1v2dA 185 :DLFLISDEVYDELYYG T0339 216 :D 1v2dA 204 :R T0339 217 :VEDL 1v2dA 206 :LREF T0339 221 :G 1v2dA 213 :R T0339 223 :DFLTIVGHK 1v2dA 214 :TFTVGSAGK T0339 232 :FY 1v2dA 224 :LE T0339 234 :GPRIGALYIR 1v2dA 228 :GYRVGWIVGP T0339 244 :GLGEFTPLYPMLFG 1v2dA 239 :EFMPRLAGMRQWTS T0339 267 :GTENTPMIAGLGKAAELVTQ 1v2dA 253 :FSAPTPLQAGVAEALKLARR T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1v2dA 275 :FYEALREGYRRRRDLLAGGLRAM T0339 314 :RIHLNSQFP 1v2dA 298 :GLRVYVPEG T0339 328 :PNTCNFSIRG 1v2dA 307 :TYFLMAELPG T0339 340 :LQGHVVLA 1v2dA 317 :WDAFRLVE T0339 351 :V 1v2dA 325 :E T0339 352 :LMASVGAACHSDHGD 1v2dA 328 :VALIPASAFYLEDPP T0339 383 :RNALRLSVGR 1v2dA 343 :KDLFRFAFCK T0339 395 :TRAEVDLVVQDLKQA 1v2dA 353 :TEEELHLALERLGRV Number of specific fragments extracted= 27 number of extra gaps= 0 total=474 Will force an alignment to be made, even if fragment is small Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v2dA/T0339-1v2dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1v2dA/T0339-1v2dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v2dA read from 1v2dA/T0339-1v2dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v2dA in template set T0339 4 :VYMDYNATT 1v2dA 28 :VNLGQGFPS T0339 13 :PLEPEVIQAMTKAMWEAWGN 1v2dA 38 :PPPPFLLEAVRRALGRQDQY T0339 33 :PSSP 1v2dA 60 :PAGL T0339 48 :NAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSVV 1v2dA 64 :PALREALAEEFAVEPESVVVTSGATEALYVLLQSLV T0339 105 :GAKPHFITSSVEHDSIRL 1v2dA 100 :GPGDEVVVLEPFFDVYLP T0339 127 :LVEEQVAAVTFVPVS 1v2dA 118 :DAFLAGAKARLVRLD T0339 142 :KVSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMP 1v2dA 135 :PEGFRLDLSALEKALTPRTRALLLNTPMNPTGLVFG T0339 178 :VPEISQRIKALN 1v2dA 174 :LEAIARLARAHD T0339 200 :ILVHTDAAQ 1v2dA 186 :LFLISDEVY T0339 209 :ALGKQRVDVEDL 1v2dA 198 :YYGERPRRLREF T0339 223 :DFLTIVGHKFY 1v2dA 214 :TFTVGSAGKRL T0339 234 :GP 1v2dA 226 :AT T0339 236 :RIGALYIRG 1v2dA 230 :RVGWIVGPK T0339 246 :GEFTPLYPMLFGGGQ 1v2dA 239 :EFMPRLAGMRQWTSF T0339 268 :TENTPMIAGLGKAAELVTQ 1v2dA 254 :SAPTPLQAGVAEALKLARR T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1v2dA 275 :FYEALREGYRRRRDLLAGGLRAM T0339 311 :G 1v2dA 298 :G T0339 315 :IHLNSQ 1v2dA 299 :LRVYVP T0339 325 :QRLP 1v2dA 305 :EGTY T0339 330 :TCNFSIRG 1v2dA 309 :FLMAELPG T0339 340 :LQGHVVLAQ 1v2dA 317 :WDAFRLVEE T0339 354 :ASVG 1v2dA 326 :ARVA T0339 358 :AACHSDH 1v2dA 334 :SAFYLED T0339 381 :VARNALRLSVGR 1v2dA 341 :PPKDLFRFAFCK T0339 395 :TRAEVDLVVQDLKQA 1v2dA 353 :TEEELHLALERLGRV Number of specific fragments extracted= 25 number of extra gaps= 0 total=499 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v2dA/T0339-1v2dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1v2dA/T0339-1v2dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v2dA read from 1v2dA/T0339-1v2dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v2dA in template set T0339 4 :VYMDYNATT 1v2dA 28 :VNLGQGFPS T0339 13 :PLEPEVIQAMTKAMWEAWGNPS 1v2dA 38 :PPPPFLLEAVRRALGRQDQYAP T0339 35 :SPYS 1v2dA 61 :AGLP T0339 49 :AARESLAKMIGGKPQDIIFTSGGTESNNLVIHSV 1v2dA 65 :ALREALAEEFAVEPESVVVTSGATEALYVLLQSL T0339 104 :KGAKPHFITSSVEHDSIRLPLEHL 1v2dA 99 :VGPGDEVVVLEPFFDVYLPDAFLA T0339 132 :VAAVTFVPVS 1v2dA 123 :GAKARLVRLD T0339 142 :KVSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMP 1v2dA 135 :PEGFRLDLSALEKALTPRTRALLLNTPMNPTGLVFG T0339 178 :VPEISQRIKA 1v2dA 174 :LEAIARLARA T0339 198 :PPILVHTDAAQALGKQRVD 1v2dA 184 :HDLFLISDEVYDELYYGER T0339 220 :LGVDFLTIVGHKFYGPR 1v2dA 211 :PERTFTVGSAGKRLEAT T0339 237 :IGALYIRGLGEFTPLYP 1v2dA 231 :VGWIVGPKEFMPRLAGM T0339 262 :RNFRPGTENTPMIAGLGKAAELVT 1v2dA 248 :RQWTSFSAPTPLQAGVAEALKLAR T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1v2dA 274 :GFYEALREGYRRRRDLLAGGLRAMGLRVYVP T0339 326 :RLPNTCNFSIRGPRLQGH 1v2dA 305 :EGTYFLMAELPGWDAFRL T0339 347 :AQCRVLMASVGAACHSDHG 1v2dA 323 :VEEARVALIPASAFYLEDP T0339 382 :ARNALRLSVG 1v2dA 342 :PKDLFRFAFC T0339 394 :TTRAEVDLVVQDLKQA 1v2dA 352 :KTEEELHLALERLGRV Number of specific fragments extracted= 17 number of extra gaps= 0 total=516 Will force an alignment to be made, even if fragment is small Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c0nA/T0339-1c0nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1c0nA expands to /projects/compbio/data/pdb/1c0n.pdb.gz 1c0nA:# T0339 read from 1c0nA/T0339-1c0nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c0nA read from 1c0nA/T0339-1c0nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1c0nA to template set # found chain 1c0nA in template set T0339 2 :RKVYMDYNATTPLEPEVIQAMTKAMWEAWGNPSSP 1c0nA 23 :PLAYLDSAASAQKPSQVIDAEAEFYRHGYAAVHAG T0339 37 :YSAGRKAKDIINAARESLAKMIGG 1c0nA 59 :HTLSAQATEKMENVRKRASLFINA T0339 61 :KPQDIIFTSGGTESNNLVIHSVVK 1c0nA 84 :SAEELVFVRGTTEGINLVANSWGN T0339 89 :NQTSKGH 1c0nA 108 :SNVRAGD T0339 109 :HFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSK 1c0nA 115 :NIIISQMEHHANIVPWQMLCARVGAELRVIPLNP T0339 144 :SGQTEVD 1c0nA 149 :DGTLQLE T0339 155 :AVRPTTRLVTIMLANNETGIVMPVPEISQ 1c0nA 160 :LFDAATRLLAITHVSNVLGTENPLAEMIT T0339 188 :LNQER 1c0nA 189 :LAHQH T0339 199 :PILVHTDAAQALGKQRVDVEDLGVDFLTIVGHK 1c0nA 194 :GAKVLVDGAQAVMHHPVDVQALDCDFYVFSGHK T0339 232 :FYGPRIGALYIR 1c0nA 228 :YGPTGIGILYVK T0339 244 :GLGEFT 1c0nA 241 :ALLQEM T0339 252 :YPMLFGGG 1c0nA 247 :PPWEGGGS T0339 260 :QERNFRPGTENTPMIAGLGKAAELVTQ 1c0nA 270 :APWRFEAGTPNTGGIIGLGAALEYVSA T0339 287 :NCEAYEAHMRDVRDYLEERLEA 1c0nA 298 :GLNNIAEYEQNLMHYALSQLES T0339 312 :QKRIHLNSQFPG 1c0nA 320 :VPDLTLYGPQAR T0339 328 :PNTCNFSIRG 1c0nA 332 :LGVIAFNLGA T0339 340 :LQGHVVLAQCRV 1c0nA 342 :HHAYDVGSFLDN T0339 352 :LMASVGAACH 1c0nA 356 :IAVRTGHHCA T0339 362 :SD 1c0nA 372 :YN T0339 377 :V 1c0nA 374 :V T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQAVAQL 1c0nA 375 :PAMCRASLAMYNTHEEVDRLVTGLQRIHRLL Number of specific fragments extracted= 21 number of extra gaps= 0 total=537 Will force an alignment to be made, even if fragment is small Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c0nA/T0339-1c0nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1c0nA/T0339-1c0nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c0nA read from 1c0nA/T0339-1c0nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1c0nA in template set T0339 2 :RKVYMDYNATTPLEPEVIQAMTKAMWEAWGN 1c0nA 23 :PLAYLDSAASAQKPSQVIDAEAEFYRHGYAA T0339 33 :PSSPYSAGRKAKDIINAARESLAKMIGG 1c0nA 55 :HAGAHTLSAQATEKMENVRKRASLFINA T0339 61 :KPQDIIFTSGGTESNNLVIHSVVKHFH 1c0nA 84 :SAEELVFVRGTTEGINLVANSWGNSNV T0339 105 :GAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSK 1c0nA 111 :RAGDNIIISQMEHHANIVPWQMLCARVGAELRVIPLNP T0339 144 :SGQTEVD 1c0nA 149 :DGTLQLE T0339 154 :AAVRPTTRLVTIMLANNETGIVMPVPEISQRIKALN 1c0nA 159 :TLFDAATRLLAITHVSNVLGTENPLAEMITLAHQHG T0339 200 :ILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFYGP 1c0nA 195 :AKVLVDGAQAVMHHPVDVQALDCDFYVFSGHKLYGP T0339 236 :RIGALYIRG 1c0nA 232 :GIGILYVKE T0339 246 :GEFTPLYPMLFGGGQ 1c0nA 241 :ALLQEMPPWEGGGSM T0339 261 :ERNFRPGTENTPMIAGLGKAAELVTQ 1c0nA 271 :PWRFEAGTPNTGGIIGLGAALEYVSA T0339 287 :NCEAYEAHMRDVRDYLEERLEAEFG 1c0nA 298 :GLNNIAEYEQNLMHYALSQLESVPD T0339 315 :IHLNSQ 1c0nA 323 :LTLYGP T0339 323 :GT 1c0nA 329 :QA T0339 326 :RLP 1c0nA 331 :RLG T0339 330 :TCNFSIRG 1c0nA 334 :VIAFNLGA T0339 340 :LQGHVVLAQCRV 1c0nA 342 :HHAYDVGSFLDN T0339 352 :LMASVGAACH 1c0nA 356 :IAVRTGHHCA T0339 369 :SPVLLSYGVPF 1c0nA 366 :MPLMAYYNVPA T0339 385 :ALRLSVGRSTTRAEVDLVVQDLKQAVAQL 1c0nA 377 :MCRASLAMYNTHEEVDRLVTGLQRIHRLL Number of specific fragments extracted= 19 number of extra gaps= 0 total=556 Will force an alignment to be made, even if fragment is small Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c0nA/T0339-1c0nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1c0nA/T0339-1c0nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c0nA read from 1c0nA/T0339-1c0nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1c0nA in template set T0339 2 :RKVYMDYNATTPLEPEVIQAMTKAMWEAWGNPS 1c0nA 23 :PLAYLDSAASAQKPSQVIDAEAEFYRHGYAAVH T0339 35 :SPYSAGRKAKDIINAARESLAKMIGG 1c0nA 57 :GAHTLSAQATEKMENVRKRASLFINA T0339 61 :KPQDIIFTSGGTESNNLVIHSV 1c0nA 84 :SAEELVFVRGTTEGINLVANSW T0339 100 :HSPVKGAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVS 1c0nA 106 :GNSNVRAGDNIIISQMEHHANIVPWQMLCARVGAELRVIPLN T0339 143 :VSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKA 1c0nA 148 :PDGTLQLETLPTLFDAATRLLAITHVSNVLGTENPLAEMITLAHQ T0339 198 :PPILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFYGPR 1c0nA 193 :HGAKVLVDGAQAVMHHPVDVQALDCDFYVFSGHKLYGPT T0339 237 :IGALYIRGLGEFTPLYPMLFGGGQ 1c0nA 233 :IGILYVKEALLQEMPPWEGGGSMI T0339 261 :ERNFRPGTENTPMIAGLGKAAELVT 1c0nA 271 :PWRFEAGTPNTGGIIGLGAALEYVS T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1c0nA 297 :LGLNNIAEYEQNLMHYALSQLESVPDLTLYG T0339 324 :TQRLPNTCNFSIRGPRLQGHVVLAQCRVLMASVGAACHSDHG 1c0nA 328 :PQARLGVIAFNLGAHHAYDVGSFLDNYGIAVRTGHHCAMPLM T0339 378 :PFDVARNALRLSVGRSTTRAEVDLVVQDLKQAVAQL 1c0nA 370 :AYYNVPAMCRASLAMYNTHEEVDRLVTGLQRIHRLL Number of specific fragments extracted= 11 number of extra gaps= 0 total=567 Will force an alignment to be made, even if fragment is small Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1elqA/T0339-1elqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1elqA expands to /projects/compbio/data/pdb/1elq.pdb.gz 1elqA:# T0339 read from 1elqA/T0339-1elqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1elqA read from 1elqA/T0339-1elqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1elqA to template set # found chain 1elqA in template set T0339 2 :RKVYMDYNATTPLEPEVIQA 1elqA 19 :NKTYFNFGGQGILPTVALEA T0339 22 :MTKAMWE 1elqA 42 :MYGYLQE T0339 32 :NPSSPYSAGRKAKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSV 1elqA 49 :NGPFSIAANQHIQQLIAQLRQALAETFNVDPNTITITDNVTTGCDIVLWGL T0339 90 :QTSKGH 1elqA 100 :DWHQGD T0339 109 :HFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSKV 1elqA 106 :EILLTDCEHPGIIAIVQAIAARFGITYRFFPVAAT T0339 144 :SGQ 1elqA 142 :NQG T0339 148 :E 1elqA 145 :D T0339 149 :VDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1elqA 147 :AAVLANHLGPKTRLVILSHLLWNTGQVLPLAEIMA T0339 188 :LNQER 1elqA 182 :VCRRH T0339 196 :GLP 1elqA 187 :QGN T0339 199 :PILVHTDAAQALGKQRVDVEDLGVDFLTIVGHK 1elqA 191 :PVRVLVDGAQSAGSLPLDFSRLEVDYYAFTGHK T0339 232 :FY 1elqA 225 :FA T0339 234 :GPRIGALYIR 1elqA 228 :PAGVGGLYIH T0339 244 :GLGEFTP 1elqA 239 :DCLGEIN T0339 251 :LYPM 1elqA 252 :RSIT T0339 260 :QERNFRPGTENTPMIAGLGKAAELVTQ 1elqA 268 :GGKRFEVATSAYPQYAGLLAALQLHQR T0339 287 :NCEAYEAHMRDVRDYLEERLEA 1elqA 297 :TAEERYQAICQRSEFLWRGLNQ T0339 312 :QKRIHLNSQFPGT 1elqA 319 :LPHVHCLATSAPQ T0339 328 :PNTCNFSIRGP 1elqA 332 :AGLVSFTVDSP T0339 340 :LQGHVVLAQCRV 1elqA 343 :LGHRAIVQKLEE T0339 352 :LMASVGAA 1elqA 357 :IYLRTIAD T0339 383 :RNALRLSVGRSTTRAEVDLVVQDL 1elqA 365 :PDCIRACCHYITDEEEINHLLARL Number of specific fragments extracted= 22 number of extra gaps= 0 total=589 Will force an alignment to be made, even if fragment is small Number of alignments=34 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1elqA/T0339-1elqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1elqA/T0339-1elqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1elqA read from 1elqA/T0339-1elqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1elqA in template set T0339 3 :KVYMDYNATTPLEPEVIQAMTKAMWEAWGN 1elqA 20 :KTYFNFGGQGILPTVALEAITAMYGYLQEN T0339 33 :PSS 1elqA 51 :PFS T0339 37 :YSAGRKAKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSV 1elqA 54 :IAANQHIQQLIAQLRQALAETFNVDPNTITITDNVTTGCDIVLWGL T0339 90 :Q 1elqA 101 :W T0339 105 :GAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSKVSGQTE 1elqA 102 :HQGDEILLTDCEHPGIIAIVQAIAARFGITYRFFPVAATLNQGD T0339 149 :VDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKALN 1elqA 147 :AAVLANHLGPKTRLVILSHLLWNTGQVLPLAEIMAVCRRHQ T0339 196 :GLPPILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFY 1elqA 188 :GNYPVRVLVDGAQSAGSLPLDFSRLEVDYYAFTGHKWF T0339 234 :GP 1elqA 227 :GP T0339 236 :RIGALYIRG 1elqA 230 :GVGGLYIHG T0339 246 :GEFTPLYPMLFGGGQ 1elqA 239 :DCLGEINPTYVGWRS T0339 261 :ERNFRPGTENTPMIAGLGKAAELVTQ 1elqA 269 :GKRFEVATSAYPQYAGLLAALQLHQR T0339 287 :NCEAYEAHMRDVRDYLEERLEAEFG 1elqA 297 :TAEERYQAICQRSEFLWRGLNQLPH T0339 315 :IHLNSQ 1elqA 322 :VHCLAT T0339 323 :GTQRLP 1elqA 328 :SAPQAG T0339 330 :TCNFSIRGP 1elqA 334 :LVSFTVDSP T0339 340 :LQGHVVLAQCRV 1elqA 343 :LGHRAIVQKLEE T0339 352 :LMASV 1elqA 357 :IYLRT T0339 377 :VPF 1elqA 362 :IAD T0339 383 :RNALRLSVGRSTTRAEVDLVVQDL 1elqA 365 :PDCIRACCHYITDEEEINHLLARL Number of specific fragments extracted= 19 number of extra gaps= 0 total=608 Will force an alignment to be made, even if fragment is small Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1elqA/T0339-1elqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1elqA/T0339-1elqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1elqA read from 1elqA/T0339-1elqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1elqA in template set T0339 3 :KVYMDYNATTPLEPEVIQAMTKAMWEAWGNPSSPYSAGRKAKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSV 1elqA 20 :KTYFNFGGQGILPTVALEAITAMYGYLQENGPFSIAANQHIQQLIAQLRQALAETFNVDPNTITITDNVTTGCDIVLWGL T0339 103 :VKGAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSKVSGQTE 1elqA 100 :DWHQGDEILLTDCEHPGIIAIVQAIAARFGITYRFFPVAATLNQGD T0339 149 :VDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKA 1elqA 147 :AAVLANHLGPKTRLVILSHLLWNTGQVLPLAEIMAVCRR T0339 194 :AAGLPPILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFYGPR 1elqA 186 :HQGNYPVRVLVDGAQSAGSLPLDFSRLEVDYYAFTGHKWFAGP T0339 237 :IGALYIRGLGEFTPLYPMLFGGGQ 1elqA 231 :VGGLYIHGDCLGEINPTYVGWRSI T0339 261 :ERNFRPGTENTPMIAGLGKAAELVT 1elqA 269 :GKRFEVATSAYPQYAGLLAALQLHQ T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1elqA 296 :GTAEERYQAICQRSEFLWRGLNQLPHVHCLA T0339 323 :GTQRLPNTCNFSIRG 1elqA 327 :TSAPQAGLVSFTVDS T0339 338 :PRLQGHVVLAQCRVLMASV 1elqA 343 :LGHRAIVQKLEEQRIYLRT T0339 380 :DVARNALRLSVGRSTTRAEVDLVVQDL 1elqA 362 :IADPDCIRACCHYITDEEEINHLLARL Number of specific fragments extracted= 10 number of extra gaps= 0 total=618 Will force an alignment to be made, even if fragment is small Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o4sA/T0339-1o4sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1o4sA expands to /projects/compbio/data/pdb/1o4s.pdb.gz 1o4sA:Skipped atom 146, because occupancy 0.330 <= existing 0.340 in 1o4sA Skipped atom 149, because occupancy 0.330 <= existing 0.340 in 1o4sA Skipped atom 152, because occupancy 0.330 <= existing 0.340 in 1o4sA Skipped atom 155, because occupancy 0.330 <= existing 0.340 in 1o4sA Skipped atom 507, because occupancy 0.500 <= existing 0.500 in 1o4sA Skipped atom 509, because occupancy 0.500 <= existing 0.500 in 1o4sA Skipped atom 511, because occupancy 0.500 <= existing 0.500 in 1o4sA Skipped atom 513, because occupancy 0.500 <= existing 0.500 in 1o4sA Skipped atom 515, because occupancy 0.500 <= existing 0.500 in 1o4sA Skipped atom 517, because occupancy 0.500 <= existing 0.500 in 1o4sA Skipped atom 709, because occupancy 0.350 <= existing 0.650 in 1o4sA Skipped atom 711, because occupancy 0.350 <= existing 0.650 in 1o4sA Skipped atom 713, because occupancy 0.350 <= existing 0.650 in 1o4sA Skipped atom 715, because occupancy 0.350 <= existing 0.650 in 1o4sA Skipped atom 1521, because occupancy 0.350 <= existing 0.650 in 1o4sA Skipped atom 1523, because occupancy 0.350 <= existing 0.650 in 1o4sA Skipped atom 1525, because occupancy 0.350 <= existing 0.650 in 1o4sA Skipped atom 1527, because occupancy 0.350 <= existing 0.650 in 1o4sA Skipped atom 2016, because occupancy 0.500 <= existing 0.500 in 1o4sA Skipped atom 2216, because occupancy 0.350 <= existing 0.650 in 1o4sA Skipped atom 2218, because occupancy 0.350 <= existing 0.650 in 1o4sA # T0339 read from 1o4sA/T0339-1o4sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o4sA read from 1o4sA/T0339-1o4sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1o4sA to template set # found chain 1o4sA in template set Warning: unaligning (T0339)A168 because of BadResidue code BAD_PEPTIDE in next template residue (1o4sA)N172 Warning: unaligning (T0339)N169 because of BadResidue code BAD_PEPTIDE at template residue (1o4sA)N172 Warning: unaligning (T0339)P266 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o4sA)S265 Warning: unaligning (T0339)G267 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o4sA)S265 T0339 1 :ERKVYMDYNATT 1o4sA 29 :EDVINLTAGEPD T0339 13 :PLEPEVIQAMTKAMWE 1o4sA 42 :PTPEPVVEEAVRFLQK T0339 33 :PSSPYSAGRKAKDIINAARESLAKMIGGK 1o4sA 58 :GEVKYTDPRGIYELREGIAKRIGERYKKD T0339 62 :PQDIIFTSGGTESNNLVIHSV 1o4sA 89 :PDQVVVTNGAKQALFNAFMAL T0339 91 :TSKGH 1o4sA 110 :LDPGD T0339 109 :HFITSSVEHDSIRLPLEHL 1o4sA 115 :EVIVFSPVWVSYIPQIILA T0339 132 :VAAVTFVPVSKV 1o4sA 134 :GGTVNVVETFMS T0339 144 :SGQTEVDDILAAVRPTTRLVTIML 1o4sA 147 :NFQPSLEEVEGLLVGKTKAVLINS T0339 170 :NETGIVMPVPEISQ 1o4sA 173 :NPTGVVYRREFLEG T0339 185 :IKALNQER 1o4sA 187 :LVRLAKKR T0339 199 :PILVHTDAAQALGKQR 1o4sA 195 :NFYIISDEVYDSLVYT T0339 216 :D 1o4sA 214 :T T0339 217 :VEDL 1o4sA 217 :LDVS T0339 221 :GV 1o4sA 222 :GF T0339 223 :DFLTIVGHK 1o4sA 226 :IVYINGFSK T0339 232 :FY 1o4sA 236 :HS T0339 234 :GPRIGALYIR 1o4sA 240 :GWRVGYLISS T0339 244 :GLGEFTPLYPMLF 1o4sA 251 :KVATAVSKIQSHT T0339 268 :TENTPMIAGLGKA 1o4sA 266 :CINTVAQYAALKA T0339 285 :TQ 1o4sA 279 :LE T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1o4sA 282 :DNSYMVQTFKERKNFVVERLKKM T0339 314 :RIHLNSQFP 1o4sA 305 :GVKFVEPEG T0339 328 :PNTCNFSIRG 1o4sA 314 :AFYLFFKVRG T0339 341 :QGHVVLAQCRV 1o4sA 324 :DDVKFCERLLE T0339 352 :LMASVGAACHS 1o4sA 338 :VALVPGSAFLK T0339 383 :RNALRLSV 1o4sA 349 :PGFVRLSF T0339 393 :STTRAEVDLVVQDLKQAV 1o4sA 357 :ATSIERLTEALDRIEDFL Number of specific fragments extracted= 27 number of extra gaps= 2 total=645 Will force an alignment to be made, even if fragment is small Number of alignments=37 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o4sA/T0339-1o4sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1o4sA/T0339-1o4sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o4sA read from 1o4sA/T0339-1o4sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o4sA in template set Warning: unaligning (T0339)A168 because of BadResidue code BAD_PEPTIDE in next template residue (1o4sA)N172 Warning: unaligning (T0339)N169 because of BadResidue code BAD_PEPTIDE at template residue (1o4sA)N172 Warning: unaligning (T0339)P266 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o4sA)S265 Warning: unaligning (T0339)G267 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o4sA)S265 T0339 2 :RKVYMDYNATT 1o4sA 30 :DVINLTAGEPD T0339 13 :PLEPEVIQAMTKAMWEAWGN 1o4sA 42 :PTPEPVVEEAVRFLQKGEVK T0339 33 :PSSPYSA 1o4sA 65 :PRGIYEL T0339 47 :INAARESLAKMIGG 1o4sA 72 :REGIAKRIGERYKK T0339 61 :KPQDIIFTSGGTESNNLVIHSVV 1o4sA 88 :SPDQVVVTNGAKQALFNAFMALL T0339 105 :GAKPHFITSSVEHDSIRLPLEHL 1o4sA 111 :DPGDEVIVFSPVWVSYIPQIILA T0339 132 :VAAVTFVPVS 1o4sA 134 :GGTVNVVETF T0339 142 :KVSGQTEVDDILAAVRPTTRLVTIML 1o4sA 145 :SKNFQPSLEEVEGLLVGKTKAVLINS T0339 170 :NETGIVMP 1o4sA 173 :NPTGVVYR T0339 178 :VPEISQRIKALN 1o4sA 184 :LEGLVRLAKKRN T0339 200 :ILVHTDAAQALGKQRVD 1o4sA 196 :FYIISDEVYDSLVYTDE T0339 217 :V 1o4sA 217 :L T0339 224 :FLTIVGHKFY 1o4sA 227 :VYINGFSKSH T0339 234 :G 1o4sA 240 :G T0339 236 :RIGALYIRG 1o4sA 242 :RVGYLISSE T0339 246 :G 1o4sA 251 :K T0339 268 :TENTPMIAGLG 1o4sA 266 :CINTVAQYAAL T0339 283 :LVTQ 1o4sA 277 :KALE T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1o4sA 282 :DNSYMVQTFKERKNFVVERLKKM T0339 311 :G 1o4sA 305 :G T0339 315 :IHLNSQ 1o4sA 306 :VKFVEP T0339 325 :QRLP 1o4sA 312 :EGAF T0339 330 :TCNFSIRG 1o4sA 316 :YLFFKVRG T0339 340 :LQGHVVLAQCRV 1o4sA 324 :DDVKFCERLLEE T0339 352 :LMASVGAAC 1o4sA 338 :VALVPGSAF T0339 381 :VARNALRLSVGR 1o4sA 347 :LKPGFVRLSFAT T0339 395 :TRAEVDLVVQDLKQAV 1o4sA 359 :SIERLTEALDRIEDFL Number of specific fragments extracted= 27 number of extra gaps= 2 total=672 Will force an alignment to be made, even if fragment is small Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o4sA/T0339-1o4sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1o4sA/T0339-1o4sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o4sA read from 1o4sA/T0339-1o4sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o4sA in template set Warning: unaligning (T0339)A168 because of BadResidue code BAD_PEPTIDE in next template residue (1o4sA)N172 Warning: unaligning (T0339)N169 because of BadResidue code BAD_PEPTIDE at template residue (1o4sA)N172 Warning: unaligning (T0339)P266 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o4sA)S265 Warning: unaligning (T0339)G267 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o4sA)S265 T0339 1 :ERKVYMDYNATT 1o4sA 29 :EDVINLTAGEPD T0339 13 :PLEPEVIQAMTKAMWE 1o4sA 42 :PTPEPVVEEAVRFLQK T0339 29 :AWGNPSSPY 1o4sA 61 :KYTDPRGIY T0339 45 :DIINAARESLAKMIGG 1o4sA 70 :ELREGIAKRIGERYKK T0339 61 :KPQDIIFTSGGTESNNLVIHSV 1o4sA 88 :SPDQVVVTNGAKQALFNAFMAL T0339 104 :KGAKPHFITSSVEHDSIRLPLEHL 1o4sA 110 :LDPGDEVIVFSPVWVSYIPQIILA T0339 132 :VAAVTFVPVS 1o4sA 134 :GGTVNVVETF T0339 142 :KVSGQTEVDDILAAVRPTTRLVTIML 1o4sA 145 :SKNFQPSLEEVEGLLVGKTKAVLINS T0339 170 :NETGIVMP 1o4sA 173 :NPTGVVYR T0339 178 :VPEISQRIKA 1o4sA 184 :LEGLVRLAKK T0339 198 :PPILVHTDAAQ 1o4sA 194 :RNFYIISDEVY T0339 209 :ALGKQRVD 1o4sA 207 :LVYTDEFT T0339 217 :VEDLGVDFLTIVGHKFYGPR 1o4sA 220 :SEGFDRIVYINGFSKSHSMT T0339 237 :IGALYIRGLGEFTPLYP 1o4sA 243 :VGYLISSEKVATAVSKI T0339 265 :R 1o4sA 263 :T T0339 268 :TENTPMIAGLGKA 1o4sA 266 :CINTVAQYAALKA T0339 284 :VTQNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1o4sA 279 :LEVDNSYMVQTFKERKNFVVERLKKMGVKFVEP T0339 326 :RLPNTCNFSIRGPRLQGHVVLAQCRVLMASVGAA 1o4sA 312 :EGAFYLFFKVRGDDVKFCERLLEEKKVALVPGSA T0339 380 :DVARNALRLSVG 1o4sA 346 :FLKPGFVRLSFA T0339 394 :TTRAEVDLVVQDLKQAV 1o4sA 358 :TSIERLTEALDRIEDFL Number of specific fragments extracted= 20 number of extra gaps= 2 total=692 Will force an alignment to be made, even if fragment is small Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m32A/T0339-1m32A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1m32A expands to /projects/compbio/data/pdb/1m32.pdb.gz 1m32A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 318, because occupancy 0.500 <= existing 0.500 in 1m32A Skipped atom 320, because occupancy 0.500 <= existing 0.500 in 1m32A Skipped atom 322, because occupancy 0.500 <= existing 0.500 in 1m32A Skipped atom 324, because occupancy 0.500 <= existing 0.500 in 1m32A Skipped atom 326, because occupancy 0.500 <= existing 0.500 in 1m32A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0339 read from 1m32A/T0339-1m32A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m32A read from 1m32A/T0339-1m32A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1m32A to template set # found chain 1m32A in template set Warning: unaligning (T0339)V4 because first residue in template chain is (1m32A)Y5 T0339 5 :YMDYNATTPLEPEVIQA 1m32A 6 :LLLTPGPLTTSRTVKEA T0339 30 :WGNPSSPYS 1m32A 23 :MLFDSCTWD T0339 40 :GRKAKDIINAARESLAKMI 1m32A 32 :DDYNIGVVEQIRQQLTALA T0339 60 :GKPQ 1m32A 51 :TASE T0339 64 :DIIFT 1m32A 57 :TSVLL T0339 69 :SGGTESNNLVIHSV 1m32A 63 :GSGSYAVEAVLGSA T0339 91 :TSKGH 1m32A 77 :LGPQD T0339 109 :HFITSSVEHDS 1m32A 82 :KVLIVSNGAYG T0339 120 :IRLPLEHL 1m32A 95 :MVEMAGLM T0339 132 :VAAVTFVPVSK 1m32A 103 :GIAHHAYDCGE T0339 144 :SGQTEVDDILAAVR 1m32A 114 :VARPDVQAIDAILN T0339 158 :PTTRLVTIMLANNETGIVMPVPEISQ 1m32A 130 :PTISHIAMVHSETTTGMLNPIDEVGA T0339 188 :LNQER 1m32A 156 :LAHRY T0339 199 :PILVHTDAAQALGKQRVDVEDLGVDFLTIVGHK 1m32A 161 :GKTYIVDAMSSFGGIPMDIAALHIDYLISSANK T0339 232 :FY 1m32A 195 :IQ T0339 234 :GPRIGALYIR 1m32A 198 :VPGFAFVIAR T0339 244 :GLGEFTPLYPMLFGGG 1m32A 209 :QKLAACKGHSRSLSLD T0339 260 :QERNFR 1m32A 235 :NHGKWR T0339 267 :GTENTPMIAGLGKAAELVTQ 1m32A 241 :FTSPTHTVLAFAQALKELAK T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1m32A 263 :GVAARHQRYQQNQRSLVAGMRAL T0339 314 :RIHLNS 1m32A 286 :GFNTLL T0339 322 :PGTQRLPNTCNFSIR 1m32A 292 :DDELHSPIITAFYSP T0339 337 :GPRLQGHVVLAQCRV 1m32A 308 :DPQYRFSEFYRRLKE T0339 352 :LMASVGAACH 1m32A 325 :FVIYPGKVSQ T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQA 1m32A 335 :SDCFRIGNIGEVYAADITALLTAIRTA Number of specific fragments extracted= 25 number of extra gaps= 0 total=717 Will force an alignment to be made, even if fragment is small Number of alignments=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m32A/T0339-1m32A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1m32A/T0339-1m32A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m32A read from 1m32A/T0339-1m32A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m32A in template set Warning: unaligning (T0339)K3 because first residue in template chain is (1m32A)Y5 T0339 4 :VYM 1m32A 6 :LLL T0339 8 :YNATTPLEPEVIQA 1m32A 9 :TPGPLTTSRTVKEA T0339 31 :GNPSSPYSAGRKAKDIINAARESLAKMI 1m32A 23 :MLFDSCTWDDDYNIGVVEQIRQQLTALA T0339 60 :GKPQ 1m32A 51 :TASE T0339 65 :IIFTSGGTESNNLVIHSVV 1m32A 59 :VLLQGSGSYAVEAVLGSAL T0339 105 :GAKPHFITSSV 1m32A 78 :GPQDKVLIVSN T0339 118 :DSIRLPLEHLVEEQVAAVTFVPVSK 1m32A 89 :GAYGARMVEMAGLMGIAHHAYDCGE T0339 144 :SGQTEVDDILAAV 1m32A 114 :VARPDVQAIDAIL T0339 157 :RPTTRLVTIMLANNETGIVMPVPEISQRIKALN 1m32A 129 :DPTISHIAMVHSETTTGMLNPIDEVGALAHRYG T0339 200 :ILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFY 1m32A 162 :KTYIVDAMSSFGGIPMDIAALHIDYLISSANKCI T0339 234 :GP 1m32A 197 :GV T0339 236 :RIGALYIRG 1m32A 200 :GFAFVIARE T0339 246 :GEFTPLYPMLFGGGQ 1m32A 209 :QKLAACKGHSRSLSL T0339 261 :ERNFRP 1m32A 236 :HGKWRF T0339 268 :TENTPMIAGLGKAAELVTQ 1m32A 242 :TSPTHTVLAFAQALKELAK T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1m32A 263 :GVAARHQRYQQNQRSLVAGMRAL T0339 311 :G 1m32A 286 :G T0339 315 :IHLNSQ 1m32A 287 :FNTLLD T0339 323 :GTQRLPNTCNFSI 1m32A 293 :DELHSPIITAFYS T0339 336 :RGPRLQGHVVLAQCRV 1m32A 307 :EDPQYRFSEFYRRLKE T0339 352 :LMASVG 1m32A 325 :FVIYPG T0339 364 :H 1m32A 331 :K T0339 377 :VPF 1m32A 332 :VSQ T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQA 1m32A 335 :SDCFRIGNIGEVYAADITALLTAIRTA Number of specific fragments extracted= 24 number of extra gaps= 0 total=741 Will force an alignment to be made, even if fragment is small Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m32A/T0339-1m32A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1m32A/T0339-1m32A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m32A read from 1m32A/T0339-1m32A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m32A in template set T0339 8 :YNATTPLEPEVIQAM 1m32A 9 :TPGPLTTSRTVKEAM T0339 32 :NPSSPYSAGRKAKDIINAARESLAKMI 1m32A 24 :LFDSCTWDDDYNIGVVEQIRQQLTALA T0339 60 :GKPQD 1m32A 51 :TASEG T0339 65 :IIFTSGGTESNNLVIHSV 1m32A 59 :VLLQGSGSYAVEAVLGSA T0339 104 :KGAKPHFITSSVE 1m32A 77 :LGPQDKVLIVSNG T0339 119 :SIRLPLEHLVEEQVAAVTFVPVS 1m32A 90 :AYGARMVEMAGLMGIAHHAYDCG T0339 143 :VSGQTEVDDILAAV 1m32A 113 :EVARPDVQAIDAIL T0339 157 :RPTTRLVTIMLANNETGIVMPVPEISQRIKA 1m32A 129 :DPTISHIAMVHSETTTGMLNPIDEVGALAHR T0339 198 :PPILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFYGPR 1m32A 160 :YGKTYIVDAMSSFGGIPMDIAALHIDYLISSANKCIQGV T0339 237 :IGALYIRGLGEFTPLYPMLFGGGQ 1m32A 201 :FAFVIAREQKLAACKGHSRSLSLD T0339 261 :ERNFRPGTENTPMIAGLGKAAELVT 1m32A 235 :NHGKWRFTSPTHTVLAFAQALKELA T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1m32A 262 :GGVAARHQRYQQNQRSLVAGMRALGFNTLLD T0339 323 :GTQRLPNTCNFSIRG 1m32A 293 :DELHSPIITAFYSPE T0339 338 :PRLQGHVVLAQCRVLMASVGAA 1m32A 311 :YRFSEFYRRLKEQGFVIYPGKV T0339 381 :VARNALRLSVGRSTTRAEVDLVVQDLKQA 1m32A 333 :SQSDCFRIGNIGEVYAADITALLTAIRTA Number of specific fragments extracted= 15 number of extra gaps= 0 total=756 Will force an alignment to be made, even if fragment is small Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b5pA/T0339-1b5pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1b5pA expands to /projects/compbio/data/pdb/1b5p.pdb.gz 1b5pA:# T0339 read from 1b5pA/T0339-1b5pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b5pA read from 1b5pA/T0339-1b5pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1b5pA to template set # found chain 1b5pA in template set T0339 2 :RKVYMDYNATTP 1b5pA 32 :DLVALTAGEPDF T0339 14 :LEPEVIQAMTKAMWE 1b5pA 45 :TPEHVKEAARRALAQ T0339 33 :PSSPYSAGRKAKDIINAARESLAKMIG 1b5pA 60 :GKTKYAPPAGIPELREALAEKFRRENG T0339 60 :GKPQDIIFTSGGTESNNLVIHSV 1b5pA 89 :VTPEETIVTVGGSQALFNLFQAI T0339 91 :TSKGH 1b5pA 112 :LDPGD T0339 109 :HFITSSVEHDSIRLPLEHL 1b5pA 117 :EVIVLSPYWVSYPEMVRFA T0339 132 :VAAVTFVPVSKV 1b5pA 136 :GGVVVEVETLPE T0339 144 :SGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1b5pA 149 :GFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEA T0339 185 :IKALNQER 1b5pA 189 :LARLAVEH T0339 199 :PILVHTDAAQALGKQR 1b5pA 197 :DFYLVSDEIYEHLLYE T0339 215 :VDVEDL 1b5pA 216 :FSPGRV T0339 223 :DFLTIVGHK 1b5pA 226 :TLTVNGAAK T0339 232 :FY 1b5pA 236 :FA T0339 234 :GPRIGALYIR 1b5pA 240 :GWRIGYACGP T0339 244 :GLGEFT 1b5pA 251 :EVIKAM T0339 250 :PLYP 1b5pA 258 :SVSR T0339 256 :FG 1b5pA 262 :QS T0339 266 :PGTENTPMIAGLGKAAE 1b5pA 264 :TTSPDTIAQWATLEALT T0339 283 :LVTQNCEAYEAHMRDVRDYLEERLEAE 1b5pA 284 :ASRAFVEMAREAYRRRRDLLLEGLTAL T0339 314 :RIHLNSQFP 1b5pA 311 :GLKAVRPSG T0339 328 :PNTCNFSIRGPRLQGHVVLAQCRV 1b5pA 320 :AFYVLMDTSPIAPDEVRAAERLLE T0339 352 :LMASVGAACHS 1b5pA 346 :VAVVPGTDFAA T0339 383 :RNALRLS 1b5pA 357 :FGHVRLS T0339 392 :RSTTRAEVDLVVQD 1b5pA 364 :YATSEENLRKALER Number of specific fragments extracted= 24 number of extra gaps= 0 total=780 Will force an alignment to be made, even if fragment is small Number of alignments=43 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b5pA/T0339-1b5pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1b5pA/T0339-1b5pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b5pA read from 1b5pA/T0339-1b5pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b5pA in template set T0339 2 :RKVYMDYNATT 1b5pA 32 :DLVALTAGEPD T0339 13 :PLEPEVIQAMTKAMWEAWGN 1b5pA 44 :DTPEHVKEAARRALAQGKTK T0339 33 :PSSP 1b5pA 67 :PAGI T0339 44 :KDIINAARESLAKMIGG 1b5pA 71 :PELREALAEKFRRENGL T0339 61 :KPQDIIFTSGGTESNNLVIHSVV 1b5pA 90 :TPEETIVTVGGSQALFNLFQAIL T0339 105 :GAKPHFITSSVE 1b5pA 113 :DPGDEVIVLSPY T0339 121 :RLPLEHLVEEQVAAVTFVPVSKVSG 1b5pA 125 :WVSYPEMVRFAGGVVVEVETLPEEG T0339 146 :QTEVDDILAAVRPTTRLVTIMLANNETGIVMP 1b5pA 151 :VPDPERVRRAITPRTKALVVNSPNNPTGAVYP T0339 178 :VPEISQRIKALN 1b5pA 186 :LEALARLAVEHD T0339 200 :ILVHTDAAQALGKQRVD 1b5pA 198 :FYLVSDEIYEHLLYEGE T0339 217 :VED 1b5pA 219 :GRV T0339 222 :V 1b5pA 222 :A T0339 223 :DFLTIVGHKFYGP 1b5pA 226 :TLTVNGAAKAFAM T0339 236 :R 1b5pA 240 :G T0339 237 :IGALYIRG 1b5pA 243 :IGYACGPK T0339 246 :G 1b5pA 251 :E T0339 261 :ER 1b5pA 264 :TT T0339 268 :TENTPMIAGLGKAAE 1b5pA 266 :SPDTIAQWATLEALT T0339 283 :LVTQNCEAYEAHMRDVRDYLEERLEAE 1b5pA 284 :ASRAFVEMAREAYRRRRDLLLEGLTAL T0339 311 :G 1b5pA 311 :G T0339 315 :IHLN 1b5pA 312 :LKAV T0339 323 :GTQR 1b5pA 316 :RPSG T0339 328 :PNTCNFSIRGPRLQGHVVLAQCRV 1b5pA 320 :AFYVLMDTSPIAPDEVRAAERLLE T0339 352 :LMASVGA 1b5pA 346 :VAVVPGT T0339 379 :FDVARNALRLSVGR 1b5pA 353 :DFAAFGHVRLSYAT T0339 395 :TRAEVDLVVQD 1b5pA 367 :SEENLRKALER Number of specific fragments extracted= 26 number of extra gaps= 0 total=806 Will force an alignment to be made, even if fragment is small Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b5pA/T0339-1b5pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1b5pA/T0339-1b5pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b5pA read from 1b5pA/T0339-1b5pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b5pA in template set T0339 2 :RKVYMDYNATT 1b5pA 32 :DLVALTAGEPD T0339 13 :PLEPEVIQAMTKAMWEAW 1b5pA 44 :DTPEHVKEAARRALAQGK T0339 31 :GNPSSPY 1b5pA 65 :APPAGIP T0339 45 :DIINAARESLAKMIGG 1b5pA 72 :ELREALAEKFRRENGL T0339 61 :KPQDIIFTSGGTESNNLVIHSV 1b5pA 90 :TPEETIVTVGGSQALFNLFQAI T0339 104 :KGAKPHFITSSVEHDSIRLPLEHL 1b5pA 112 :LDPGDEVIVLSPYWVSYPEMVRFA T0339 132 :VAAVTFVPVS 1b5pA 136 :GGVVVEVETL T0339 142 :KVSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMP 1b5pA 147 :EEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYP T0339 178 :VPEISQRIKA 1b5pA 186 :LEALARLAVE T0339 198 :PPILVHTDAAQALGKQRVD 1b5pA 196 :HDFYLVSDEIYEHLLYEGE T0339 217 :VEDLGVDFLTIVGHKFYGPR 1b5pA 220 :RVAPEHTLTVNGAAKAFAMT T0339 237 :IGALYIRGLGEFTPLYPM 1b5pA 243 :IGYACGPKEVIKAMASVS T0339 263 :NFRPGTENTPMIAGLGKAAELVT 1b5pA 261 :RQSTTSPDTIAQWATLEALTNQE T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1b5pA 287 :AFVEMAREAYRRRRDLLLEGLTALGLKAVRP T0339 326 :RLPNTCNFSIRG 1b5pA 318 :SGAFYVLMDTSP T0339 338 :PRLQGHVVLAQCRVLMASVG 1b5pA 332 :PDEVRAAERLLEAGVAVVPG T0339 378 :PFDVARNALRLSVG 1b5pA 352 :TDFAAFGHVRLSYA T0339 394 :TTRAEVDLVVQD 1b5pA 366 :TSEENLRKALER Number of specific fragments extracted= 18 number of extra gaps= 0 total=824 Will force an alignment to be made, even if fragment is small Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wyuB/T0339-1wyuB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wyuB expands to /projects/compbio/data/pdb/1wyu.pdb.gz 1wyuB:# T0339 read from 1wyuB/T0339-1wyuB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wyuB read from 1wyuB/T0339-1wyuB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wyuB to template set # found chain 1wyuB in template set T0339 4 :VYMDYNATT 1wyuB 68 :FYPLGSCTM T0339 13 :PLEPEVIQAM 1wyuB 78 :YNPKLHEEAA T0339 28 :EAW 1wyuB 88 :RLF T0339 31 :GNPSSPYSAGRKAKDIINAARESLAKMIGG 1wyuB 93 :LHPYQDPRTAQGALRLMWELGEYLKALTGM T0339 63 :QDIIFTSG 1wyuB 123 :DAITLEPA T0339 71 :GTESNNLVIHSVVKHFHANQTSKGH 1wyuB 132 :GAHGELTGILIIRAYHEDRGEGRTR T0339 108 :PHFITSSVEHDSIRLPLEHL 1wyuB 157 :RVVLVPDSAHGSNPATASMA T0339 132 :VAAVTFVPVSK 1wyuB 177 :GYQVREIPSGP T0339 144 :SGQTEVDDILAAVRPTTRLVTIMLANNETGIVM 1wyuB 188 :EGEVDLEALKRELGPHVAALMLTNPNTLGLFER T0339 180 :EISQ 1wyuB 221 :RILE T0339 185 :IKALNQER 1wyuB 225 :ISRLCKEA T0339 199 :PILVHTDAAQALGKQRVD 1wyuB 233 :GVQLYYDGANLNAIMGWA T0339 217 :VEDLGVDFLTIVGHK 1wyuB 252 :PGDMGFDVVHLNLHK T0339 232 :F 1wyuB 268 :F T0339 234 :GPRIGALYIR 1wyuB 276 :GPGSGPVGVK T0339 244 :GLGEFTPLYPMLFGG 1wyuB 287 :HLAPYLPVPLVERGE T0339 260 :QERNFRPGTENTPMIAGLGKAAELVTQ 1wyuB 313 :SIGRVRSFYGNFLALVRAWAYIRTLGL T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1wyuB 341 :GLKKAAALAVLNARYLKELLKEK T0339 314 :RIHLNSQFP 1wyuB 364 :GYRVPYDGP T0339 327 :LPNTCNFSIRGP 1wyuB 373 :SMHEFVAQPPEG T0339 340 :LQGHVVLAQCRVLMASVGAACHSDHG 1wyuB 385 :FRALDLAKGLLELGFHPPTVYFPLIV T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQAVA 1wyuB 411 :KEALMVEPTETEAKETLEAFAEAMGALLK T0339 412 :QLE 1wyuB 444 :WLE Number of specific fragments extracted= 23 number of extra gaps= 0 total=847 Will force an alignment to be made, even if fragment is small Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wyuB/T0339-1wyuB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1wyuB/T0339-1wyuB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wyuB read from 1wyuB/T0339-1wyuB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wyuB in template set T0339 9 :NATTPLEPEVIQA 1wyuB 74 :CTMKYNPKLHEEA T0339 26 :M 1wyuB 87 :A T0339 28 :EAWGN 1wyuB 88 :RLFAD T0339 33 :PSSPYSAGRKAKDIINAARESLAKMIGGKP 1wyuB 95 :PYQDPRTAQGALRLMWELGEYLKALTGMDA T0339 65 :IIF 1wyuB 125 :ITL T0339 68 :TSGGTESNNLVIHSVVKHFHANQTS 1wyuB 129 :PAAGAHGELTGILIIRAYHEDRGEG T0339 105 :GAKPHFITSSVEHDSIRL 1wyuB 154 :RTRRVVLVPDSAHGSNPA T0339 127 :LVEEQVAAVTFVPVSK 1wyuB 172 :TASMAGYQVREIPSGP T0339 144 :SGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKALN 1wyuB 188 :EGEVDLEALKRELGPHVAALMLTNPNTLGLFERRILEISRLCKEAG T0339 200 :ILVHTDAAQ 1wyuB 234 :VQLYYDGAN T0339 209 :ALGKQRVDV 1wyuB 245 :AIMGWARPG T0339 219 :DLGVDFLTIVGHKFY 1wyuB 254 :DMGFDVVHLNLHKTF T0339 235 :P 1wyuB 271 :P T0339 236 :R 1wyuB 273 :G T0339 237 :IGALYIRG 1wyuB 279 :SGPVGVKA T0339 246 :GEFTPLYPMLFGGGQ 1wyuB 287 :HLAPYLPVPLVERGE T0339 261 :ERNFRPGTENTPMIAGLGKAAELVTQ 1wyuB 314 :IGRVRSFYGNFLALVRAWAYIRTLGL T0339 289 :EAYEAHMRDVRDYLE 1wyuB 340 :EGLKKAAALAVLNAR T0339 304 :ERLEAE 1wyuB 358 :ELLKEK T0339 311 :G 1wyuB 364 :G T0339 315 :IHLNSQ 1wyuB 365 :YRVPYD T0339 323 :GT 1wyuB 371 :GP T0339 327 :LPNTCNFSIRGP 1wyuB 373 :SMHEFVAQPPEG T0339 340 :LQGHVVLAQCRV 1wyuB 385 :FRALDLAKGLLE T0339 356 :VG 1wyuB 397 :LG T0339 367 :QPSPV 1wyuB 400 :HPPTV T0339 377 :VPFDVARNALRLSVGRSTTRAEVDLVVQDLKQAVA 1wyuB 405 :YFPLIVKEALMVEPTETEAKETLEAFAEAMGALLK Number of specific fragments extracted= 27 number of extra gaps= 0 total=874 Will force an alignment to be made, even if fragment is small Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wyuB/T0339-1wyuB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1wyuB/T0339-1wyuB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wyuB read from 1wyuB/T0339-1wyuB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wyuB in template set T0339 8 :YNATTPLEPEVIQAM 1wyuB 73 :SCTMKYNPKLHEEAA T0339 28 :EAWGNPS 1wyuB 88 :RLFADLH T0339 35 :SPYSAGRKAKDIINAARESLAKMIGG 1wyuB 97 :QDPRTAQGALRLMWELGEYLKALTGM T0339 64 :DIIF 1wyuB 124 :AITL T0339 68 :TSGGTESNNLVIHSVVKHFHAN 1wyuB 129 :PAAGAHGELTGILIIRAYHEDR T0339 102 :PVKGAKPHFITSSVEHDSIRLPLEHL 1wyuB 151 :GEGRTRRVVLVPDSAHGSNPATASMA T0339 132 :VAAVTFVPVS 1wyuB 177 :GYQVREIPSG T0339 143 :VSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKA 1wyuB 187 :PEGEVDLEALKRELGPHVAALMLTNPNTLGLFERRILEISRLCKE T0339 198 :PPILVHTDAAQALGKQRVD 1wyuB 232 :AGVQLYYDGANLNAIMGWA T0339 217 :VEDLGVDFLTIVGHKFYGPR 1wyuB 252 :PGDMGFDVVHLNLHKTFTVP T0339 237 :IGALYIRGLGEFTPLYPMLFGGGQ 1wyuB 279 :SGPVGVKAHLAPYLPVPLVERGEE T0339 261 :ERNFRPGTENTPMIAGLGKAAELVT 1wyuB 314 :IGRVRSFYGNFLALVRAWAYIRTLG T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1wyuB 340 :EGLKKAAALAVLNARYLKELLKEKGYRVPYD T0339 325 :QRLPNTCNFSIRG 1wyuB 371 :GPSMHEFVAQPPE T0339 338 :PRLQGHVVLAQCRVLMASV 1wyuB 385 :FRALDLAKGLLELGFHPPT T0339 376 :GVPFDVARNALRLSVGRSTTRAEVDLVVQDLKQAVA 1wyuB 404 :VYFPLIVKEALMVEPTETEAKETLEAFAEAMGALLK Number of specific fragments extracted= 16 number of extra gaps= 0 total=890 Will force an alignment to be made, even if fragment is small Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m6sA/T0339-1m6sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1m6sA expands to /projects/compbio/data/pdb/1m6s.pdb.gz 1m6sA:Bad short name: N1 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: C2' for alphabet: pdb_atoms Bad short name: C3 for alphabet: pdb_atoms Bad short name: O3 for alphabet: pdb_atoms Bad short name: C4 for alphabet: pdb_atoms Bad short name: C4' for alphabet: pdb_atoms Bad short name: C5 for alphabet: pdb_atoms Bad short name: C6 for alphabet: pdb_atoms Bad short name: C5' for alphabet: pdb_atoms Bad short name: OP4 for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms # T0339 read from 1m6sA/T0339-1m6sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m6sA read from 1m6sA/T0339-1m6sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1m6sA to template set # found chain 1m6sA in template set Warning: unaligning (T0339)K3 because first residue in template chain is (1m6sA)M1 Warning: unaligning (T0339)L167 because of BadResidue code BAD_PEPTIDE in next template residue (1m6sA)T137 Warning: unaligning (T0339)A168 because of BadResidue code BAD_PEPTIDE at template residue (1m6sA)T137 Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1m6sA)G200 T0339 4 :VYMDYNATTPLEPEVIQAMT 1m6sA 2 :IDLRSDTVTKPTEEMRKAMA T0339 33 :PSSPYSAGRKAKDIINAARESLAKMIGG 1m6sA 22 :QAEVGDDVYGEDPTINELERLAAETFGK T0339 63 :QDIIFTSGGTESNNLVIHSV 1m6sA 50 :EAALFVPSGTMGNQVSIMAH T0339 91 :TSKGH 1m6sA 70 :TQRGD T0339 109 :HFITSSVEHDSIR 1m6sA 75 :EVILEADSHIFWY T0339 122 :LPLEHL 1m6sA 91 :AMAVLS T0339 132 :VAAVTFVPVS 1m6sA 97 :GVMPHPVPGK T0339 144 :SGQTEVDDILAAVRPT 1m6sA 107 :NGAMDPDDVRKAIRPR T0339 160 :TRLVTIM 1m6sA 129 :TSLIAIE T0339 169 :NNE 1m6sA 138 :HNR T0339 172 :TGIVMPVPEISQ 1m6sA 142 :GGRVVPLENIKE T0339 185 :IKALNQER 1m6sA 154 :ICTIAKEH T0339 199 :PILVHTDAAQ 1m6sA 162 :GINVHIDGAR T0339 209 :ALGKQRVDVEDL 1m6sA 175 :ASIASGVPVKEY T0339 221 :GVDFLTIVG 1m6sA 189 :YADSVMFCL T0339 232 :FYGPRIGALYIR 1m6sA 201 :LCAPVGSVVVGD T0339 244 :GLGEFTPLYPMLFGG 1m6sA 214 :DFIERARKARKMLGG T0339 266 :PGTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEER 1m6sA 229 :GMRQAGVLAAAGIIALTKMVDRLKEDHENARFLALKLKEI T0339 314 :RIHLNSQ 1m6sA 269 :GYSVNPE T0339 325 :QRLPNTCNFSIRGPRLQGHVVLAQCRV 1m6sA 276 :DVKTNMVILRTDNLKVNAHGFIEALRN T0339 352 :LMASVGA 1m6sA 305 :VLANAVS T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQAVAQL 1m6sA 312 :DTEIRLVTHKDVSRNDIEEALNIFEKLFRKF Number of specific fragments extracted= 22 number of extra gaps= 1 total=912 Will force an alignment to be made, even if fragment is small Number of alignments=49 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m6sA/T0339-1m6sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1m6sA/T0339-1m6sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m6sA read from 1m6sA/T0339-1m6sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m6sA in template set Warning: unaligning (T0339)K3 because first residue in template chain is (1m6sA)M1 Warning: unaligning (T0339)L167 because of BadResidue code BAD_PEPTIDE in next template residue (1m6sA)T137 Warning: unaligning (T0339)A168 because of BadResidue code BAD_PEPTIDE at template residue (1m6sA)T137 Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1m6sA)G200 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1m6sA)G200 T0339 4 :VYMDYNATTPLEPEVIQAM 1m6sA 2 :IDLRSDTVTKPTEEMRKAM T0339 28 :EAWGNPSSPYSAG 1m6sA 21 :AQAEVGDDVYGED T0339 45 :DIINAARESLAKMIGGKP 1m6sA 34 :PTINELERLAAETFGKEA T0339 65 :IIFTSGGTESNNLVIHSVV 1m6sA 52 :ALFVPSGTMGNQVSIMAHT T0339 105 :GAKPHFITSSVEH 1m6sA 71 :QRGDEVILEADSH T0339 120 :IRL 1m6sA 84 :IFW T0339 123 :PLEHL 1m6sA 91 :AMAVL T0339 131 :QVAAVTFVPVS 1m6sA 96 :SGVMPHPVPGK T0339 144 :SGQTEVDDILAAVRP 1m6sA 107 :NGAMDPDDVRKAIRP T0339 160 :TRLVTIM 1m6sA 129 :TSLIAIE T0339 169 :NNETG 1m6sA 138 :HNRSG T0339 174 :IVMP 1m6sA 144 :RVVP T0339 178 :VPEISQRIKALN 1m6sA 151 :IKEICTIAKEHG T0339 200 :ILVHTDAAQALG 1m6sA 163 :INVHIDGARIFN T0339 214 :RVDVEDL 1m6sA 180 :GVPVKEY T0339 221 :GVDFLTIVG 1m6sA 189 :YADSVMFCL T0339 233 :Y 1m6sA 201 :L T0339 234 :GPR 1m6sA 203 :APV T0339 238 :GALYIRGLGEF 1m6sA 206 :GSVVVGDRDFI T0339 256 :FGGGQ 1m6sA 226 :LGGGM T0339 268 :TENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEER 1m6sA 231 :RQAGVLAAAGIIALTKMVDRLKEDHENARFLALKLKEI T0339 311 :G 1m6sA 269 :G T0339 315 :IHL 1m6sA 270 :YSV T0339 322 :PGTQRLPNTCNFSIRGPRLQGHVVLAQCRV 1m6sA 273 :NPEDVKTNMVILRTDNLKVNAHGFIEALRN T0339 352 :LMASV 1m6sA 305 :VLANA T0339 381 :VARNALRLSVGRSTTRAEVDLVVQDLKQAVAQL 1m6sA 310 :VSDTEIRLVTHKDVSRNDIEEALNIFEKLFRKF Number of specific fragments extracted= 26 number of extra gaps= 1 total=938 Will force an alignment to be made, even if fragment is small Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m6sA/T0339-1m6sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1m6sA/T0339-1m6sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m6sA read from 1m6sA/T0339-1m6sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m6sA in template set Warning: unaligning (T0339)K3 because first residue in template chain is (1m6sA)M1 Warning: unaligning (T0339)L167 because of BadResidue code BAD_PEPTIDE in next template residue (1m6sA)T137 Warning: unaligning (T0339)A168 because of BadResidue code BAD_PEPTIDE at template residue (1m6sA)T137 Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1m6sA)G200 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1m6sA)G200 T0339 4 :VYMDYNATTPLEPEVIQAMT 1m6sA 2 :IDLRSDTVTKPTEEMRKAMA T0339 29 :AWGNPSSPYSAG 1m6sA 22 :QAEVGDDVYGED T0339 45 :DIINAARESLAKMIGG 1m6sA 34 :PTINELERLAAETFGK T0339 64 :DIIFTSGGTESNNLVIHSV 1m6sA 51 :AALFVPSGTMGNQVSIMAH T0339 104 :KGAKPHFITSSVEHDSIR 1m6sA 70 :TQRGDEVILEADSHIFWY T0339 123 :PLEHL 1m6sA 91 :AMAVL T0339 131 :QVAAVTFVPVS 1m6sA 96 :SGVMPHPVPGK T0339 144 :SGQTEVDDILAAV 1m6sA 107 :NGAMDPDDVRKAI T0339 157 :RPT 1m6sA 123 :NIH T0339 160 :TRLVTIM 1m6sA 129 :TSLIAIE T0339 169 :NNET 1m6sA 138 :HNRS T0339 173 :GIVMP 1m6sA 143 :GRVVP T0339 178 :VPEISQRIKA 1m6sA 151 :IKEICTIAKE T0339 198 :PPILVHTDAAQ 1m6sA 161 :HGINVHIDGAR T0339 209 :ALG 1m6sA 177 :IAS T0339 214 :RVDVEDL 1m6sA 180 :GVPVKEY T0339 221 :GVDFLTIVG 1m6sA 189 :YADSVMFCL T0339 233 :YGPR 1m6sA 201 :LCAP T0339 237 :IGALYIRGLGEFTPLYPMLFGGG 1m6sA 206 :GSVVVGDRDFIERARKARKMLGG T0339 266 :PGTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEER 1m6sA 229 :GMRQAGVLAAAGIIALTKMVDRLKEDHENARFLALKLKEI T0339 311 :G 1m6sA 269 :G T0339 315 :IH 1m6sA 270 :YS T0339 321 :FPGTQRLPNTCNFSIRG 1m6sA 272 :VNPEDVKTNMVILRTDN T0339 338 :PRLQGHVVLAQCRVLMASVG 1m6sA 291 :VNAHGFIEALRNSGVLANAV T0339 382 :ARNALRLSVGRSTTRAEVDLVVQDLKQAVAQL 1m6sA 311 :SDTEIRLVTHKDVSRNDIEEALNIFEKLFRKF Number of specific fragments extracted= 25 number of extra gaps= 1 total=963 Will force an alignment to be made, even if fragment is small Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gdeA/T0339-1gdeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gdeA expands to /projects/compbio/data/pdb/1gde.pdb.gz 1gdeA:# T0339 read from 1gdeA/T0339-1gdeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gdeA read from 1gdeA/T0339-1gdeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gdeA to template set # found chain 1gdeA in template set T0339 1 :ERKVYMDYNATTP 1gdeA 26 :KDVISLGIGEPDF T0339 14 :LEPEVIQAMTKAMWE 1gdeA 40 :TPQHIKEYAKEALDK T0339 33 :PSSPYSAGRKAKDIINAARESLAKMIG 1gdeA 55 :GLTHYGPNIGLLELREAIAEKLKKQNG T0339 60 :GKPQ 1gdeA 84 :ADPK T0339 64 :DIIFTSGGTESNNLVIHSV 1gdeA 89 :EIMVLLGANQAFLMGLSAF T0339 91 :TSKGH 1gdeA 108 :LKDGE T0339 109 :HFITSSVEHDSIRLPLEHL 1gdeA 113 :EVLIPTPAFVSYAPAVILA T0339 132 :VAAVTFVPVSKV 1gdeA 132 :GGKPVEVPTYEE T0339 144 :SGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1gdeA 145 :EFRLNVDELKKYVTDKTRALIINSPCNPTGAVLTKKDLEE T0339 185 :IKALNQER 1gdeA 185 :IADFVVEH T0339 199 :PILVHTDAAQALGKQR 1gdeA 193 :DLIVISDEVYEHFIYD T0339 215 :VD 1gdeA 212 :HY T0339 217 :VEDL 1gdeA 215 :IASL T0339 221 :GV 1gdeA 220 :GM T0339 223 :DFLTIVGHK 1gdeA 225 :TITVNGFSK T0339 232 :FY 1gdeA 235 :FA T0339 234 :GPRIGALYIR 1gdeA 239 :GWRLGFVAAP T0339 244 :GLGEFTPLYPMLF 1gdeA 250 :WIIERMVKFQMYN T0339 266 :PGTENTPMIAGLGKAAE 1gdeA 263 :ATCPVTFIQYAAAKALK T0339 283 :LVTQNCEAYEAHMRDVRDYLEERLEAE 1gdeA 282 :RSWKAVEEMRKEYDRRRKLVWKRLNEM T0339 314 :RIHLNSQFP 1gdeA 309 :GLPTVKPKG T0339 328 :PNTCNFSIRGPRLQGHVVLAQCRV 1gdeA 318 :AFYIFPRIRDTGLTSKKFSELMLK T0339 352 :LMASVGAACH 1gdeA 345 :VAVVPGSAFG T0339 380 :DVARNALRLS 1gdeA 355 :KAGEGYVRIS T0339 392 :RSTTRAEVDLVVQDLKQAVAQL 1gdeA 365 :YATAYEKLEEAMDRMERVLKER Number of specific fragments extracted= 25 number of extra gaps= 0 total=988 Will force an alignment to be made, even if fragment is small Number of alignments=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gdeA/T0339-1gdeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1gdeA/T0339-1gdeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gdeA read from 1gdeA/T0339-1gdeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gdeA in template set T0339 2 :RKVYMDYNATT 1gdeA 27 :DVISLGIGEPD T0339 13 :PLEPEVIQAMTKA 1gdeA 39 :DTPQHIKEYAKEA T0339 27 :WEAWGNPSSPYSA 1gdeA 52 :LDKGLTHYGPNIG T0339 43 :AKDIINAARESLAKMIGG 1gdeA 65 :LLELREAIAEKLKKQNGI T0339 61 :KPQ 1gdeA 85 :DPK T0339 64 :DIIFTSGGTESNNLVIHSVV 1gdeA 89 :EIMVLLGANQAFLMGLSAFL T0339 105 :GAKPHFITSSVEHDSIRLPLEHL 1gdeA 109 :KDGEEVLIPTPAFVSYAPAVILA T0339 132 :VAAVTFVPVSKVSG 1gdeA 132 :GGKPVEVPTYEEDE T0339 146 :QTEVDDILAAVRPTTRLVTIMLANNETGIVMP 1gdeA 147 :RLNVDELKKYVTDKTRALIINSPCNPTGAVLT T0339 178 :VPEISQRIKALN 1gdeA 182 :LEEIADFVVEHD T0339 200 :ILVHTDAAQALGKQ 1gdeA 194 :LIVISDEVYEHFIY T0339 214 :RVDVEDLG 1gdeA 212 :HYSIASLD T0339 223 :DFLTIVGHKFYGP 1gdeA 225 :TITVNGFSKTFAM T0339 236 :R 1gdeA 239 :G T0339 237 :IGALYIRG 1gdeA 242 :LGFVAAPS T0339 246 :GEFTPLYPMLF 1gdeA 250 :WIIERMVKFQM T0339 265 :RPG 1gdeA 261 :YNA T0339 268 :TENTPMIAGLGKAA 1gdeA 265 :CPVTFIQYAAAKAL T0339 282 :ELVTQNCEAYEAHMRDVRDYLEERLEAE 1gdeA 281 :ERSWKAVEEMRKEYDRRRKLVWKRLNEM T0339 311 :G 1gdeA 309 :G T0339 315 :IHLNSQ 1gdeA 310 :LPTVKP T0339 326 :RLPNTCNFSIRGPRLQGHVVLAQCRV 1gdeA 316 :KGAFYIFPRIRDTGLTSKKFSELMLK T0339 352 :LMASVGAACH 1gdeA 345 :VAVVPGSAFG T0339 380 :DVARNALRLSVGR 1gdeA 355 :KAGEGYVRISYAT T0339 395 :TRAEVDLVVQDLKQAVAQ 1gdeA 368 :AYEKLEEAMDRMERVLKE Number of specific fragments extracted= 25 number of extra gaps= 0 total=1013 Will force an alignment to be made, even if fragment is small Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gdeA/T0339-1gdeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1gdeA/T0339-1gdeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gdeA read from 1gdeA/T0339-1gdeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gdeA in template set T0339 4 :VYMDYNATT 1gdeA 29 :ISLGIGEPD T0339 13 :PLEPEVIQAMTKAMWEAWGNPS 1gdeA 39 :DTPQHIKEYAKEALDKGLTHYG T0339 35 :SPY 1gdeA 62 :NIG T0339 43 :AKDIINAARESLAKMIGG 1gdeA 65 :LLELREAIAEKLKKQNGI T0339 61 :KPQD 1gdeA 85 :DPKT T0339 65 :IIFTSGGTESNNLVIHSV 1gdeA 90 :IMVLLGANQAFLMGLSAF T0339 104 :KGAKPHFITSSVEHDSIRLPLEHL 1gdeA 108 :LKDGEEVLIPTPAFVSYAPAVILA T0339 132 :VAAVTFVPVS 1gdeA 132 :GGKPVEVPTY T0339 142 :KVSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMP 1gdeA 143 :EDEFRLNVDELKKYVTDKTRALIINSPCNPTGAVLT T0339 178 :VPEISQRIKA 1gdeA 182 :LEEIADFVVE T0339 198 :PPILVHTDAAQ 1gdeA 192 :HDLIVISDEVY T0339 209 :ALGKQRVD 1gdeA 204 :HFIYDDAR T0339 217 :VEDLGV 1gdeA 216 :ASLDGM T0339 223 :DFLTIVGHKFYGPR 1gdeA 225 :TITVNGFSKTFAMT T0339 237 :IGALYIRGLGEFTPLYPMLFG 1gdeA 242 :LGFVAAPSWIIERMVKFQMYN T0339 266 :PGTENTPMIAGLGKAAELVT 1gdeA 263 :ATCPVTFIQYAAAKALKDER T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1gdeA 285 :KAVEEMRKEYDRRRKLVWKRLNEMGLPTVKP T0339 326 :RLPNTCNFSIR 1gdeA 316 :KGAFYIFPRIR T0339 337 :GPRLQGHVVLAQ 1gdeA 329 :GLTSKKFSELML T0339 349 :CRVLMASVGAACH 1gdeA 342 :EARVAVVPGSAFG T0339 380 :DVARNALRLSVG 1gdeA 355 :KAGEGYVRISYA T0339 394 :TTRAEVDLVVQDLKQAVAQ 1gdeA 367 :TAYEKLEEAMDRMERVLKE Number of specific fragments extracted= 22 number of extra gaps= 0 total=1035 Will force an alignment to be made, even if fragment is small Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iugA/T0339-1iugA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1iugA expands to /projects/compbio/data/pdb/1iug.pdb.gz 1iugA:Bad short name: N1 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: C2' for alphabet: pdb_atoms Bad short name: C3 for alphabet: pdb_atoms Bad short name: O3 for alphabet: pdb_atoms Bad short name: C4 for alphabet: pdb_atoms Bad short name: C4' for alphabet: pdb_atoms Bad short name: C5 for alphabet: pdb_atoms Bad short name: C6 for alphabet: pdb_atoms Bad short name: C5' for alphabet: pdb_atoms Bad short name: OP4 for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms # T0339 read from 1iugA/T0339-1iugA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iugA read from 1iugA/T0339-1iugA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1iugA to template set # found chain 1iugA in template set Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1iugA)G186 Warning: unaligning (T0339)E414 because last residue in template chain is (1iugA)L349 T0339 5 :YMDYNATTPLEPEVIQAMT 1iugA 3 :WLLTPGPVRLHPKALEALA T0339 33 :PSSPYSAGRKAKDIINAARESLAKMIGG 1iugA 22 :RPQLHHRTEAAREVFLKARGLLREAFRT T0339 63 :Q 1iugA 50 :E T0339 64 :DIIFTSG 1iugA 52 :EVLILTG T0339 71 :GTESNNLVIHSV 1iugA 60 :GTLAMEALVKNL T0339 91 :TSKGH 1iugA 72 :FAPGE T0339 109 :HFITSSVEHDS 1iugA 77 :RVLVPVYGKFS T0339 120 :IRLPLEHL 1iugA 90 :FYEIALEA T0339 132 :VAAVTFVPVSK 1iugA 98 :GLVVERLDYPY T0339 144 :SGQTEVDD 1iugA 109 :GDTPRPED T0339 156 :VR 1iugA 117 :VA T0339 158 :PTTRLVTIMLANNETGIVMPVPEISQR 1iugA 120 :EGYAGLLLVHSETSTGALADLPALARA T0339 188 :LNQER 1iugA 147 :FKEKN T0339 198 :PPILVHTDAAQALGKQRVDVEDLGVDFLTIVG 1iugA 152 :PEGLVGADMVTSLLVGEVALEAMGVDAAASGS T0339 232 :FY 1iugA 187 :LM T0339 234 :GPRIGALYIR 1iugA 190 :PPGLGFVALS T0339 244 :GLGEFTPLYPMLFG 1iugA 201 :RALERLKPRGYYLD T0339 260 :QERNFRPGTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEERLEAE 1iugA 222 :QKEGESAWTPAINLVLAVAAVLEEVLPRLEEHLALKAWQNALLYGVGEEG T0339 314 :RIHLNSQ 1iugA 272 :GLRPVPK T0339 325 :QRLPNTCNFSIRGP 1iugA 279 :RFSPAVAAFYLPEG T0339 340 :LQGHVVLAQCRVLMASVGAACHSDH 1iugA 293 :VPYARVKEAFAQRGAVIAGGQGPLK T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQAVAQL 1iugA 318 :GKVFRLSLMGAYDRYEALGVAGMFREVLEEI Number of specific fragments extracted= 22 number of extra gaps= 0 total=1057 Will force an alignment to be made, even if fragment is small Number of alignments=55 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iugA/T0339-1iugA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1iugA/T0339-1iugA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iugA read from 1iugA/T0339-1iugA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1iugA in template set Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1iugA)G186 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1iugA)G186 T0339 5 :YMDYNATTPLEPEVIQAM 1iugA 3 :WLLTPGPVRLHPKALEAL T0339 24 :K 1iugA 21 :A T0339 33 :PSSPYSAGRKAKDIINAARESLAKMIGGKP 1iugA 22 :RPQLHHRTEAAREVFLKARGLLREAFRTEG T0339 64 :DIIFTSG 1iugA 52 :EVLILTG T0339 71 :GTESNNLVIHSVV 1iugA 60 :GTLAMEALVKNLF T0339 105 :GAKPHFITSS 1iugA 73 :APGERVLVPV T0339 117 :HDSIRLPLEHLVEEQVAAVTFVPVSK 1iugA 83 :YGKFSERFYEIALEAGLVVERLDYPY T0339 144 :SGQTEVD 1iugA 109 :GDTPRPE T0339 155 :AV 1iugA 116 :DV T0339 157 :RPTTRLVTIMLANNETGIVMPVPEISQRIKALN 1iugA 119 :KEGYAGLLLVHSETSTGALADLPALARAFKEKN T0339 198 :PPILVHTDAAQALGKQRVDVEDLGVDFLTIVG 1iugA 152 :PEGLVGADMVTSLLVGEVALEAMGVDAAASGS T0339 233 :Y 1iugA 187 :L T0339 234 :GP 1iugA 189 :CP T0339 236 :RIGALYIRG 1iugA 192 :GLGFVALSP T0339 246 :GEFTPLYPMLFGGGQ 1iugA 201 :RALERLKPRGYYLDL T0339 261 :ERNFRP 1iugA 224 :EGESAW T0339 268 :TENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEERLEAE 1iugA 230 :TPAINLVLAVAAVLEEVLPRLEEHLALKAWQNALLYGVGEEG T0339 311 :G 1iugA 272 :G T0339 315 :IHLNSQ 1iugA 273 :LRPVPK T0339 325 :QRLPNTCNFSIRGP 1iugA 279 :RFSPAVAAFYLPEG T0339 340 :LQGHVVLAQCRVLMASVG 1iugA 293 :VPYARVKEAFAQRGAVIA T0339 377 :VPFDVARNALRLSVGRSTTRAEVDLVVQDLKQAVAQL 1iugA 312 :GQGPLKGKVFRLSLMGAYDRYEALGVAGMFREVLEEI Number of specific fragments extracted= 22 number of extra gaps= 0 total=1079 Will force an alignment to be made, even if fragment is small Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iugA/T0339-1iugA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1iugA/T0339-1iugA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iugA read from 1iugA/T0339-1iugA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1iugA in template set Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1iugA)G186 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1iugA)G186 T0339 5 :YMDYNATTPLEPEVIQAMTK 1iugA 3 :WLLTPGPVRLHPKALEALAR T0339 34 :SSPYSAGRKAKDIINAARESLAKMIGGKP 1iugA 23 :PQLHHRTEAAREVFLKARGLLREAFRTEG T0339 65 :IIFTSGGTESNNLVIHSV 1iugA 54 :LILTGSGTLAMEALVKNL T0339 104 :KGAKPHFITSSVE 1iugA 72 :FAPGERVLVPVYG T0339 119 :SIRLPLEHLVEEQVAAVTFVPVS 1iugA 85 :KFSERFYEIALEAGLVVERLDYP T0339 143 :VSGQTEVDD 1iugA 108 :YGDTPRPED T0339 156 :V 1iugA 117 :V T0339 157 :RPTTRLVTIMLANNETGIVMPVPEISQRIKA 1iugA 119 :KEGYAGLLLVHSETSTGALADLPALARAFKE T0339 196 :GLPPILVHTDAAQALGKQRVDVEDLGVDFLTIVG 1iugA 150 :KNPEGLVGADMVTSLLVGEVALEAMGVDAAASGS T0339 233 :YGPR 1iugA 187 :LMCP T0339 237 :IGALYIRGLGEFTPLY 1iugA 193 :LGFVALSPRALERLKP T0339 256 :FGGGQ 1iugA 209 :RGYYL T0339 261 :ERNFRPGTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEERLEA 1iugA 223 :KEGESAWTPAINLVLAVAAVLEEVLPRLEEHLALKAWQNALLYGVGEE T0339 310 :FGQKRIH 1iugA 271 :GGLRPVP T0339 324 :TQRLPNTCNFSIRG 1iugA 278 :KRFSPAVAAFYLPE T0339 338 :PRLQGHVVLAQCRVLMASVG 1iugA 293 :VPYARVKEAFAQRGAVIAGG T0339 378 :PFDVARNALRLSVGRSTTRAEVDLVVQDLKQAVAQL 1iugA 313 :QGPLKGKVFRLSLMGAYDRYEALGVAGMFREVLEEI Number of specific fragments extracted= 17 number of extra gaps= 0 total=1096 Will force an alignment to be made, even if fragment is small Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cl1A/T0339-1cl1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cl1A expands to /projects/compbio/data/pdb/1cl1.pdb.gz 1cl1A:Bad short name: N1 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: C2' for alphabet: pdb_atoms Bad short name: C3 for alphabet: pdb_atoms Bad short name: O3 for alphabet: pdb_atoms Bad short name: C4 for alphabet: pdb_atoms Bad short name: C4' for alphabet: pdb_atoms Bad short name: C5 for alphabet: pdb_atoms Bad short name: C6 for alphabet: pdb_atoms Bad short name: C5' for alphabet: pdb_atoms Bad short name: OP4 for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms # T0339 read from 1cl1A/T0339-1cl1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cl1A read from 1cl1A/T0339-1cl1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cl1A to template set # found chain 1cl1A in template set Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cl1A)Y211 T0339 10 :ATTPLEPEVIQ 1cl1A 33 :SLVFDSVEAKK T0339 25 :AMWEAWGNPSS 1cl1A 44 :HATRNRANGEL T0339 38 :SAGRKAKDIINAARESLAKMIGG 1cl1A 55 :FYGRRGTLTHFSLQQAMCELEGG T0339 63 :QDIIFTSGGTESNNLVIHSV 1cl1A 78 :AGCVLFPCGAAAVANSILAF T0339 91 :TSKGH 1cl1A 98 :IEQGD T0339 109 :HFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSKV 1cl1A 103 :HVLMTNTAYEPSQDFCSKILSKLGVTTSWFDPLIG T0339 151 :DILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1cl1A 139 :DIVKHLQPNTKIVFLESPGSITMEVHDVPAIVA T0339 188 :LNQER 1cl1A 172 :AVRSV T0339 197 :LPPILVHTDAAQALGKQRVDV 1cl1A 177 :VPDAIIMIDNTWAAGVLFKAL T0339 219 :DLGVDFLTIVG 1cl1A 198 :DFGIDVSIQAA T0339 232 :FYGPR 1cl1A 212 :LVGHS T0339 237 :IGALYIR 1cl1A 220 :IGTAVCN T0339 244 :GLGEFTPLYPMLFG 1cl1A 228 :RCWEQLRENAYLMG T0339 267 :GTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEE 1cl1A 242 :QMVDADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAE T0339 312 :QKRI 1cl1A 280 :HPQV T0339 316 :HLNSQFPGT 1cl1A 285 :RVNHPALPG T0339 325 :QRLPNTCNFSIR 1cl1A 305 :TGSSGLFSFVLK T0339 337 :G 1cl1A 318 :K T0339 340 :LQGHVVLAQCRV 1cl1A 319 :LNNEELANYLDN T0339 352 :LMASVGAACH 1cl1A 333 :LFSMAYSWGG T0339 367 :QPSPVLLS 1cl1A 351 :QPEHIAAI T0339 375 :YGVPFDVARNALRLSVGRS 1cl1A 360 :PQGEIDFSGTLIRLHIGLE T0339 395 :T 1cl1A 379 :D T0339 399 :VDLVVQDLKQAVAQL 1cl1A 380 :VDDLIADLDAGFARI Number of specific fragments extracted= 24 number of extra gaps= 0 total=1120 Will force an alignment to be made, even if fragment is small Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cl1A/T0339-1cl1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1cl1A/T0339-1cl1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cl1A read from 1cl1A/T0339-1cl1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cl1A in template set Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cl1A)Y211 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cl1A)Y211 T0339 44 :KDIINAARESLAKMIGG 1cl1A 61 :TLTHFSLQQAMCELEGG T0339 63 :QDIIFTSGGTESNNLVIHSVV 1cl1A 78 :AGCVLFPCGAAAVANSILAFI T0339 105 :GAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPV 1cl1A 99 :EQGDHVLMTNTAYEPSQDFCSKILSKLGVTTSWFDP T0339 141 :SK 1cl1A 137 :GA T0339 151 :DILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKALN 1cl1A 139 :DIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVV T0339 198 :PPILVHTDAAQALGKQRVDV 1cl1A 178 :PDAIIMIDNTWAAGVLFKAL T0339 219 :DLGVDFLTIVG 1cl1A 198 :DFGIDVSIQAA T0339 233 :Y 1cl1A 212 :L T0339 234 :GP 1cl1A 214 :GH T0339 236 :R 1cl1A 217 :D T0339 237 :IGALYIRG 1cl1A 220 :IGTAVCNA T0339 246 :GEFTPLYPMLFGGGQERNFR 1cl1A 228 :RCWEQLRENAYLMGQMVDAD T0339 276 :GLGKAAELVTQ 1cl1A 248 :TAYITSRGLRT T0339 287 :NCEAYEAHMRDVRDYLE 1cl1A 262 :RLRQHHESSLKVAEWLA T0339 308 :AEFG 1cl1A 279 :EHPQ T0339 315 :I 1cl1A 283 :V T0339 316 :HLNSQFPGT 1cl1A 285 :RVNHPALPG T0339 325 :QRLPNTCNFSIRGP 1cl1A 305 :TGSSGLFSFVLKKK T0339 340 :LQGHVVLAQCRV 1cl1A 319 :LNNEELANYLDN T0339 352 :LMA 1cl1A 336 :MAY T0339 374 :SYGVPFDVARNALRLSVGR 1cl1A 359 :RPQGEIDFSGTLIRLHIGL T0339 397 :AEVDLVVQDLKQAVAQL 1cl1A 378 :EDVDDLIADLDAGFARI Number of specific fragments extracted= 22 number of extra gaps= 0 total=1142 Will force an alignment to be made, even if fragment is small Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cl1A/T0339-1cl1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1cl1A/T0339-1cl1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cl1A read from 1cl1A/T0339-1cl1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cl1A in template set Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cl1A)Y211 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cl1A)Y211 T0339 24 :KAMWEAWGNPS 1cl1A 43 :KHATRNRANGE T0339 37 :YSAGRKAKDIINAARESLAKMIGG 1cl1A 54 :LFYGRRGTLTHFSLQQAMCELEGG T0339 64 :DIIFTSGGTESNNLVIHSV 1cl1A 79 :GCVLFPCGAAAVANSILAF T0339 104 :KGAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVS 1cl1A 98 :IEQGDHVLMTNTAYEPSQDFCSKILSKLGVTTSWFDPL T0339 148 :EVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKA 1cl1A 136 :IGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRS T0339 196 :GLPPILVHTDAAQALGKQ 1cl1A 176 :VVPDAIIMIDNTWAAGVL T0339 215 :VDVEDLGVDFLTIVG 1cl1A 194 :FKALDFGIDVSIQAA T0339 233 :YGPR 1cl1A 212 :LVGH T0339 237 :IGALYIRGLGEFTPLYPMLFGGGQ 1cl1A 220 :IGTAVCNARCWEQLRENAYLMGQM T0339 274 :IAGLGKAAELVT 1cl1A 246 :ADTAYITSRGLR T0339 286 :QNCEAYEAHMR 1cl1A 261 :VRLRQHHESSL T0339 301 :YLEERLEAEFGQKRIHLNSQFP 1cl1A 272 :KVAEWLAEHPQVARVNHPALPG T0339 323 :GTQRLPNTCNFSIRG 1cl1A 303 :DFTGSSGLFSFVLKK T0339 338 :PRLQGHVVLAQCR 1cl1A 319 :LNNEELANYLDNF T0339 358 :AACHS 1cl1A 332 :SLFSM T0339 369 :SPVLLSY 1cl1A 352 :PEHIAAI T0339 376 :GVPFDVARNALRLSVGRSTTR 1cl1A 361 :QGEIDFSGTLIRLHIGLEDVD T0339 401 :LVVQDLKQAVAQL 1cl1A 382 :DLIADLDAGFARI Number of specific fragments extracted= 18 number of extra gaps= 0 total=1160 Will force an alignment to be made, even if fragment is small Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yjsA/T0339-1yjsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yjsA expands to /projects/compbio/data/pdb/1yjs.pdb.gz 1yjsA:# T0339 read from 1yjsA/T0339-1yjsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yjsA read from 1yjsA/T0339-1yjsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yjsA to template set # found chain 1yjsA in template set Warning: unaligning (T0339)L255 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yjsA)P252 Warning: unaligning (T0339)F256 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yjsA)P252 T0339 4 :VYM 1yjsA 26 :IEL T0339 8 :YNATTPLEPEVIQA 1yjsA 29 :IASENFVSRAVMEA T0339 31 :GNPSSP 1yjsA 54 :GYPGRR T0339 37 :YSAGRKAKDIINAARESLAKMIGG 1yjsA 61 :YGGCEYVDIVEELARERAKQLFGA T0339 63 :QDIIFTS 1yjsA 85 :EHANVQP T0339 70 :GGTESNNLVIHSV 1yjsA 93 :SGAQANMAVYFTV T0339 91 :TSKGH 1yjsA 106 :LEHGD T0339 109 :HFITSSVEHDS 1yjsA 111 :TVLGMNLSHGG T0339 122 :LPLEHL 1yjsA 131 :FSGVQY T0339 134 :AVTFVPVSKVSGQTEVDDILAAVR 1yjsA 137 :NFVAYGVDPETHVIDYDDVREKAR T0339 158 :PTTRLVT 1yjsA 162 :HRPKLIV T0339 167 :LANNETGIVMPVPEISQ 1yjsA 169 :AAASAYPRIIDFAKFRE T0339 188 :LNQER 1yjsA 186 :IADEV T0339 199 :PILVHTDAAQ 1yjsA 191 :GAYLMVDMAH T0339 209 :ALGKQ 1yjsA 203 :GLVAA T0339 215 :VD 1yjsA 210 :HP T0339 217 :VED 1yjsA 214 :VPY T0339 222 :VDFLTIVGHK 1yjsA 217 :AHFVTTTTHQ T0339 232 :FYGPRIGALYIR 1yjsA 228 :LRGPRGGMILCQ T0339 244 :GLGEFT 1yjsA 241 :QFAKQI T0339 251 :LYPM 1yjsA 247 :DKAI T0339 257 :G 1yjsA 253 :G T0339 266 :PGTENTPM 1yjsA 254 :IQGGPLMH T0339 274 :IAGLGKAAELVTQ 1yjsA 263 :IAAKAVAFGEALQ T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1yjsA 277 :DFKAYAKRVVDNAKRLASALQNE T0339 314 :RIHLNS 1yjsA 300 :GFTLVS T0339 322 :PGTQ 1yjsA 306 :GGTD T0339 328 :PNTCNFSIRGPRLQGHVVLAQCRV 1yjsA 310 :NHLLLVDLRPQQLTGKTAEKVLDE T0339 352 :LMASVGAACHSDHGDQP 1yjsA 336 :ITVNKNTIPYDPESPFV T0339 383 :RNALRLSV 1yjsA 353 :TSGIRIGT T0339 391 :GRSTTRAEVDLVVQDLKQAV 1yjsA 365 :TRGFGLEEMDEIAAIIGLVL T0339 411 :AQLED 1yjsA 394 :EEARQ Number of specific fragments extracted= 32 number of extra gaps= 1 total=1192 Will force an alignment to be made, even if fragment is small Number of alignments=61 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yjsA/T0339-1yjsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1yjsA/T0339-1yjsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yjsA read from 1yjsA/T0339-1yjsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yjsA in template set Warning: unaligning (T0339)E28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yjsA)N49 Warning: unaligning (T0339)F256 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yjsA)P252 Warning: unaligning (T0339)G257 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yjsA)P252 T0339 4 :VYM 1yjsA 26 :IEL T0339 8 :YNATTPLEPEVIQAM 1yjsA 29 :IASENFVSRAVMEAQ T0339 29 :AWGN 1yjsA 50 :KYAE T0339 33 :P 1yjsA 56 :P T0339 34 :SSPYSA 1yjsA 61 :YGGCEY T0339 43 :AKDIINAARESLAKMIGGKP 1yjsA 67 :VDIVEELARERAKQLFGAEH T0339 65 :IIFTS 1yjsA 87 :ANVQP T0339 70 :GGTESNNLVIHSVV 1yjsA 93 :SGAQANMAVYFTVL T0339 105 :GAKPHFITSSVEHDSI 1yjsA 107 :EHGDTVLGMNLSHGGH T0339 121 :RLPL 1yjsA 130 :NFSG T0339 129 :EE 1yjsA 134 :VQ T0339 133 :AAVTFVPVSKVSGQTEVDDILAAV 1yjsA 136 :YNFVAYGVDPETHVIDYDDVREKA T0339 159 :TTRLVTIMLAN 1yjsA 163 :RPKLIVAAASA T0339 172 :TGIVMPVPEISQRIKALN 1yjsA 174 :YPRIIDFAKFREIADEVG T0339 200 :ILVHTDAAQ 1yjsA 192 :AYLMVDMAH T0339 209 :ALGKQRVDVE 1yjsA 206 :AAGLHPNPVP T0339 221 :GVDFLTIVGHKFY 1yjsA 216 :YAHFVTTTTHQTL T0339 234 :GPRIGALYIRG 1yjsA 230 :GPRGGMILCQE T0339 246 :GEFTPLYPML 1yjsA 241 :QFAKQIDKAI T0339 258 :G 1yjsA 253 :G T0339 265 :RPGTENTPMIAGLGKAAELVTQ 1yjsA 254 :IQGGPLMHVIAAKAVAFGEALQ T0339 287 :NCEAYEAHMRDVRDYLEERLEA 1yjsA 277 :DFKAYAKRVVDNAKRLASALQN T0339 310 :FG 1yjsA 299 :EG T0339 315 :IHLNSQ 1yjsA 301 :FTLVSG T0339 323 :GTQ 1yjsA 307 :GTD T0339 328 :PNTCNFSIRGPRLQGHVVLAQCRVLMASVG 1yjsA 310 :NHLLLVDLRPQQLTGKTAEKVLDEVGITVN T0339 360 :CHSDHGD 1yjsA 341 :NTIPYDP T0339 377 :VPFDVA 1yjsA 348 :ESPFVT T0339 384 :NALRLSV 1yjsA 354 :SGIRIGT T0339 391 :GRSTTRAEVDLVVQDLKQAV 1yjsA 365 :TRGFGLEEMDEIAAIIGLVL Number of specific fragments extracted= 30 number of extra gaps= 2 total=1222 Will force an alignment to be made, even if fragment is small Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yjsA/T0339-1yjsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1yjsA/T0339-1yjsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yjsA read from 1yjsA/T0339-1yjsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yjsA in template set Warning: unaligning (T0339)L255 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yjsA)P252 Warning: unaligning (T0339)F256 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yjsA)P252 T0339 9 :NATTPLEPEVIQAM 1yjsA 30 :ASENFVSRAVMEAQ T0339 30 :WGNPS 1yjsA 53 :EGYPG T0339 35 :SPYSAGRKAKDIINAARESLAKMIGG 1yjsA 59 :RYYGGCEYVDIVEELARERAKQLFGA T0339 65 :IIFTSGGTESNNLVIHSV 1yjsA 88 :NVQPHSGAQANMAVYFTV T0339 104 :KGAKPHFITSSVEHDSIR 1yjsA 106 :LEHGDTVLGMNLSHGGHL T0339 122 :LPLEH 1yjsA 131 :FSGVQ T0339 133 :AAVTFVPVSKVSGQTEVDDILAAV 1yjsA 136 :YNFVAYGVDPETHVIDYDDVREKA T0339 161 :R 1yjsA 165 :K T0339 164 :TIMLANNETGIVMPVPEISQRIKA 1yjsA 166 :LIVAAASAYPRIIDFAKFREIADE T0339 198 :PPILVHTDAAQ 1yjsA 190 :VGAYLMVDMAH T0339 209 :ALGKQRVDVE 1yjsA 206 :AAGLHPNPVP T0339 221 :GVDFLTIVGHKFYGPR 1yjsA 216 :YAHFVTTTTHQTLRGP T0339 237 :IGALYIRGLGEFTPLYPM 1yjsA 233 :GGMILCQEQFAKQIDKAI T0339 257 :GG 1yjsA 253 :GI T0339 266 :PGTENTPMIAGLGKAAELVT 1yjsA 255 :QGGPLMHVIAAKAVAFGEAL T0339 286 :QNCEAYEAHMRDVRDYLEERLEAE 1yjsA 276 :DDFKAYAKRVVDNAKRLASALQNE T0339 311 :GQKRIH 1yjsA 300 :GFTLVS T0339 322 :PGTQRLPNTCNFSIRGPRLQGHVVLAQCRVLMASVGAACHSDHG 1yjsA 306 :GGTDNHLLLVDLRPQQLTGKTAEKVLDEVGITVNKNTIPYDPES T0339 380 :DVARNALRLSVG 1yjsA 350 :PFVTSGIRIGTA T0339 392 :RSTTRAEVDLVVQDLK 1yjsA 366 :RGFGLEEMDEIAAIIG Number of specific fragments extracted= 20 number of extra gaps= 1 total=1242 Will force an alignment to be made, even if fragment is small Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kl1A/T0339-1kl1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kl1A expands to /projects/compbio/data/pdb/1kl1.pdb.gz 1kl1A:# T0339 read from 1kl1A/T0339-1kl1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kl1A read from 1kl1A/T0339-1kl1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kl1A to template set # found chain 1kl1A in template set Warning: unaligning (T0339)L255 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1kl1A)P252 Warning: unaligning (T0339)F256 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1kl1A)P252 T0339 4 :VYM 1kl1A 26 :IEL T0339 8 :YNATTPLEPEVIQA 1kl1A 29 :IASENFVSRAVMEA T0339 31 :GNPSSP 1kl1A 54 :GYPGRR T0339 37 :YSAGRKAKDIINAARESLAKMIGG 1kl1A 61 :YGGCEYVDIVEELARERAKQLFGA T0339 63 :QDIIFTS 1kl1A 85 :EHANVQP T0339 70 :GGTESNNLVIHSV 1kl1A 93 :SGAQANMAVYFTV T0339 91 :TSKGH 1kl1A 106 :LEHGD T0339 109 :HFITSSVEHDSIR 1kl1A 111 :TVLGMNLSHGGHL T0339 122 :LPLEHL 1kl1A 131 :FSGVQY T0339 134 :AVTFVPVSKVSGQTEVDDILAAVR 1kl1A 137 :NFVAYGVDPETHVIDYDDVREKAR T0339 158 :PTTRLVT 1kl1A 162 :HRPKLIV T0339 167 :LANNETGIVMPVPEISQ 1kl1A 169 :AAASAYPRIIDFAKFRE T0339 188 :LNQER 1kl1A 186 :IADEV T0339 199 :PILVHTDAAQ 1kl1A 191 :GAYLMVDMAH T0339 209 :ALGKQ 1kl1A 203 :GLVAA T0339 215 :VD 1kl1A 210 :HP T0339 217 :VED 1kl1A 214 :VPY T0339 222 :VDFLTIVGHK 1kl1A 217 :AHFVTTTTHK T0339 232 :FYGPRIGALYIR 1kl1A 228 :LRGPRGGMILCQ T0339 244 :GLGEFT 1kl1A 241 :QFAKQI T0339 251 :LYPM 1kl1A 247 :DKAI T0339 257 :G 1kl1A 253 :G T0339 266 :PGTENTPMIAGLGK 1kl1A 254 :IQGGPLMHVIAAKA T0339 280 :AAELVTQ 1kl1A 269 :AFGEALQ T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1kl1A 277 :DFKAYAKRVVDNAKRLASALQNE T0339 314 :RIHLNS 1kl1A 300 :GFTLVS T0339 322 :PGTQ 1kl1A 306 :GGTD T0339 328 :PNTCNFSIRGPRLQGHVVLAQCRV 1kl1A 310 :NHLLLVDLRPQQLTGKTAEKVLDE T0339 352 :LMASVGAACHSDHGDQP 1kl1A 336 :ITVNKNTIPYDPESPFV T0339 383 :RNALRLSV 1kl1A 353 :TSGIRIGT T0339 391 :GRSTTRAEVDLVVQDLKQA 1kl1A 365 :TRGFGLEEMDEIAAIIGLV T0339 410 :VAQLED 1kl1A 393 :LEEARQ Number of specific fragments extracted= 32 number of extra gaps= 1 total=1274 Will force an alignment to be made, even if fragment is small Number of alignments=64 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kl1A/T0339-1kl1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1kl1A/T0339-1kl1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kl1A read from 1kl1A/T0339-1kl1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kl1A in template set Warning: unaligning (T0339)G257 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1kl1A)P252 Warning: unaligning (T0339)G258 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1kl1A)P252 T0339 3 :KVYM 1kl1A 25 :KIEL T0339 8 :YNATTPLEPEVIQAM 1kl1A 29 :IASENFVSRAVMEAQ T0339 27 :WEAWGN 1kl1A 48 :TNKYAE T0339 33 :P 1kl1A 56 :P T0339 34 :SSPYSA 1kl1A 61 :YGGCEY T0339 43 :AKDIINAARESLAKMIGG 1kl1A 67 :VDIVEELARERAKQLFGA T0339 63 :QDIIFTS 1kl1A 85 :EHANVQP T0339 70 :GGTESNNLVIHSVV 1kl1A 93 :SGAQANMAVYFTVL T0339 105 :GAKPHFITSSVEHDSI 1kl1A 107 :EHGDTVLGMNLSHGGH T0339 122 :L 1kl1A 131 :F T0339 124 :LE 1kl1A 132 :SG T0339 129 :EE 1kl1A 134 :VQ T0339 133 :AAVTFVPVSKVSGQTEVDDILAAV 1kl1A 136 :YNFVAYGVDPETHVIDYDDVREKA T0339 159 :TTRLVTIMLAN 1kl1A 163 :RPKLIVAAASA T0339 172 :TGIVMPVPEISQRIKALN 1kl1A 174 :YPRIIDFAKFREIADEVG T0339 200 :ILVHTDAAQ 1kl1A 192 :AYLMVDMAH T0339 209 :ALGKQRVDV 1kl1A 206 :AAGLHPNPV T0339 219 :DL 1kl1A 215 :PY T0339 222 :VDFLTIVGHKFY 1kl1A 217 :AHFVTTTTHKTL T0339 234 :GPRIGALYIRG 1kl1A 230 :GPRGGMILCQE T0339 246 :GEFTPLYP 1kl1A 241 :QFAKQIDK T0339 255 :LF 1kl1A 249 :AI T0339 259 :GQ 1kl1A 253 :GI T0339 266 :PGTENTPMIAGLGKAAELVTQ 1kl1A 255 :QGGPLMHVIAAKAVAFGEALQ T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1kl1A 277 :DFKAYAKRVVDNAKRLASALQNE T0339 311 :G 1kl1A 300 :G T0339 315 :IHLNSQ 1kl1A 301 :FTLVSG T0339 323 :GTQ 1kl1A 307 :GTD T0339 328 :PNTCNFSIRGPRLQGHVVLAQCRVLMASVG 1kl1A 310 :NHLLLVDLRPQQLTGKTAEKVLDEVGITVN T0339 360 :CHSDHG 1kl1A 341 :NTIPYD T0339 376 :GVPFDVA 1kl1A 347 :PESPFVT T0339 384 :NALRLSV 1kl1A 354 :SGIRIGT T0339 391 :GRSTTRAEVDLVVQDLKQA 1kl1A 365 :TRGFGLEEMDEIAAIIGLV T0339 410 :VAQLED 1kl1A 393 :LEEARQ Number of specific fragments extracted= 34 number of extra gaps= 1 total=1308 Will force an alignment to be made, even if fragment is small Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kl1A/T0339-1kl1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1kl1A/T0339-1kl1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kl1A read from 1kl1A/T0339-1kl1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kl1A in template set Warning: unaligning (T0339)L255 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1kl1A)P252 Warning: unaligning (T0339)F256 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1kl1A)P252 T0339 9 :NATTPLEPEVIQAMTKAMWEAW 1kl1A 30 :ASENFVSRAVMEAQGSVLTNKY T0339 31 :GNPS 1kl1A 54 :GYPG T0339 35 :SPYSAGRKAKDIINAARESLAKMIGG 1kl1A 59 :RYYGGCEYVDIVEELARERAKQLFGA T0339 65 :IIFTSGGTESNNLVIHSV 1kl1A 88 :NVQPHSGAQANMAVYFTV T0339 104 :KGAKPHFITSSVEHDSIRLP 1kl1A 106 :LEHGDTVLGMNLSHGGHLTH T0339 124 :LEHL 1kl1A 132 :SGVQ T0339 133 :AAVTFVPVSKVSGQTEVDDILAAV 1kl1A 136 :YNFVAYGVDPETHVIDYDDVREKA T0339 161 :R 1kl1A 165 :K T0339 164 :TIMLANNETGIVMPVPEISQRIKA 1kl1A 166 :LIVAAASAYPRIIDFAKFREIADE T0339 198 :PPILVHTDAAQ 1kl1A 190 :VGAYLMVDMAH T0339 209 :ALGKQRVDVE 1kl1A 206 :AAGLHPNPVP T0339 221 :GVDFLTIVGHKFYGPR 1kl1A 216 :YAHFVTTTTHKTLRGP T0339 237 :IGALYIRGLGEFTPLYPM 1kl1A 233 :GGMILCQEQFAKQIDKAI T0339 257 :GG 1kl1A 253 :GI T0339 266 :PGTENTPMIAGLGKAAELVT 1kl1A 255 :QGGPLMHVIAAKAVAFGEAL T0339 286 :QNCEAYEAHMRDVRDYLEERLEAE 1kl1A 276 :DDFKAYAKRVVDNAKRLASALQNE T0339 311 :GQKRIH 1kl1A 300 :GFTLVS T0339 322 :PGTQRLPNTCNFSIRGPRLQGHVVLAQCRVLMASVGAACHSDHG 1kl1A 306 :GGTDNHLLLVDLRPQQLTGKTAEKVLDEVGITVNKNTIPYDPES T0339 380 :DVARNALRLSVG 1kl1A 350 :PFVTSGIRIGTA T0339 392 :RSTTRAEVDLVVQDLK 1kl1A 366 :RGFGLEEMDEIAAIIG T0339 408 :QAVAQLED 1kl1A 391 :QALEEARQ Number of specific fragments extracted= 21 number of extra gaps= 1 total=1329 Will force an alignment to be made, even if fragment is small Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mdoA/T0339-1mdoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mdoA expands to /projects/compbio/data/pdb/1mdo.pdb.gz 1mdoA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 199, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 255, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 257, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 259, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 261, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 263, because occupancy 0.500 <= existing 0.500 in 1mdoA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 575, because occupancy 0.350 <= existing 0.650 in 1mdoA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 577, because occupancy 0.350 <= existing 0.650 in 1mdoA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 579, because occupancy 0.350 <= existing 0.650 in 1mdoA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 581, because occupancy 0.350 <= existing 0.650 in 1mdoA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1058, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 1060, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 1062, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 1064, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 1066, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 1068, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 1070, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 1814, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 1816, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 1818, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 1820, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 1822, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 1824, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 1826, because occupancy 0.500 <= existing 0.500 in 1mdoA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2634, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 2636, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 2638, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 2640, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 2642, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 2673, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 2675, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 2677, because occupancy 0.500 <= existing 0.500 in 1mdoA Skipped atom 2679, because occupancy 0.500 <= existing 0.500 in 1mdoA # T0339 read from 1mdoA/T0339-1mdoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mdoA read from 1mdoA/T0339-1mdoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mdoA to template set # found chain 1mdoA in template set Warning: unaligning (T0339)A359 because of BadResidue code BAD_PEPTIDE in next template residue (1mdoA)F330 Warning: unaligning (T0339)C360 because of BadResidue code BAD_PEPTIDE at template residue (1mdoA)F330 T0339 10 :ATTPLEPEVIQAMTKAMWE 1mdoA 14 :SRPAMGAEELAAVKTVLDS T0339 36 :PYSAG 1mdoA 33 :GWITT T0339 44 :KDIINAARESLAKMIGG 1mdoA 38 :GPKNQELEAAFCRLTGN T0339 63 :QDIIFTSGGTESNNLVIHSV 1mdoA 55 :QYAVAVSSATAGMHIALMAL T0339 90 :QTSKGH 1mdoA 75 :GIGEGD T0339 109 :HFITSSVEHDSIRLPLEHL 1mdoA 81 :EVITPSMTWVSTLNMIVLL T0339 132 :VAAVTFVPVSKVSGQTEVDDILAAVRPTTRLVT 1mdoA 100 :GANPVMVDVDRDTLMVTPEHIEAAITPQTKAII T0339 168 :ANNETGIVMPVPEISQ 1mdoA 133 :PVHYAGAPADLDAIYA T0339 188 :LNQER 1mdoA 149 :LGERY T0339 199 :PILVHTDAAQALGKQR 1mdoA 154 :GIPVIEDAAHATGTSY T0339 215 :VDV 1mdoA 172 :RHI T0339 221 :GV 1mdoA 175 :GA T0339 223 :DFLTIVGH 1mdoA 178 :GTAIFSFH T0339 231 :K 1mdoA 188 :K T0339 232 :FYGPRIGALYIR 1mdoA 190 :ITCAEGGIVVTD T0339 244 :G 1mdoA 203 :P T0339 245 :LGEFT 1mdoA 205 :FADKL T0339 251 :LYPMLFGGG 1mdoA 210 :RSLKFHGLG T0339 260 :QERNFRPGTENTPMIAGLGKAAE 1mdoA 235 :VLAPGYKYNLPDLNAAIALAQLQ T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1mdoA 258 :KLDALNARRAAIAAQYHQAMADL T0339 314 :RIHLNSQFPGT 1mdoA 281 :PFQPLSLPSWE T0339 325 :QRLPNTCNFSIR 1mdoA 293 :IHAWHLFIIRVD T0339 337 :G 1mdoA 309 :G T0339 340 :LQGHVVLAQCRVLMASVGA 1mdoA 310 :ITRDALMASLKTKGIGTGL T0339 361 :H 1mdoA 331 :R T0339 362 :SD 1mdoA 343 :FP T0339 365 :GDQPSPVLL 1mdoA 345 :TLTLPDTEW T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQAV 1mdoA 356 :ERICSLPLFPDMTESDFDRVITALHQIA Number of specific fragments extracted= 28 number of extra gaps= 1 total=1357 Will force an alignment to be made, even if fragment is small Number of alignments=67 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mdoA/T0339-1mdoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1mdoA/T0339-1mdoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mdoA read from 1mdoA/T0339-1mdoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mdoA in template set Warning: unaligning (T0339)P250 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mdoA)Q232 Warning: unaligning (T0339)A359 because of BadResidue code BAD_PEPTIDE in next template residue (1mdoA)F330 Warning: unaligning (T0339)C360 because of BadResidue code BAD_PEPTIDE at template residue (1mdoA)F330 T0339 10 :ATTPLEPEVIQA 1mdoA 14 :SRPAMGAEELAA T0339 23 :TKAMWEAWGNPSS 1mdoA 26 :VKTVLDSGWITTG T0339 45 :DIINAARESLAKMIGGKP 1mdoA 39 :PKNQELEAAFCRLTGNQY T0339 65 :IIFTSGGTESNNLVIHSV 1mdoA 57 :AVAVSSATAGMHIALMAL T0339 105 :GAKPHFITSSV 1mdoA 77 :GEGDEVITPSM T0339 120 :IRLPLEHLVEEQVAAVTFVPVSKVSGQTEVDDILAAVRPTTRLV 1mdoA 88 :TWVSTLNMIVLLGANPVMVDVDRDTLMVTPEHIEAAITPQTKAI T0339 167 :LANNETGIVMPVPEISQRIKALN 1mdoA 132 :IPVHYAGAPADLDAIYALGERYG T0339 200 :ILVHTDAAQALGK 1mdoA 155 :IPVIEDAAHATGT T0339 215 :VDV 1mdoA 172 :RHI T0339 223 :DFLTIVGHKFY 1mdoA 178 :GTAIFSFHAIK T0339 234 :GPRIGALYIRG 1mdoA 192 :CAEGGIVVTDN T0339 245 :LGEFT 1mdoA 215 :HGLGV T0339 261 :ERNFRPGTENTPMIAGLG 1mdoA 237 :APGYKYNLPDLNAAIALA T0339 284 :VTQNCEAYEAHMRDVRDYLEERLEAEF 1mdoA 255 :QLQKLDALNARRAAIAAQYHQAMADLP T0339 315 :IHLNSQFPGT 1mdoA 282 :FQPLSLPSWE T0339 325 :QRLPNTCNFSIR 1mdoA 293 :IHAWHLFIIRVD T0339 337 :G 1mdoA 309 :G T0339 340 :LQGHVVLAQCRVLMASVGA 1mdoA 310 :ITRDALMASLKTKGIGTGL T0339 361 :HSDH 1mdoA 331 :RAAH T0339 366 :DQPSPVLLSYGVPFD 1mdoA 335 :TQKYYRERFPTLTLP T0339 381 :VARNALRLSVGRSTTRAEVDLVVQDLKQAV 1mdoA 354 :NSERICSLPLFPDMTESDFDRVITALHQIA Number of specific fragments extracted= 21 number of extra gaps= 1 total=1378 Will force an alignment to be made, even if fragment is small Number of alignments=68 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mdoA/T0339-1mdoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1mdoA/T0339-1mdoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mdoA read from 1mdoA/T0339-1mdoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mdoA in template set Warning: unaligning (T0339)A359 because of BadResidue code BAD_PEPTIDE in next template residue (1mdoA)F330 Warning: unaligning (T0339)C360 because of BadResidue code BAD_PEPTIDE at template residue (1mdoA)F330 T0339 10 :ATTPLEPEVIQAMTKAMWEAWGNPS 1mdoA 14 :SRPAMGAEELAAVKTVLDSGWITTG T0339 45 :DIINAARESLAKMIGG 1mdoA 39 :PKNQELEAAFCRLTGN T0339 63 :QDIIFTSGGTESNNLVIHSV 1mdoA 55 :QYAVAVSSATAGMHIALMAL T0339 103 :VKGAKPHFITSSVEHDSIRLPLEHL 1mdoA 75 :GIGEGDEVITPSMTWVSTLNMIVLL T0339 132 :VAAVTFVPVSKVSGQTEVDDILAAVRPTTRLV 1mdoA 100 :GANPVMVDVDRDTLMVTPEHIEAAITPQTKAI T0339 167 :LANNETGIVMPVPEISQRIKA 1mdoA 132 :IPVHYAGAPADLDAIYALGER T0339 198 :PPILVHTDAAQALGK 1mdoA 153 :YGIPVIEDAAHATGT T0339 223 :DFLTIVGHKFYGPR 1mdoA 178 :GTAIFSFHAIKNIT T0339 237 :IGALYIRGLGEFTPLYPMLFGGGQ 1mdoA 195 :GGIVVTDNPQFADKLRSLKFHGLG T0339 261 :ERNFRPGTENTPMIAGLGKA 1mdoA 237 :APGYKYNLPDLNAAIALAQL T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1mdoA 257 :QKLDALNARRAAIAAQYHQAMADLPFQPLSL T0339 320 :QFPGTQRLPNTCNFSIR 1mdoA 288 :PSWEHIHAWHLFIIRVD T0339 337 :GPRLQGHVVLAQCRVLM 1mdoA 309 :GITRDALMASLKTKGIG T0339 356 :VGA 1mdoA 326 :TGL T0339 361 :HSDHG 1mdoA 331 :RAAHT T0339 367 :QPSPVLLSYGVPFDVAR 1mdoA 336 :QKYYRERFPTLTLPDTE T0339 384 :NALRLSVGRSTTRAEVDLVVQDLKQA 1mdoA 357 :RICSLPLFPDMTESDFDRVITALHQI Number of specific fragments extracted= 17 number of extra gaps= 1 total=1395 Will force an alignment to be made, even if fragment is small Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bw0A/T0339-1bw0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bw0A expands to /projects/compbio/data/pdb/1bw0.pdb.gz 1bw0A:Bad short name: N1 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: C2' for alphabet: pdb_atoms Bad short name: C3 for alphabet: pdb_atoms Bad short name: O3 for alphabet: pdb_atoms Bad short name: C4 for alphabet: pdb_atoms Bad short name: C4' for alphabet: pdb_atoms Bad short name: C5 for alphabet: pdb_atoms Bad short name: C6 for alphabet: pdb_atoms Bad short name: C5' for alphabet: pdb_atoms Bad short name: OP4 for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms # T0339 read from 1bw0A/T0339-1bw0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bw0A read from 1bw0A/T0339-1bw0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1bw0A to template set # found chain 1bw0A in template set Warning: unaligning (T0339)N169 because of BadResidue code BAD_PEPTIDE in next template residue (1bw0A)N188 Warning: unaligning (T0339)N170 because of BadResidue code BAD_PEPTIDE at template residue (1bw0A)N188 Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bw0A)N254 T0339 2 :RKVYMDYNA 1bw0A 34 :PIIKLSVGD T0339 11 :TTPLEPEVIQAMTKAMWEAWGNPSSPYSAG 1bw0A 48 :NLLTSAAQIKKLKEAIDSQECNGYFPTVGS T0339 44 :KDIINAARESLAKMI 1bw0A 78 :PEAREAVATWWRNSF T0339 60 :GKPQDIIFTSGGTESNNLVIHSV 1bw0A 102 :IVKDNVVLCSGGSHGILMAITAI T0339 91 :TSKGH 1bw0A 125 :CDAGD T0339 109 :HFITSSVEHDSIRLPLEHL 1bw0A 130 :YALVPQPGFPHYETVCKAY T0339 132 :VAAVTFVPVSKV 1bw0A 149 :GIGMHFYNCRPE T0339 144 :SGQTEVDDILAAVRPTTRLVTIMLA 1bw0A 162 :DWEADLDEIRRLKDDKTKLLIVTNP T0339 171 :ETGIVMPVPEISQ 1bw0A 189 :PCGSNFSRKHVED T0339 185 :IKALNQER 1bw0A 202 :IVRLAEEL T0339 199 :PILVHTDAAQALGKQR 1bw0A 210 :RLPLFSDEIYAGMVFK T0339 216 :D 1bw0A 234 :T T0339 217 :VEDLGV 1bw0A 236 :VADFET T0339 223 :DFLTIVG 1bw0A 245 :RVILGGT T0339 232 :FY 1bw0A 255 :LV T0339 234 :GPRIGALYIR 1bw0A 259 :GWRLGWLLYV T0339 244 :G 1bw0A 270 :P T0339 245 :LGEFT 1bw0A 277 :FLEGL T0339 266 :PGTENTPMIAGLGKAAELVTQ 1bw0A 288 :VCGPCTVVQAALGEALLNTPQ T0339 287 :NCEAYEAHMRDVRDYLEERLEA 1bw0A 310 :HLDQIVAKIEESAMYLYNHIGE T0339 312 :QKRIHLNSQFP 1bw0A 332 :CIGLAPTMPRG T0339 328 :PNTCNFSIRGPR 1bw0A 343 :AMYLMSRIDLEK T0339 340 :LQ 1bw0A 358 :IK T0339 342 :GHVVLAQCRV 1bw0A 361 :DVEFFEKLLE T0339 352 :LMASVGAACHS 1bw0A 374 :VQVLPGTIFHA T0339 383 :RNALRLSVGR 1bw0A 385 :PGFTRLTTTR T0339 395 :TRAEVDLVVQDLKQAVAQL 1bw0A 395 :PVEVYREAVERIKAFCQRH Number of specific fragments extracted= 27 number of extra gaps= 1 total=1422 Will force an alignment to be made, even if fragment is small Number of alignments=70 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bw0A/T0339-1bw0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1bw0A/T0339-1bw0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bw0A read from 1bw0A/T0339-1bw0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bw0A in template set Warning: unaligning (T0339)N169 because of BadResidue code BAD_PEPTIDE in next template residue (1bw0A)N188 Warning: unaligning (T0339)N170 because of BadResidue code BAD_PEPTIDE at template residue (1bw0A)N188 Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bw0A)N254 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bw0A)N254 T0339 12 :TPLEPEVIQAMTKAMWEAWGNPSSPYSA 1bw0A 74 :TVGSPEAREAVATWWRNSFVHKEELKST T0339 60 :GKPQDIIFTSGGTESNNLVIHSVV 1bw0A 102 :IVKDNVVLCSGGSHGILMAITAIC T0339 105 :GAKPHFITSSVEHD 1bw0A 126 :DAGDYALVPQPGFP T0339 123 :PLEHLVEEQVAAVTFVP 1bw0A 140 :HYETVCKAYGIGMHFYN T0339 140 :VSK 1bw0A 159 :PEN T0339 144 :SGQTEVDDILAAVRPTTRLVTIMLA 1bw0A 162 :DWEADLDEIRRLKDDKTKLLIVTNP T0339 171 :ETGIVMP 1bw0A 189 :PCGSNFS T0339 178 :VPEISQRIKALN 1bw0A 199 :VEDIVRLAEELR T0339 200 :ILVHTDAAQALGKQR 1bw0A 211 :LPLFSDEIYAGMVFK T0339 219 :DLGVDFLTIV 1bw0A 240 :ETTVPRVILG T0339 229 :G 1bw0A 251 :T T0339 233 :Y 1bw0A 255 :L T0339 234 :GP 1bw0A 257 :VP T0339 236 :RIGALYIRGLG 1bw0A 261 :RLGWLLYVDPH T0339 258 :GGQ 1bw0A 272 :GNG T0339 267 :GTENTPMIAGLGKAA 1bw0A 289 :CGPCTVVQAALGEAL T0339 285 :TQ 1bw0A 304 :LN T0339 287 :NCEAYEAHMRDVRD 1bw0A 307 :PQEHLDQIVAKIEE T0339 301 :YLEERLEAEFG 1bw0A 324 :YLYNHIGECIG T0339 315 :IHLNSQ 1bw0A 335 :LAPTMP T0339 326 :RLPNTCNFSIRGPRLQ 1bw0A 341 :RGAMYLMSRIDLEKYR T0339 342 :GHVVLAQCRV 1bw0A 361 :DVEFFEKLLE T0339 352 :LMASVGA 1bw0A 374 :VQVLPGT T0339 379 :FDVARNALRLSVGR 1bw0A 381 :IFHAPGFTRLTTTR T0339 395 :TRAEVDLVVQDLKQAVAQL 1bw0A 395 :PVEVYREAVERIKAFCQRH Number of specific fragments extracted= 25 number of extra gaps= 1 total=1447 Will force an alignment to be made, even if fragment is small Number of alignments=71 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bw0A/T0339-1bw0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1bw0A/T0339-1bw0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bw0A read from 1bw0A/T0339-1bw0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bw0A in template set Warning: unaligning (T0339)N169 because of BadResidue code BAD_PEPTIDE in next template residue (1bw0A)N188 Warning: unaligning (T0339)N170 because of BadResidue code BAD_PEPTIDE at template residue (1bw0A)N188 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bw0A)N254 T0339 2 :RKVYMDYNATT 1bw0A 34 :PIIKLSVGDPT T0339 13 :PLEPEVIQAMTKAMWEAWGNPSSPYSAGRKAKDIINAARESLA 1bw0A 50 :LTSAAQIKKLKEAIDSQECNGYFPTVGSPEAREAVATWWRNSF T0339 60 :GKPQDIIFTSGGTESNNLVIHSV 1bw0A 102 :IVKDNVVLCSGGSHGILMAITAI T0339 104 :KGAKPHFITSSVEHDSIRLPLEHL 1bw0A 125 :CDAGDYALVPQPGFPHYETVCKAY T0339 132 :VAAVTFVPVS 1bw0A 149 :GIGMHFYNCR T0339 142 :KVSGQTEVDDILAAVRPTTRLVTIMLA 1bw0A 160 :ENDWEADLDEIRRLKDDKTKLLIVTNP T0339 171 :ETGIVMP 1bw0A 189 :PCGSNFS T0339 178 :VPEISQRIKA 1bw0A 199 :VEDIVRLAEE T0339 198 :PPILVHTDAAQALGKQRVD 1bw0A 209 :LRLPLFSDEIYAGMVFKGK T0339 219 :DLGVDFLTIVGH 1bw0A 240 :ETTVPRVILGGT T0339 233 :YGPR 1bw0A 255 :LVVP T0339 237 :IGALYI 1bw0A 262 :LGWLLY T0339 254 :MLFGGGQ 1bw0A 268 :VDPHGNG T0339 267 :GTENTPMIAGLGKAAELVT 1bw0A 289 :CGPCTVVQAALGEALLNTP T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1bw0A 309 :EHLDQIVAKIEESAMYLYNHIGECIGLAPTM T0339 325 :QRLPNTCNFSIRG 1bw0A 340 :PRGAMYLMSRIDL T0339 338 :PR 1bw0A 359 :KT T0339 340 :LQGHVVLAQCRVLMASVGAA 1bw0A 362 :VEFFEKLLEEENVQVLPGTI T0339 380 :DVARNALRLSVGR 1bw0A 382 :FHAPGFTRLTTTR T0339 395 :TRAEVDLVVQDLKQAVAQL 1bw0A 395 :PVEVYREAVERIKAFCQRH Number of specific fragments extracted= 20 number of extra gaps= 1 total=1467 Will force an alignment to be made, even if fragment is small Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e5eA/T0339-1e5eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1e5eA expands to /projects/compbio/data/pdb/1e5e.pdb.gz 1e5eA:Skipped atom 813, because occupancy 0.500 <= existing 0.500 in 1e5eA Skipped atom 1030, because occupancy 0.400 <= existing 0.600 in 1e5eA Skipped atom 1032, because occupancy 0.400 <= existing 0.600 in 1e5eA Skipped atom 1034, because occupancy 0.400 <= existing 0.600 in 1e5eA Skipped atom 1036, because occupancy 0.400 <= existing 0.600 in 1e5eA Skipped atom 1560, because occupancy 0.500 <= existing 0.500 in 1e5eA Skipped atom 1562, because occupancy 0.500 <= existing 0.500 in 1e5eA Skipped atom 1564, because occupancy 0.500 <= existing 0.500 in 1e5eA Skipped atom 1566, because occupancy 0.500 <= existing 0.500 in 1e5eA Skipped atom 1726, because occupancy 0.500 <= existing 0.500 in 1e5eA Skipped atom 1728, because occupancy 0.500 <= existing 0.500 in 1e5eA Skipped atom 1730, because occupancy 0.500 <= existing 0.500 in 1e5eA Skipped atom 1732, because occupancy 0.500 <= existing 0.500 in 1e5eA Skipped atom 1758, because occupancy 0.500 <= existing 0.500 in 1e5eA Skipped atom 1760, because occupancy 0.500 <= existing 0.500 in 1e5eA Skipped atom 1762, because occupancy 0.500 <= existing 0.500 in 1e5eA Skipped atom 2077, because occupancy 0.500 <= existing 0.500 in 1e5eA Skipped atom 2079, because occupancy 0.500 <= existing 0.500 in 1e5eA Skipped atom 2081, because occupancy 0.500 <= existing 0.500 in 1e5eA Skipped atom 2083, because occupancy 0.500 <= existing 0.500 in 1e5eA Skipped atom 2329, because occupancy 0.500 <= existing 0.500 in 1e5eA Skipped atom 2331, because occupancy 0.500 <= existing 0.500 in 1e5eA Skipped atom 2333, because occupancy 0.500 <= existing 0.500 in 1e5eA # T0339 read from 1e5eA/T0339-1e5eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e5eA read from 1e5eA/T0339-1e5eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1e5eA to template set # found chain 1e5eA in template set Warning: unaligning (T0339)D415 because last residue in template chain is (1e5eA)R397 T0339 27 :WEAWGNPSSPYSAGRKAKDIINAARESLAKMIGG 1e5eA 44 :GNRFAGQESGYIYTRLGNPTVSNLEGKIAFLEKT T0339 63 :QDIIFTSGGTESNNLVIHSV 1e5eA 78 :EACVATSSGMGAIAATVLTI T0339 91 :TSKGH 1e5eA 98 :LKAGD T0339 109 :HFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSK 1e5eA 103 :HLISDECLYGCTHALFEHALTKFGIQVDFINTAI T0339 144 :SG 1e5eA 137 :PG T0339 151 :DILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1e5eA 139 :EVKKHMKPNTKIVYFETPANPTLKIIDMERVCK T0339 188 :LNQER 1e5eA 172 :DAHSQ T0339 196 :G 1e5eA 177 :E T0339 199 :PILVHTDAAQALGKQRVDV 1e5eA 178 :GVLVIADNTFCSPMITNPV T0339 219 :DLGVDFLTIVGHK 1e5eA 197 :DFGVDVVVHSATK T0339 232 :FYGPR 1e5eA 211 :INGHT T0339 237 :IGALYIR 1e5eA 219 :AGLICGK T0339 244 :GLGEFT 1e5eA 227 :DLLQQI T0339 250 :PLYPMLFG 1e5eA 235 :VGIKDITG T0339 267 :GTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLE 1e5eA 243 :SVISPHDAWLITRGLSTLNIRMKAESENAMKVAEYLK T0339 308 :A 1e5eA 280 :S T0339 312 :QKRI 1e5eA 281 :HPAV T0339 316 :HLNS 1e5eA 286 :KVYY T0339 320 :QFP 1e5eA 294 :DHE T0339 324 :TQRLPNTCNFSIRGPRLQGHVVLAQCRV 1e5eA 305 :MRMYGSMITFILKSGFEGAKKLLDNLKL T0339 352 :LMASVGAACH 1e5eA 335 :LAVSLGGCES T0339 362 :SDHGDQPSPVLLSYGVPFDVARNALRLSVGR 1e5eA 348 :HPASMTHAVVPKEEREAAGITDGMIRLSVGI T0339 394 :TTRAE 1e5eA 379 :EDADE T0339 402 :VVQDLKQAVAQLE 1e5eA 384 :LIADFKQGLDALL Number of specific fragments extracted= 24 number of extra gaps= 0 total=1491 Will force an alignment to be made, even if fragment is small Number of alignments=73 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e5eA/T0339-1e5eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1e5eA/T0339-1e5eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e5eA read from 1e5eA/T0339-1e5eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1e5eA in template set T0339 28 :EAWGNPSSPYSAGRKAKDIINAARESLAKMIGGKP 1e5eA 45 :NRFAGQESGYIYTRLGNPTVSNLEGKIAFLEKTEA T0339 65 :IIFTSGGTESNNLVIHSVV 1e5eA 80 :CVATSSGMGAIAATVLTIL T0339 105 :GAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSK 1e5eA 99 :KAGDHLISDECLYGCTHALFEHALTKFGIQVDFINTAI T0339 144 :SG 1e5eA 137 :PG T0339 151 :DILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKAL 1e5eA 139 :EVKKHMKPNTKIVYFETPANPTLKIIDMERVCKDAHSQ T0339 189 :N 1e5eA 178 :G T0339 200 :ILVHTDAAQALGKQRVDV 1e5eA 179 :VLVIADNTFCSPMITNPV T0339 219 :DLGVDFLTIVGHKFY 1e5eA 197 :DFGVDVVVHSATKYI T0339 234 :GP 1e5eA 213 :GH T0339 236 :RI 1e5eA 216 :DV T0339 238 :GALYIRGLG 1e5eA 219 :AGLICGKAD T0339 261 :ERNFRPGTENTPMIAGLGKAAE 1e5eA 244 :VISPHDAWLITRGLSTLNIRMK T0339 290 :AYEAHMRDVRDY 1e5eA 266 :AESENAMKVAEY T0339 306 :LEAEFGQKRIHLNSQFP 1e5eA 278 :LKSHPAVEKVYYPGFED T0339 324 :TQRLPNTCNFSIRGPRLQGHVVLAQCRV 1e5eA 305 :MRMYGSMITFILKSGFEGAKKLLDNLKL T0339 352 :LMASVG 1e5eA 335 :LAVSLG T0339 358 :AACHSDHGDQPSPVLLSYGVPFDVARNALRLSVGRSTTRA 1e5eA 344 :SLIQHPASMTHAVVPKEEREAAGITDGMIRLSVGIEDADE T0339 402 :VVQDLKQAVAQLE 1e5eA 384 :LIADFKQGLDALL Number of specific fragments extracted= 18 number of extra gaps= 0 total=1509 Will force an alignment to be made, even if fragment is small Number of alignments=74 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e5eA/T0339-1e5eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1e5eA/T0339-1e5eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e5eA read from 1e5eA/T0339-1e5eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1e5eA in template set T0339 45 :DIINAARESLAKMIGG 1e5eA 62 :PTVSNLEGKIAFLEKT T0339 64 :DIIFTSGGTESNNLVIHSV 1e5eA 79 :ACVATSSGMGAIAATVLTI T0339 104 :KGAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSKVS 1e5eA 98 :LKAGDHLISDECLYGCTHALFEHALTKFGIQVDFINTAIPG T0339 151 :DILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKA 1e5eA 139 :EVKKHMKPNTKIVYFETPANPTLKIIDMERVCKDAHS T0339 197 :LPPILVHTDAAQALGKQRVDVE 1e5eA 176 :QEGVLVIADNTFCSPMITNPVD T0339 220 :LGVDFLTIVGHKFYGPR 1e5eA 198 :FGVDVVVHSATKYINGH T0339 237 :IGALYIRGLGEFTPLYP 1e5eA 219 :AGLICGKADLLQQIRMV T0339 266 :PGTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYL 1e5eA 242 :GSVISPHDAWLITRGLSTLNIRMKAESENAMKVAEYL T0339 307 :EAEFGQKRIHL 1e5eA 279 :KSHPAVEKVYY T0339 319 :SQFPG 1e5eA 290 :PGFED T0339 324 :TQRLPNTCNFSIRG 1e5eA 305 :MRMYGSMITFILKS T0339 340 :LQGHVVLAQCRV 1e5eA 320 :FEGAKKLLDNLK T0339 352 :LMASVGAACHSDHG 1e5eA 344 :SLIQHPASMTHAVV T0339 368 :PSPVLLSYGVP 1e5eA 358 :PKEEREAAGIT T0339 383 :RNALRLSVGRSTTRA 1e5eA 369 :DGMIRLSVGIEDADE T0339 402 :VVQDLKQAVAQLE 1e5eA 384 :LIADFKQGLDALL Number of specific fragments extracted= 16 number of extra gaps= 0 total=1525 Will force an alignment to be made, even if fragment is small Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vefA/T0339-1vefA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vefA expands to /projects/compbio/data/pdb/1vef.pdb.gz 1vefA:# T0339 read from 1vefA/T0339-1vefA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vefA read from 1vefA/T0339-1vefA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vefA to template set # found chain 1vefA in template set T0339 1 :ERKVYMDYNA 1vefA 43 :EGNEYIDCVG T0339 11 :TTPLEPEVIQAMTKAMWEAWGNPSSP 1vefA 59 :LGHGNPEVVEAVKRQAETLMAMPQTL T0339 41 :R 1vefA 85 :P T0339 44 :KDIINAARESLAKMIG 1vefA 86 :TPMRGEFYRTLTAILP T0339 60 :G 1vefA 104 :L T0339 63 :QDIIFTSGGTESNNLVIHSVVKHF 1vefA 105 :NRVFPVNSGTEANEAALKFARAHT T0339 93 :KGH 1vefA 129 :GRK T0339 109 :HFITSSVEHDSIRLPLEHLV 1vefA 132 :KFVAAMRGFSGRTMGSLSVT T0339 129 :EEQ 1vefA 158 :EPF T0339 132 :VA 1vefA 162 :PL T0339 134 :AVTFVPVS 1vefA 166 :PVEFIPYN T0339 148 :EVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKALNQER 1vefA 174 :DVEALKRAVDEETAAVILEPVQGEGGVRPATPEFLRAAREITQEK T0339 199 :PILVHTDAAQ 1vefA 219 :GALLILDEIQ T0339 209 :ALGKQRVD 1vefA 230 :GMGRTGKR T0339 217 :VEDLGV 1vefA 240 :FEHFGI T0339 223 :DFLTIV 1vefA 248 :DILTLA T0339 231 :K 1vefA 254 :K T0339 232 :FY 1vefA 256 :LG T0339 234 :GPRIGALYIR 1vefA 259 :GVPLGVAVMR T0339 244 :GLGEFTP 1vefA 270 :EVARSMP T0339 252 :YPMLFG 1vefA 277 :KGGHGT T0339 266 :PGTENTPMIAGLGKAAELVTQ 1vefA 283 :TFGGNPLAMAAGVAAIRYLER T0339 289 :EAYEAHMRDVRDYLEERLEA 1vefA 304 :TRLWERAAELGPWFMEKLRA T0339 310 :FGQKRI 1vefA 324 :IPSPKI T0339 322 :PGTQRLPNTCNFSIR 1vefA 330 :REVRGMGLMVGLELK T0339 340 :LQGHVVLAQCRV 1vefA 345 :EKAAPYIARLEK T0339 352 :LMASVGA 1vefA 360 :VLALQAG T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQAV 1vefA 367 :PTVIRFLPPLVIEKEDLERVVEAVRAVL Number of specific fragments extracted= 28 number of extra gaps= 0 total=1553 Will force an alignment to be made, even if fragment is small Number of alignments=76 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vefA/T0339-1vefA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1vefA/T0339-1vefA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vefA read from 1vefA/T0339-1vefA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vefA in template set T0339 6 :MDY 1vefA 48 :IDC T0339 9 :NATTPLEPEVIQAMTKAMWEAWGNPSSP 1vefA 57 :ANLGHGNPEVVEAVKRQAETLMAMPQTL T0339 37 :Y 1vefA 86 :T T0339 45 :DIINAARESLAKMI 1vefA 87 :PMRGEFYRTLTAIL T0339 62 :PQ 1vefA 101 :PP T0339 64 :DIIFTSGGTESNNLVIHSVVKHF 1vefA 106 :RVFPVNSGTEANEAALKFARAHT T0339 106 :AKPHFITSSVEHDSIRLPLEHL 1vefA 129 :GRKKFVAAMRGFSGRTMGSLSV T0339 128 :VEEQ 1vefA 157 :REPF T0339 135 :VTFVPVS 1vefA 167 :VEFIPYN T0339 148 :EVDDILAAVRPTTRLVTIMLANNETGIVMP 1vefA 174 :DVEALKRAVDEETAAVILEPVQGEGGVRPA T0339 178 :VPEISQRIKALN 1vefA 208 :LRAAREITQEKG T0339 200 :ILVHTDAAQALG 1vefA 220 :ALLILDEIQTGM T0339 212 :KQ 1vefA 236 :KR T0339 217 :VEDLGV 1vefA 240 :FEHFGI T0339 223 :DFLTIVGHKFYGPRIGALYIRG 1vefA 248 :DILTLAKALGGGVPLGVAVMRE T0339 246 :G 1vefA 270 :E T0339 251 :LYPMLFGGGQERNF 1vefA 271 :VARSMPKGGHGTTF T0339 268 :TENTPMIAGLGKAAELVTQ 1vefA 285 :GGNPLAMAAGVAAIRYLER T0339 291 :YEAHMRDVRDYLEERLEAE 1vefA 306 :LWERAAELGPWFMEKLRAI T0339 310 :FG 1vefA 327 :PK T0339 315 :IH 1vefA 329 :IR T0339 323 :GTQRLPNTCNFSIR 1vefA 331 :EVRGMGLMVGLELK T0339 340 :LQGHVVLAQCRV 1vefA 345 :EKAAPYIARLEK T0339 352 :LMAS 1vefA 361 :LALQ T0339 381 :VARNALRLSVGRSTTRAEVDLVVQDLKQAV 1vefA 365 :AGPTVIRFLPPLVIEKEDLERVVEAVRAVL Number of specific fragments extracted= 25 number of extra gaps= 0 total=1578 Will force an alignment to be made, even if fragment is small Number of alignments=77 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vefA/T0339-1vefA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1vefA/T0339-1vefA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vefA read from 1vefA/T0339-1vefA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vefA in template set T0339 9 :NATTPLEPEVIQAMTKAMWEAWGNPSSPYS 1vefA 57 :ANLGHGNPEVVEAVKRQAETLMAMPQTLPT T0339 45 :DIINAARESLAKMI 1vefA 87 :PMRGEFYRTLTAIL T0339 62 :PQD 1vefA 101 :PPE T0339 65 :IIFTSGGTESNNLVIHSVV 1vefA 107 :VFPVNSGTEANEAALKFAR T0339 103 :VKGAKPHFITSSVEHDSIRLPLEHL 1vefA 126 :AHTGRKKFVAAMRGFSGRTMGSLSV T0339 135 :VTFVPVS 1vefA 167 :VEFIPYN T0339 148 :EVDDILAAVRPTTRLVTIMLANNETGIVMP 1vefA 174 :DVEALKRAVDEETAAVILEPVQGEGGVRPA T0339 178 :VPEISQRIKA 1vefA 208 :LRAAREITQE T0339 198 :PPILVHTDAAQALGKQRVD 1vefA 218 :KGALLILDEIQTGMGRTGK T0339 217 :VEDLGV 1vefA 240 :FEHFGI T0339 223 :DFLTIVGHKFYGPRIGALYIRGLGEFTPL 1vefA 248 :DILTLAKALGGGVPLGVAVMREEVARSMP T0339 254 :MLFGGG 1vefA 277 :KGGHGT T0339 266 :PGTENTPMIAGLGKAAELVT 1vefA 283 :TFGGNPLAMAAGVAAIRYLE T0339 290 :AYEAHMRDVRDYLEERLEAEFG 1vefA 305 :RLWERAAELGPWFMEKLRAIPS T0339 312 :QK 1vefA 330 :RE T0339 324 :TQRLPNTCNFSIRGPRLQGHVVLAQCRVLMASV 1vefA 332 :VRGMGLMVGLELKEKAAPYIARLEKEHRVLALQ T0339 381 :VARNALRLSVGRSTTRAEVDLVVQDLKQAV 1vefA 365 :AGPTVIRFLPPLVIEKEDLERVVEAVRAVL Number of specific fragments extracted= 17 number of extra gaps= 0 total=1595 Will force an alignment to be made, even if fragment is small Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fc4A/T0339-1fc4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fc4A expands to /projects/compbio/data/pdb/1fc4.pdb.gz 1fc4A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0339 read from 1fc4A/T0339-1fc4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fc4A read from 1fc4A/T0339-1fc4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fc4A to template set # found chain 1fc4A in template set T0339 1 :ER 1fc4A 40 :DG T0339 3 :KVYMD 1fc4A 44 :VINFC T0339 8 :YNATT 1fc4A 50 :NNYLG T0339 13 :PLEPEVIQAMTKAMWE 1fc4A 56 :ANHPDLIAAAKAGMDS T0339 30 :WGNPSSPYSAGRKAKDIINAARESLAKMIGG 1fc4A 72 :HGFGMASVRFICGTQDSHKELEQKLAAFLGM T0339 63 :QDIIFTSGGTESNNLVIHSV 1fc4A 103 :EDAILYSSCFDANGGLFETL T0339 91 :TSKGH 1fc4A 123 :LGAED T0339 109 :HFITSSVEHDSIRLPLEHL 1fc4A 128 :AIISDALNHASIIDGVRLC T0339 132 :VAAVTFVPVS 1fc4A 147 :KAKRYRYANN T0339 148 :EVDDILAAVR 1fc4A 157 :DMQELEARLK T0339 158 :PTT 1fc4A 171 :AGA T0339 161 :RLVTIMLANNETGIVMPVPEISQ 1fc4A 176 :VLIATDGVFSMDGVIANLKGVCD T0339 188 :LNQER 1fc4A 199 :LADKY T0339 199 :PILVHTDAAQALGKQR 1fc4A 204 :DALVMVDDSHAVGFVG T0339 215 :VDVEDL 1fc4A 223 :RGSHEY T0339 221 :GVDFLTIVGHK 1fc4A 234 :RVDIITGTLGK T0339 232 :FYGPRIGALYIR 1fc4A 246 :LGGASGGYTAAR T0339 244 :GLGEFT 1fc4A 259 :EVVEWL T0339 250 :PLYPMLFG 1fc4A 266 :QRSRPYLF T0339 266 :PGTENTPMIAGLGKAAELVTQ 1fc4A 274 :SNSLAPAIVAASIKVLEMVEA T0339 288 :CEAYEAHMRDVRDYLEERLEAE 1fc4A 295 :GSELRDRLWANARQFREQMSAA T0339 314 :RIHLNSQF 1fc4A 317 :GFTLAGAD T0339 328 :PNTCNFSIRG 1fc4A 325 :HAIIPVMLGD T0339 340 :LQ 1fc4A 335 :AV T0339 342 :GHVVLAQCRV 1fc4A 338 :AQKFARELQK T0339 352 :LMASVGAACHSDHG 1fc4A 350 :IYVTGFFYPVVPKG T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQAVAQL 1fc4A 364 :QARIRTQMSAAHTPEQITRAVEAFTRIGKQL Number of specific fragments extracted= 27 number of extra gaps= 0 total=1622 Will force an alignment to be made, even if fragment is small Number of alignments=79 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fc4A/T0339-1fc4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1fc4A/T0339-1fc4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fc4A read from 1fc4A/T0339-1fc4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fc4A in template set T0339 3 :KVYMDYNATTPL 1fc4A 44 :VINFCANNYLGL T0339 15 :EPEVIQA 1fc4A 58 :HPDLIAA T0339 23 :TKAMWEAWGN 1fc4A 65 :AKAGMDSHGF T0339 33 :PSSP 1fc4A 76 :MASV T0339 37 :YSAG 1fc4A 81 :FICG T0339 43 :AKDIINAARESLAKMIGG 1fc4A 85 :TQDSHKELEQKLAAFLGM T0339 63 :QDIIFTSGGTESNNLVIHSVV 1fc4A 103 :EDAILYSSCFDANGGLFETLL T0339 105 :GAKPHFITSSV 1fc4A 124 :GAEDAIISDAL T0339 120 :IRLPLEHLVEEQVAAVTFVPVS 1fc4A 135 :NHASIIDGVRLCKAKRYRYANN T0339 148 :EVDDILAAV 1fc4A 157 :DMQELEARL T0339 157 :RPTTR 1fc4A 170 :EAGAR T0339 162 :LVTIMLANNETGIVMPVPEISQRIKALN 1fc4A 177 :LIATDGVFSMDGVIANLKGVCDLADKYD T0339 200 :ILVHTDAAQALGKQ 1fc4A 205 :ALVMVDDSHAVGFV T0339 217 :VEDLG 1fc4A 229 :CDVMG T0339 222 :VDFLTIVGHKFY 1fc4A 235 :VDIITGTLGKAL T0339 234 :GPRIGALYIRG 1fc4A 248 :GASGGYTAARK T0339 246 :GEFTP 1fc4A 259 :EVVEW T0339 265 :RPGTENTPMIAGLGKAAELVTQ 1fc4A 273 :FSNSLAPAIVAASIKVLEMVEA T0339 289 :EAYEAHMRDVRDYLEERLEAE 1fc4A 296 :SELRDRLWANARQFREQMSAA T0339 311 :G 1fc4A 317 :G T0339 315 :IHLNSQF 1fc4A 318 :FTLAGAD T0339 328 :PNTCNFSIRG 1fc4A 325 :HAIIPVMLGD T0339 339 :RLQGHVVLAQCRV 1fc4A 335 :AVVAQKFARELQK T0339 352 :LMASV 1fc4A 350 :IYVTG T0339 360 :CHSDH 1fc4A 355 :FFYPV T0339 377 :VPFD 1fc4A 360 :VPKG T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQAVAQL 1fc4A 364 :QARIRTQMSAAHTPEQITRAVEAFTRIGKQL Number of specific fragments extracted= 27 number of extra gaps= 0 total=1649 Will force an alignment to be made, even if fragment is small Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fc4A/T0339-1fc4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1fc4A/T0339-1fc4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fc4A read from 1fc4A/T0339-1fc4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fc4A in template set T0339 4 :VYMDYNATTPL 1fc4A 45 :INFCANNYLGL T0339 15 :EPEVIQAMTKAMWEA 1fc4A 58 :HPDLIAAAKAGMDSH T0339 31 :GNPSSPYSAGRKAKDIINAARESLAKMIGG 1fc4A 73 :GFGMASVRFICGTQDSHKELEQKLAAFLGM T0339 63 :QDIIFTSGGTESNNLVIHSV 1fc4A 103 :EDAILYSSCFDANGGLFETL T0339 104 :KGAKPHFITSSVEHDSIRLPLEHL 1fc4A 123 :LGAEDAIISDALNHASIIDGVRLC T0339 132 :VAA 1fc4A 147 :KAK T0339 137 :FVPVS 1fc4A 150 :RYRYA T0339 143 :VS 1fc4A 155 :NN T0339 148 :EVDDILAAV 1fc4A 157 :DMQELEARL T0339 157 :RPTTR 1fc4A 170 :EAGAR T0339 162 :LVTIMLANNETGIVMPVPEISQRIKA 1fc4A 177 :LIATDGVFSMDGVIANLKGVCDLADK T0339 198 :PPILVHTDAAQALGKQR 1fc4A 203 :YDALVMVDDSHAVGFVG T0339 217 :VEDLG 1fc4A 229 :CDVMG T0339 222 :VDFLTIVGHKFYGPR 1fc4A 235 :VDIITGTLGKALGGA T0339 237 :IGALYIRGLGEFTPLY 1fc4A 251 :GGYTAARKEVVEWLRQ T0339 264 :FRPGTENTPMIAGLGKAAELVT 1fc4A 272 :LFSNSLAPAIVAASIKVLEMVE T0339 289 :EAYEAHMRDVRDYLEERLEAE 1fc4A 296 :SELRDRLWANARQFREQMSAA T0339 311 :GQKRIH 1fc4A 317 :GFTLAG T0339 326 :RLPNTCNFSIRG 1fc4A 323 :ADHAIIPVMLGD T0339 339 :RLQGHVVLAQCRVLMASV 1fc4A 337 :VAQKFARELQKEGIYVTG T0339 360 :CHSDHG 1fc4A 355 :FFYPVV T0339 380 :DVARNALRLSVGRSTTRAEVDLVVQDLKQAVAQL 1fc4A 361 :PKGQARIRTQMSAAHTPEQITRAVEAFTRIGKQL Number of specific fragments extracted= 22 number of extra gaps= 0 total=1671 Will force an alignment to be made, even if fragment is small Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ecxA/T0339-1ecxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ecxA expands to /projects/compbio/data/pdb/1ecx.pdb.gz 1ecxA:# T0339 read from 1ecxA/T0339-1ecxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ecxA read from 1ecxA/T0339-1ecxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ecxA to template set # found chain 1ecxA in template set Warning: unaligning (T0339)V356 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ecxA)H333 Warning: unaligning (T0339)P370 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ecxA)H333 Warning: unaligning (T0339)V390 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ecxA)C354 Warning: unaligning (T0339)G391 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ecxA)C354 Warning: unaligning (T0339)L413 because last residue in template chain is (1ecxA)L376 T0339 3 :KVYMDYNATTPLEPEVIQAMTKAMWEAWGNPSSPYSAGRKAKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSVVKHFHAN 1ecxA 2 :RVYFDNNATTRVDDRVLEEMIVFYREKYGNPNSAHGMGIEANLHMEKAREKVAKVLGVSPSEIFFTSCATESINWILKTVAETFEKR T0339 94 :GH 1ecxA 89 :KR T0339 109 :HFITSSVEHDSIRLPLEHL 1ecxA 91 :TIITTPIEHKAVLETMKYL T0339 129 :EEQVAAVTFVPVSK 1ecxA 110 :SMKGFKVKYVPVDS T0339 144 :SGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1ecxA 124 :RGVVKLEELEKLVDEDTFLVSIMAANNEVGTIQPVEDVTR T0339 188 :LNQER 1ecxA 164 :IVKKK T0339 197 :LPPILVHTDAAQALGKQRVDVEDLGVDFLTIVGHK 1ecxA 169 :NKETLVHVDAVQTIGKIPFSLEKLEVDYASFSAHK T0339 232 :FYGPRIGALYIR 1ecxA 205 :HGPKGVGITYIR T0339 247 :EFTPLYPMLFGGGQERNFRPGTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEERLEAE 1ecxA 217 :KGVPIRPLIHGGGQERGLRSGTQNVPGIVGAARAMEIAVEELSEAAKHMEKLRSKLVSGLMNL T0339 314 :RIHLNSQFP 1ecxA 280 :GAHIITPLE T0339 325 :QRLPNTCNFSIRG 1ecxA 289 :ISLPNTLSVSFPN T0339 340 :LQGHVVLAQCRV 1ecxA 302 :IRGSTLQNLLSG T0339 352 :LMAS 1ecxA 316 :IYVS T0339 371 :VLLSYGVPFDVARNALRLS 1ecxA 334 :VLDAMGVDRRIAQGAIRIS T0339 392 :RSTTRAEVDLVVQDLKQAVAQ 1ecxA 355 :KYNTEEEVDYFLKKIEEILSF Number of specific fragments extracted= 15 number of extra gaps= 1 total=1686 Will force an alignment to be made, even if fragment is small Number of alignments=82 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ecxA/T0339-1ecxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1ecxA/T0339-1ecxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ecxA read from 1ecxA/T0339-1ecxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ecxA in template set Warning: unaligning (T0339)V356 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ecxA)H333 Warning: unaligning (T0339)P370 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ecxA)H333 Warning: unaligning (T0339)V390 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ecxA)C354 Warning: unaligning (T0339)G391 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ecxA)C354 Warning: unaligning (T0339)L413 because last residue in template chain is (1ecxA)L376 T0339 3 :KVYMDYNATTPLEPEVIQAMTKAMWEAWGNPSSPYSAGRKAKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSVVKHFH 1ecxA 2 :RVYFDNNATTRVDDRVLEEMIVFYREKYGNPNSAHGMGIEANLHMEKAREKVAKVLGVSPSEIFFTSCATESINWILKTVAETFE T0339 105 :GAKPHFITSSVEHDSIRLPLEHL 1ecxA 87 :KRKRTIITTPIEHKAVLETMKYL T0339 129 :EEQVAAVTFVPVSK 1ecxA 110 :SMKGFKVKYVPVDS T0339 144 :SGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKALN 1ecxA 124 :RGVVKLEELEKLVDEDTFLVSIMAANNEVGTIQPVEDVTRIVKKKN T0339 198 :PPILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFYGP 1ecxA 170 :KETLVHVDAVQTIGKIPFSLEKLEVDYASFSAHKFHGP T0339 236 :RIGALYIRG 1ecxA 209 :GVGITYIRK T0339 246 :G 1ecxA 218 :G T0339 249 :TPLYPMLFGGGQERNFRPGTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEERLEAE 1ecxA 219 :VPIRPLIHGGGQERGLRSGTQNVPGIVGAARAMEIAVEELSEAAKHMEKLRSKLVSGLMNL T0339 311 :G 1ecxA 280 :G T0339 315 :IHLNSQ 1ecxA 281 :AHIITP T0339 323 :GTQRLPNTCNFSIRG 1ecxA 287 :LEISLPNTLSVSFPN T0339 340 :LQGHVVLAQCRV 1ecxA 302 :IRGSTLQNLLSG T0339 352 :LMAS 1ecxA 316 :IYVS T0339 371 :VLLSYGVPFDVARNALRLS 1ecxA 334 :VLDAMGVDRRIAQGAIRIS T0339 392 :RSTTRAEVDLVVQDLKQAVAQ 1ecxA 355 :KYNTEEEVDYFLKKIEEILSF Number of specific fragments extracted= 15 number of extra gaps= 1 total=1701 Will force an alignment to be made, even if fragment is small Number of alignments=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ecxA/T0339-1ecxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1ecxA/T0339-1ecxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ecxA read from 1ecxA/T0339-1ecxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ecxA in template set Warning: unaligning (T0339)V356 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ecxA)H333 Warning: unaligning (T0339)P370 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ecxA)H333 Warning: unaligning (T0339)V390 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ecxA)C354 Warning: unaligning (T0339)G391 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ecxA)C354 T0339 4 :VYMDYNATTPLEPEVIQAMTKAMWEAWGNPSSPYSAGRKAKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSV 1ecxA 3 :VYFDNNATTRVDDRVLEEMIVFYREKYGNPNSAHGMGIEANLHMEKAREKVAKVLGVSPSEIFFTSCATESINWILKTV T0339 100 :HSPVKGAKPHFITSSVEHDSIRLPLEHL 1ecxA 82 :AETFEKRKRTIITTPIEHKAVLETMKYL T0339 129 :EEQVAAVTFVPVS 1ecxA 110 :SMKGFKVKYVPVD T0339 143 :VSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKA 1ecxA 123 :SRGVVKLEELEKLVDEDTFLVSIMAANNEVGTIQPVEDVTRIVKK T0339 196 :GLPPILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFYGPR 1ecxA 168 :KNKETLVHVDAVQTIGKIPFSLEKLEVDYASFSAHKFHGPK T0339 237 :IGALYIRGLGEFT 1ecxA 210 :VGITYIRKGVPIR T0339 253 :PMLFGGGQERNFRPGTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1ecxA 223 :PLIHGGGQERGLRSGTQNVPGIVGAARAMEIAVEELSEAAKHMEKLRSKLVSGLMNLGAHIITP T0339 323 :GTQRLPNTCNFSIRGPRLQGHVVLAQCRVLMAS 1ecxA 287 :LEISLPNTLSVSFPNIRGSTLQNLLSGYGIYVS T0339 371 :VLLSYGVPFDVARNALRLS 1ecxA 334 :VLDAMGVDRRIAQGAIRIS T0339 392 :RSTTRAEVDLVVQDLKQAVAQ 1ecxA 355 :KYNTEEEVDYFLKKIEEILSF Number of specific fragments extracted= 10 number of extra gaps= 1 total=1711 Will force an alignment to be made, even if fragment is small Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fg7A/T0339-1fg7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fg7A expands to /projects/compbio/data/pdb/1fg7.pdb.gz 1fg7A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0339 read from 1fg7A/T0339-1fg7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fg7A read from 1fg7A/T0339-1fg7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fg7A to template set # found chain 1fg7A in template set T0339 2 :RKVYMD 1fg7A 30 :GDVWLN T0339 8 :YNA 1fg7A 37 :NEY T0339 14 :LE 1fg7A 47 :LT T0339 29 :AWGNPSSPYS 1fg7A 52 :LNRYPECQPK T0339 49 :AARESLAKMIGGKPQDIIFTSGGTESNNLVIHSV 1fg7A 62 :AVIENYAQYAGVKPEQVLVSRGADEGIELLIRAF T0339 91 :TSKG 1fg7A 96 :CEPG T0339 95 :H 1fg7A 101 :D T0339 109 :HFITSSVEHDSIRLPLEHL 1fg7A 102 :AILYCPPTYGMYSVSAETI T0339 132 :VAAVTFVPVSK 1fg7A 121 :GVECRTVPTLD T0339 144 :SGQTEVDDILA 1fg7A 132 :NWQLDLQGISD T0339 158 :PTTRLVTIMLANNETGIVMPVPEISQ 1fg7A 145 :DGVKVVYVCSPNNPTGQLINPQDFRT T0339 185 :IKALNQE 1fg7A 171 :LLELTRG T0339 199 :PILVHTDAAQALGKQR 1fg7A 178 :KAIVVADEAYIEFCPQ T0339 216 :D 1fg7A 195 :S T0339 217 :VEDL 1fg7A 197 :AGWL T0339 221 :GV 1fg7A 202 :EY T0339 223 :DFLTIVGHK 1fg7A 206 :LAILRTLSK T0339 232 :FY 1fg7A 216 :FA T0339 234 :GPRIGALYIR 1fg7A 220 :GLRCGFTLAN T0339 244 :G 1fg7A 231 :E T0339 245 :LGEFTP 1fg7A 236 :LMKVIA T0339 266 :PGTENTPMIAGLGKAA 1fg7A 242 :PYPLSTPVADIAAQAL T0339 285 :TQNCEAYEAHMRDVRDYLEERLEA 1fg7A 262 :IVAMRERVAQIIAEREYLIAALKE T0339 312 :QKRIHLNSQFP 1fg7A 286 :IPCVEQVFDSE T0339 328 :PNTCNFSIRG 1fg7A 297 :TNYILARFKA T0339 342 :GHVVLAQCRVLMASVGAACHSDHG 1fg7A 307 :SSAVFKSLWDQGIILRDQNKQPSL T0339 383 :RNALRLSVG 1fg7A 331 :SGCLRITVG T0339 395 :TRAEVDLVVQDLK 1fg7A 340 :TREESQRVIDALR Number of specific fragments extracted= 28 number of extra gaps= 0 total=1739 Will force an alignment to be made, even if fragment is small Number of alignments=85 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fg7A/T0339-1fg7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1fg7A/T0339-1fg7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fg7A read from 1fg7A/T0339-1fg7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fg7A in template set T0339 49 :AARESLAKMIGGKPQDIIFTSGGTESNNLVIHSVV 1fg7A 62 :AVIENYAQYAGVKPEQVLVSRGADEGIELLIRAFC T0339 104 :KGAKPHFITSSVEHDSIRLPLEHL 1fg7A 97 :EPGKDAILYCPPTYGMYSVSAETI T0339 132 :VAAVTFVPVSK 1fg7A 121 :GVECRTVPTLD T0339 144 :SGQTEVDDILAAV 1fg7A 132 :NWQLDLQGISDKL T0339 158 :PTTRLVTIMLANNETGIVMP 1fg7A 145 :DGVKVVYVCSPNNPTGQLIN T0339 178 :VPEISQRIKALN 1fg7A 168 :FRTLLELTRGKA T0339 200 :ILVHTDAAQALGKQRVDVEDLG 1fg7A 180 :IVVADEAYIEFCPQASLAGWLA T0339 224 :FLTIVGHKFYGP 1fg7A 207 :AILRTLSKAFAL T0339 236 :R 1fg7A 220 :G T0339 237 :IGALYIRG 1fg7A 223 :CGFTLANE T0339 246 :G 1fg7A 231 :E T0339 261 :ERNFRP 1fg7A 241 :APYPLS T0339 268 :T 1fg7A 247 :T T0339 275 :AGLGKAAELVTQ 1fg7A 248 :PVADIAAQALSP T0339 287 :NCEAYEAHMRDVRD 1fg7A 261 :GIVAMRERVAQIIA T0339 301 :YLEERLEAEFG 1fg7A 278 :YLIAALKEIPC T0339 315 :IHLNSQFP 1fg7A 289 :VEQVFDSE T0339 328 :PNTCNFSIRG 1fg7A 297 :TNYILARFKA T0339 342 :GHVVLAQCRV 1fg7A 307 :SSAVFKSLWD T0339 352 :LMASV 1fg7A 319 :IILRD T0339 362 :S 1fg7A 324 :Q T0339 377 :VPFDVARNALRLSVGR 1fg7A 325 :NKQPSLSGCLRITVGT T0339 396 :RAEVDLVVQDLK 1fg7A 341 :REESQRVIDALR Number of specific fragments extracted= 23 number of extra gaps= 0 total=1762 Will force an alignment to be made, even if fragment is small Number of alignments=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fg7A/T0339-1fg7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1fg7A/T0339-1fg7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fg7A read from 1fg7A/T0339-1fg7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fg7A in template set T0339 13 :PLEPEVIQAMTKAM 1fg7A 58 :CQPKAVIENYAQYA T0339 59 :GGKPQDIIFTSGGTESNNLVIHSV 1fg7A 72 :GVKPEQVLVSRGADEGIELLIRAF T0339 103 :VKGAKPHFITSSVEHDSIRLPLEHL 1fg7A 96 :CEPGKDAILYCPPTYGMYSVSAETI T0339 132 :VAAVTFVPVS 1fg7A 121 :GVECRTVPTL T0339 143 :VSGQTEVDDILAAV 1fg7A 131 :DNWQLDLQGISDKL T0339 158 :PTTRLVTIMLANNETGIVMP 1fg7A 145 :DGVKVVYVCSPNNPTGQLIN T0339 178 :VPEISQRIK 1fg7A 168 :FRTLLELTR T0339 198 :PPILVHTDAAQALGKQRVD 1fg7A 177 :GKAIVVADEAYIEFCPQAS T0339 217 :VEDLGVDFLTIVGHKFYGPR 1fg7A 200 :LAEYPHLAILRTLSKAFALA T0339 237 :IGALYIRGLGEFTPLYPMLFGGGQ 1fg7A 223 :CGFTLANEEVINLLMKVIAPYPLS T0339 269 :EN 1fg7A 247 :TP T0339 276 :GLGKAAELVT 1fg7A 249 :VADIAAQALS T0339 286 :QNCEAYEAHMR 1fg7A 260 :QGIVAMRERVA T0339 297 :DVRDYLEERLEAEFGQKRIH 1fg7A 274 :AEREYLIAALKEIPCVEQVF T0339 325 :QRLPNTCNFSIRG 1fg7A 294 :DSETNYILARFKA T0339 340 :LQGHVVLAQCRVLMASVG 1fg7A 307 :SSAVFKSLWDQGIILRDQ T0339 377 :VPFDVARNALRLSVG 1fg7A 325 :NKQPSLSGCLRITVG T0339 395 :TRAEVDLVVQDLK 1fg7A 340 :TREESQRVIDALR Number of specific fragments extracted= 18 number of extra gaps= 0 total=1780 Will force an alignment to be made, even if fragment is small Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bwnA/T0339-2bwnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bwnA expands to /projects/compbio/data/pdb/2bwn.pdb.gz 2bwnA:Skipped atom 279, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 281, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 283, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 285, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 287, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 289, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 291, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 293, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 295, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 740, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 742, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 983, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 985, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 987, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 989, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 991, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 993, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 995, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 997, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 999, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 1001, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 1003, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 1216, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 1218, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 1220, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 1222, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 1224, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 1226, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 1228, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 1230, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 1232, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 1609, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 1611, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 1613, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 1615, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 1617, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 1619, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 1621, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 1623, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 1625, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 1848, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 1850, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 1852, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 1854, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 1856, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 1858, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 1860, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 1862, because occupancy 0.500 <= existing 0.500 in 2bwnA Bad short name: N1 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: C2' for alphabet: pdb_atoms Bad short name: C3 for alphabet: pdb_atoms Bad short name: O3 for alphabet: pdb_atoms Bad short name: C4 for alphabet: pdb_atoms Bad short name: C4' for alphabet: pdb_atoms Bad short name: C5 for alphabet: pdb_atoms Bad short name: C6 for alphabet: pdb_atoms Bad short name: C5' for alphabet: pdb_atoms Bad short name: OP4 for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms Skipped atom 2412, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 2414, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 2416, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 2418, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 2420, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 2422, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 2424, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 2426, because occupancy 0.300 <= existing 0.700 in 2bwnA Skipped atom 2544, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2546, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2548, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2550, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2552, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2554, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2556, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2558, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2676, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2678, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2680, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2682, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2684, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2686, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2688, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2690, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2692, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2694, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2738, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2740, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2742, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2744, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2746, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2748, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2750, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 2752, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 3021, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 3023, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 3025, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 3027, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 3029, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 3031, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 3033, because occupancy 0.500 <= existing 0.500 in 2bwnA Skipped atom 3035, because occupancy 0.500 <= existing 0.500 in 2bwnA # T0339 read from 2bwnA/T0339-2bwnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bwnA read from 2bwnA/T0339-2bwnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bwnA to template set # found chain 2bwnA in template set Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bwnA)A249 Warning: unaligning (T0339)A239 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bwnA)I257 Warning: unaligning (T0339)L240 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bwnA)I257 T0339 2 :RK 2bwnA 44 :GK T0339 4 :VYMDYNATT 2bwnA 50 :VWCGNDYLG T0339 13 :PLEPEVIQAMTKAMWE 2bwnA 60 :GQHPVVLAAMHEALEA T0339 30 :WGNPSSPYSAGRKAKDIINAARESLAKMIGG 2bwnA 76 :VGAGSGGTRNISGTTAYHRRLEAEIAGLHQK T0339 63 :QDIIFTSGGTESNNLVIHSVVK 2bwnA 107 :EAALVFSSAYNANDATLSTLRV T0339 91 :TSKGH 2bwnA 129 :LFPGL T0339 109 :HFITSSVEHDSIRLPLEHL 2bwnA 134 :IIYSDSLNHASMIEGIKRN T0339 132 :VAAVTFVPVS 2bwnA 153 :AGPKRIFRHN T0339 148 :EVDDILAAVR 2bwnA 163 :DVAHLRELIA T0339 158 :PT 2bwnA 176 :PA T0339 160 :TRLVTIMLANNETGIVMPVPEISQ 2bwnA 179 :PKLIAFESVYSMDGDFGPIKEICD T0339 188 :LNQER 2bwnA 203 :IAEEF T0339 199 :PILVHTDAAQALGKQR 2bwnA 208 :GALTYIDEVHAVGMYG T0339 217 :VED 2bwnA 236 :MHR T0339 222 :VDFLTIVG 2bwnA 239 :IDIFNGTL T0339 232 :FYGP 2bwnA 250 :YGVF T0339 237 :IG 2bwnA 254 :GG T0339 241 :YIR 2bwnA 258 :AAS T0339 244 :GLGEFT 2bwnA 262 :RMVDAV T0339 250 :PLYPMLFG 2bwnA 269 :SYAPGFIF T0339 266 :PGTENTPMIAGLGKAAELVTQ 2bwnA 277 :STSLPPAIAAGAQASIAFLKT T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 2bwnA 299 :EGQKLRDAQQMHAKVLKMRLKAL T0339 314 :RIHLNSQ 2bwnA 322 :GMPIIDH T0339 322 :P 2bwnA 329 :G T0339 328 :PNTCNFSIRGP 2bwnA 330 :SHIVPVVIGDP T0339 340 :LQGHVVLAQCRV 2bwnA 341 :VHTKAVSDMLLS T0339 352 :LMASVGAACHSDHG 2bwnA 356 :VYVQPINFPTVPRG T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQA 2bwnA 370 :TERLRFTPSPVHDLKQIDGLVHAMDLL Number of specific fragments extracted= 28 number of extra gaps= 1 total=1808 Will force an alignment to be made, even if fragment is small Number of alignments=88 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bwnA/T0339-2bwnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 2bwnA/T0339-2bwnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bwnA read from 2bwnA/T0339-2bwnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bwnA in template set Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bwnA)A249 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bwnA)A249 Warning: unaligning (T0339)A239 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bwnA)I257 Warning: unaligning (T0339)L240 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bwnA)I257 T0339 4 :VYMDYNATTPL 2bwnA 48 :ITVWCGNDYLG T0339 15 :EPEVIQAMTKAMWEAWGN 2bwnA 62 :HPVVLAAMHEALEAVGAG T0339 33 :PSSPYSAG 2bwnA 86 :ISGTTAYH T0339 48 :NAARESLAKMIGGKP 2bwnA 94 :RRLEAEIAGLHQKEA T0339 65 :IIFTSGGTESNNLVIHSVVKH 2bwnA 109 :ALVFSSAYNANDATLSTLRVL T0339 105 :GAKPHFITSSV 2bwnA 130 :FPGLIIYSDSL T0339 120 :IRLPLEHLVEEQVAAVTFVPVS 2bwnA 141 :NHASMIEGIKRNAGPKRIFRHN T0339 148 :EVDDILAAV 2bwnA 163 :DVAHLRELI T0339 157 :RPT 2bwnA 175 :DPA T0339 160 :TRLVTIMLANNETGIVMPVPEISQRIKALN 2bwnA 179 :PKLIAFESVYSMDGDFGPIKEICDIAEEFG T0339 200 :ILVHTDAAQALGKQ 2bwnA 209 :ALTYIDEVHAVGMY T0339 217 :VED 2bwnA 236 :MHR T0339 222 :VDFLTIVG 2bwnA 239 :IDIFNGTL T0339 233 :YGPRIG 2bwnA 250 :YGVFGG T0339 241 :YIRG 2bwnA 258 :AASA T0339 246 :G 2bwnA 262 :R T0339 265 :RPGTENTPMIAGLGKAAELVTQ 2bwnA 276 :FSTSLPPAIAAGAQASIAFLKT T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 2bwnA 299 :EGQKLRDAQQMHAKVLKMRLKAL T0339 311 :G 2bwnA 322 :G T0339 315 :IHLNSQ 2bwnA 323 :MPIIDH T0339 323 :G 2bwnA 329 :G T0339 328 :PNTCNFSIR 2bwnA 330 :SHIVPVVIG T0339 341 :QGHVVLAQCRVLMASVG 2bwnA 339 :DPVHTKAVSDMLLSDYG T0339 358 :AACHSDH 2bwnA 359 :QPINFPT T0339 377 :VPFD 2bwnA 366 :VPRG T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQA 2bwnA 370 :TERLRFTPSPVHDLKQIDGLVHAMDLL Number of specific fragments extracted= 26 number of extra gaps= 1 total=1834 Will force an alignment to be made, even if fragment is small Number of alignments=89 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bwnA/T0339-2bwnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 2bwnA/T0339-2bwnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bwnA read from 2bwnA/T0339-2bwnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bwnA in template set Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bwnA)A249 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bwnA)A249 Warning: unaligning (T0339)A239 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bwnA)I257 Warning: unaligning (T0339)L240 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bwnA)I257 T0339 15 :EPEVIQAMTKAMWEAWGNPS 2bwnA 62 :HPVVLAAMHEALEAVGAGSG T0339 35 :SPYSAG 2bwnA 83 :TRNISG T0339 45 :DIINAARESLAKMIGG 2bwnA 91 :AYHRRLEAEIAGLHQK T0339 64 :DIIFTSGGTESNNLVIHSV 2bwnA 108 :AALVFSSAYNANDATLSTL T0339 102 :PVKGAKPHFITSSVEHDSIRLPL 2bwnA 127 :RVLFPGLIIYSDSLNHASMIEGI T0339 129 :EEQVAAVTFVPVS 2bwnA 150 :KRNAGPKRIFRHN T0339 148 :EVDDILAAV 2bwnA 163 :DVAHLRELI T0339 157 :RPTTRLVTIMLANNETGIVMPVPEISQRIKA 2bwnA 176 :PAAPKLIAFESVYSMDGDFGPIKEICDIAEE T0339 198 :PPILVHTDAAQALGKQRVD 2bwnA 207 :FGALTYIDEVHAVGMYGPR T0339 217 :VED 2bwnA 236 :MHR T0339 222 :VDFLTIVG 2bwnA 239 :IDIFNGTL T0339 233 :YGPRIG 2bwnA 250 :YGVFGG T0339 241 :YIRGLGEFTPLYPMLFG 2bwnA 258 :AASARMVDAVRSYAPGF T0339 264 :FRPGTENTPMIAGLGKAAELVT 2bwnA 275 :IFSTSLPPAIAAGAQASIAFLK T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 2bwnA 298 :AEGQKLRDAQQMHAKVLKMRLKALGMPIIDH T0339 327 :LPNTCNFSIR 2bwnA 329 :GSHIVPVVIG T0339 339 :RLQGHVV 2bwnA 339 :DPVHTKA T0339 346 :LAQCRVLMASVGAACHSDHG 2bwnA 350 :LLSDYGVYVQPINFPTVPRG T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQA 2bwnA 370 :TERLRFTPSPVHDLKQIDGLVHAMDLL Number of specific fragments extracted= 19 number of extra gaps= 1 total=1853 Will force an alignment to be made, even if fragment is small Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m7yA/T0339-1m7yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1m7yA expands to /projects/compbio/data/pdb/1m7y.pdb.gz 1m7yA:Skipped atom 393, because occupancy 0.500 <= existing 0.500 in 1m7yA Skipped atom 1568, because occupancy 0.500 <= existing 0.500 in 1m7yA Skipped atom 1570, because occupancy 0.500 <= existing 0.500 in 1m7yA Skipped atom 2408, because occupancy 0.500 <= existing 0.500 in 1m7yA Skipped atom 2410, because occupancy 0.500 <= existing 0.500 in 1m7yA Skipped atom 2412, because occupancy 0.500 <= existing 0.500 in 1m7yA Skipped atom 2483, because occupancy 0.500 <= existing 0.500 in 1m7yA Skipped atom 2485, because occupancy 0.500 <= existing 0.500 in 1m7yA Skipped atom 2487, because occupancy 0.500 <= existing 0.500 in 1m7yA # T0339 read from 1m7yA/T0339-1m7yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m7yA read from 1m7yA/T0339-1m7yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1m7yA to template set # found chain 1m7yA in template set T0339 3 :KVYMDYNATTPLEPEVIQAMTK 1m7yA 39 :GIIQMGLAENQLCFDLLESWLA T0339 25 :AMWE 1m7yA 78 :ELAL T0339 34 :SSPYSA 1m7yA 82 :FQDYHG T0339 43 :AKDIINAARESLAKMIG 1m7yA 88 :LPAFKKAMVDFMAEIRG T0339 60 :GKPQDIIFTSGGTESNNLVIHSV 1m7yA 109 :FDPNHLVLTAGATSANETFIFCL T0339 91 :TSKGH 1m7yA 132 :ADPGE T0339 109 :HFITSSVEHDSIRLPL 1m7yA 137 :AVLIPTPYYPGFDRDL T0339 128 :VEEQVAAVTFVPVSKV 1m7yA 153 :KWRTGVEIVPIHCTSS T0339 144 :SGQTEVDDILAAVR 1m7yA 170 :GFQITETALEEAYQ T0339 158 :PT 1m7yA 188 :RN T0339 160 :TRLVTIMLANNETGIVMPVPEISQ 1m7yA 192 :VKGVLVTNPSNPLGTTMTRNELYL T0339 185 :IKALNQER 1m7yA 216 :LLSFVEDK T0339 199 :PILVHTDAAQALGKQR 1m7yA 224 :GIHLISDEIYSGTAFS T0339 215 :V 1m7yA 259 :S T0339 218 :EDLGVDFLTIVGHK 1m7yA 260 :EVWQRVHVVYSLSK T0339 232 :FY 1m7yA 275 :LG T0339 234 :GPRIGALYIR 1m7yA 279 :GFRVGAIYSN T0339 244 :G 1m7yA 290 :D T0339 245 :LGEFTPLYPM 1m7yA 292 :VVAAATKMSS T0339 266 :PGTENTPMIAGLGKAAE 1m7yA 302 :FGLVSSQTQHLLSAMLS T0339 283 :LVTQNCEAYEAHMRDVRDYLEERLEAE 1m7yA 322 :LTKNYIAENHKRLKQRQKKLVSGLQKS T0339 314 :RIHLNSQFP 1m7yA 349 :GISCLNGNA T0339 328 :PNTCNFSIR 1m7yA 358 :GLFCWVDMR T0339 337 :GP 1m7yA 370 :RS T0339 340 :LQGHVVLAQCRV 1m7yA 372 :NTFEAEMELWKK T0339 352 :LMASVGAACHSDH 1m7yA 390 :LNISPGSSCHCTE T0339 383 :RNALRLSVG 1m7yA 403 :PGWFRVCFA T0339 393 :STTRAEVDLVVQDLKQAVAQ 1m7yA 412 :NLPERTLDLAMQRLKAFVGE Number of specific fragments extracted= 28 number of extra gaps= 0 total=1881 Will force an alignment to be made, even if fragment is small Number of alignments=91 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m7yA/T0339-1m7yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1m7yA/T0339-1m7yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m7yA read from 1m7yA/T0339-1m7yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m7yA in template set T0339 14 :LEPEVIQAMTKAMWEAWGNPSS 1m7yA 87 :GLPAFKKAMVDFMAEIRGNKVT T0339 60 :GKPQDIIFTSGGTESNNLVIHSVV 1m7yA 109 :FDPNHLVLTAGATSANETFIFCLA T0339 105 :GAKPHFITSSVEHDSIRLPLE 1m7yA 133 :DPGEAVLIPTPYYPGFDRDLK T0339 129 :EEQVAAVTFVPVSKVSG 1m7yA 154 :WRTGVEIVPIHCTSSNG T0339 146 :QTEVDDILAAV 1m7yA 172 :QITETALEEAY T0339 157 :RP 1m7yA 188 :RN T0339 159 :TTRLVTIMLANNETGIVMP 1m7yA 191 :RVKGVLVTNPSNPLGTTMT T0339 178 :VPEISQRIKALN 1m7yA 213 :LYLLLSFVEDKG T0339 200 :ILVHTDAAQALGKQRVD 1m7yA 225 :IHLISDEIYSGTAFSSP T0339 217 :VEDLGVD 1m7yA 250 :LKDRNCD T0339 224 :FLTIVGHKFYGP 1m7yA 266 :HVVYSLSKDLGL T0339 236 :R 1m7yA 279 :G T0339 237 :IGALYIRG 1m7yA 282 :VGAIYSND T0339 246 :GE 1m7yA 290 :DM T0339 264 :FRPGTENTPMIAGLGKAAE 1m7yA 300 :SSFGLVSSQTQHLLSAMLS T0339 283 :LVTQNCEAYEAHMRDVRDYLEERLEAE 1m7yA 322 :LTKNYIAENHKRLKQRQKKLVSGLQKS T0339 311 :G 1m7yA 349 :G T0339 315 :IHLNSQ 1m7yA 350 :ISCLNG T0339 326 :RLPNTCNFSI 1m7yA 356 :NAGLFCWVDM T0339 336 :RG 1m7yA 370 :RS T0339 340 :LQGHVVLAQCRV 1m7yA 372 :NTFEAEMELWKK T0339 352 :LMASVGAACHSDH 1m7yA 390 :LNISPGSSCHCTE T0339 383 :RNALRLSVGR 1m7yA 403 :PGWFRVCFAN T0339 394 :TTRAEVDLVVQDLKQAVAQ 1m7yA 413 :LPERTLDLAMQRLKAFVGE Number of specific fragments extracted= 24 number of extra gaps= 0 total=1905 Will force an alignment to be made, even if fragment is small Number of alignments=92 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m7yA/T0339-1m7yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1m7yA/T0339-1m7yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m7yA read from 1m7yA/T0339-1m7yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m7yA in template set T0339 15 :EPEVIQAMTKAMWEAWGNPS 1m7yA 88 :LPAFKKAMVDFMAEIRGNKV T0339 59 :GGKPQDIIFTSGGTESNNLVIHSV 1m7yA 108 :TFDPNHLVLTAGATSANETFIFCL T0339 104 :KGAKPHFITSSVEHDSIRLPLE 1m7yA 132 :ADPGEAVLIPTPYYPGFDRDLK T0339 129 :EEQVAAVTFVPVS 1m7yA 154 :WRTGVEIVPIHCT T0339 142 :KVSGQTEVDDILAAV 1m7yA 168 :SNGFQITETALEEAY T0339 159 :TTRLVTIMLANNETGIVMP 1m7yA 191 :RVKGVLVTNPSNPLGTTMT T0339 178 :VPEISQRIKA 1m7yA 213 :LYLLLSFVED T0339 198 :PPILVHTDAAQALGKQRVD 1m7yA 223 :KGIHLISDEIYSGTAFSSP T0339 217 :VEDLGVD 1m7yA 250 :LKDRNCD T0339 224 :FLTIVGHKFYGPR 1m7yA 266 :HVVYSLSKDLGLP T0339 237 :IGALYIRGLGEFTPLYPMLF 1m7yA 282 :VGAIYSNDDMVVAAATKMSS T0339 266 :PGTENTPMIAGLGKAAE 1m7yA 302 :FGLVSSQTQHLLSAMLS T0339 283 :LVTQNCEAYEAHMRDVRDYLEERLEA 1m7yA 322 :LTKNYIAENHKRLKQRQKKLVSGLQK T0339 310 :FGQKRIH 1m7yA 348 :SGISCLN T0339 325 :QRLPNTCNFSI 1m7yA 355 :GNAGLFCWVDM T0339 336 :RGPRLQGHVVLAQ 1m7yA 370 :RSNTFEAEMELWK T0339 349 :CRVLMASVGAACHSDHG 1m7yA 387 :EVHLNISPGSSCHCTEP T0339 384 :NALRLSVGR 1m7yA 404 :GWFRVCFAN T0339 394 :TTRAEVDLVVQDLKQAVAQ 1m7yA 413 :LPERTLDLAMQRLKAFVGE Number of specific fragments extracted= 19 number of extra gaps= 0 total=1924 Will force an alignment to be made, even if fragment is small Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pmmA/T0339-1pmmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pmmA expands to /projects/compbio/data/pdb/1pmm.pdb.gz 1pmmA:Skipped atom 1019, because occupancy 0.500 <= existing 0.500 in 1pmmA Skipped atom 1021, because occupancy 0.500 <= existing 0.500 in 1pmmA Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 1pmmA Skipped atom 1947, because occupancy 0.500 <= existing 0.500 in 1pmmA Skipped atom 3346, because occupancy 0.500 <= existing 0.500 in 1pmmA Skipped atom 3348, because occupancy 0.500 <= existing 0.500 in 1pmmA Skipped atom 3350, because occupancy 0.500 <= existing 0.500 in 1pmmA # T0339 read from 1pmmA/T0339-1pmmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pmmA read from 1pmmA/T0339-1pmmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1pmmA to template set # found chain 1pmmA in template set T0339 5 :YMDYNATTPLEPE 1pmmA 59 :NLATFCQTWDDEN T0339 22 :MTKAMWEAWGNPSSPYSAGRKAKDIINAARESLAKMIGGK 1pmmA 72 :VHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAP T0339 62 :PQ 1pmmA 113 :PK T0339 64 :DIIFTSGGTESNNLVIHSVVKHFHANQTSKGH 1pmmA 119 :VGTNTIGSSEACMLGGMAMKWRWRKRMEAAGK T0339 104 :KGAKPHFITS 1pmmA 151 :PTDKPNLVCG T0339 115 :VEHDSIRLPLEHL 1pmmA 161 :PVQICWHKFARYW T0339 132 :VAAVTFVPVSKVSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKALNQER 1pmmA 174 :DVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADT T0339 196 :GL 1pmmA 235 :GI T0339 199 :PILVHTDAAQALGKQR 1pmmA 237 :DIDMHIDAASGGFLAP T0339 215 :VDVEDLGVDFLTIVGHKFY 1pmmA 260 :WDFRLPRVKSISASGHKFG T0339 234 :GPRIGALYIR 1pmmA 281 :PLGCGWVIWR T0339 244 :G 1pmmA 292 :E T0339 245 :LGEFTPLYPMLFGGGQERNFRPGTENTPMIAGLGKAAELVTQ 1pmmA 295 :LPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGR T0339 287 :NCEAYEAHMRDVRDYLEERLEA 1pmmA 338 :GYTKVQNASYQVAAYLADEIAK T0339 312 :QKRIHLNSQFPGTQR 1pmmA 360 :LGPYEFICTGRPDEG T0339 328 :PNTCNFSIRGPR 1pmmA 375 :IPAVCFKLKDGE T0339 340 :LQGHVVLAQCRV 1pmmA 390 :YTLYDLSERLRL T0339 352 :LMASVGAACHSDHG 1pmmA 404 :WQVPAFTLGGEATD T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQAVAQLEDQ 1pmmA 418 :IVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDH Number of specific fragments extracted= 19 number of extra gaps= 0 total=1943 Will force an alignment to be made, even if fragment is small Number of alignments=94 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pmmA/T0339-1pmmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1pmmA/T0339-1pmmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pmmA read from 1pmmA/T0339-1pmmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pmmA in template set T0339 11 :TTPLEPEVIQAMTK 1pmmA 65 :QTWDDENVHKLMDL T0339 28 :EAWGNPSSPYSAGRKAKDII 1pmmA 79 :SINKNWIDKEEYPQSAAIDL T0339 49 :AARESLAKMIGG 1pmmA 99 :RCVNMVADLWHA T0339 61 :KPQ 1pmmA 112 :APK T0339 65 :IIFTSGGTESNNLVIHSVVKHFHANQTSKGHT 1pmmA 120 :GTNTIGSSEACMLGGMAMKWRWRKRMEAAGKP T0339 105 :GAKPHFITSS 1pmmA 152 :TDKPNLVCGP T0339 120 :IRLPLEHLVEEQVAAVTFVPVSKVSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKALN 1pmmA 162 :VQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQ T0339 194 :AAGLPPILVHTDAAQAL 1pmmA 232 :ADTGIDIDMHIDAASGG T0339 211 :GKQRVDV 1pmmA 256 :PDIVWDF T0339 219 :DLG 1pmmA 263 :RLP T0339 222 :VDFLTIVGHKFY 1pmmA 267 :VKSISASGHKFG T0339 234 :GP 1pmmA 280 :AP T0339 236 :RIGALYIRGLGEFTP 1pmmA 283 :GCGWVIWRDEEALPQ T0339 251 :LYPMLFGGGQ 1pmmA 299 :LVFNVDYLGG T0339 261 :ERNFRP 1pmmA 316 :NFSRPA T0339 272 :PMIAGLGKAAELVTQ 1pmmA 322 :GQVIAQYYEFLRLGR T0339 289 :EAYEAHMRDVRDYLE 1pmmA 337 :EGYTKVQNASYQVAA T0339 304 :ERLEAEFG 1pmmA 355 :DEIAKLGP T0339 315 :IHLNSQFPGTQRLP 1pmmA 363 :YEFICTGRPDEGIP T0339 330 :TCNFSIRGP 1pmmA 377 :AVCFKLKDG T0339 339 :RLQGHVVLAQCRV 1pmmA 389 :GYTLYDLSERLRL T0339 352 :LM 1pmmA 404 :WQ T0339 377 :VPFDVARN 1pmmA 406 :VPAFTLGG T0339 385 :ALRLSVGRSTTRAEVDLVVQDLKQAVAQLEDQ 1pmmA 420 :VMRIMCRRGFEMDFAELLLEDYKASLKYLSDH Number of specific fragments extracted= 24 number of extra gaps= 0 total=1967 Will force an alignment to be made, even if fragment is small Number of alignments=95 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pmmA/T0339-1pmmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1pmmA/T0339-1pmmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pmmA read from 1pmmA/T0339-1pmmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pmmA in template set T0339 9 :NATTPLEPEVIQAMTKA 1pmmA 63 :FCQTWDDENVHKLMDLS T0339 29 :AWGNPS 1pmmA 80 :INKNWI T0339 36 :PYSAGRKAKDIINAARESLAKMIGG 1pmmA 86 :DKEEYPQSAAIDLRCVNMVADLWHA T0339 61 :KPQD 1pmmA 112 :APKN T0339 65 :IIFTSGGTESNNLVIHSVVKHFHANQTSKGH 1pmmA 120 :GTNTIGSSEACMLGGMAMKWRWRKRMEAAGK T0339 104 :KGAKPHFITSSV 1pmmA 151 :PTDKPNLVCGPV T0339 121 :RLPLEHLVEEQVAAVTFVPVSKVSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKALNQERV 1pmmA 163 :QICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTG T0339 198 :PPILVHTDAAQALGK 1pmmA 236 :IDIDMHIDAASGGFL T0339 213 :QRVDVEDLGVDFLTIVGHKFYGPR 1pmmA 258 :IVWDFRLPRVKSISASGHKFGLAP T0339 237 :IGALYIRGLGEFTPLYPM 1pmmA 284 :CGWVIWRDEEALPQELVF T0339 261 :ERNFRPGTENTPMIAGLGKAAELVT 1pmmA 311 :GTFAINFSRPAGQVIAQYYEFLRLG T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1pmmA 337 :EGYTKVQNASYQVAAYLADEIAKLGPYEFIC T0339 320 :QFPGTQRLPNTCNFSIRG 1pmmA 368 :TGRPDEGIPAVCFKLKDG T0339 338 :PRLQGHVVLAQCRVLMASV 1pmmA 390 :YTLYDLSERLRLRGWQVPA T0339 380 :DVARN 1pmmA 409 :FTLGG T0339 385 :ALRLSVGRSTTRAEVDLVVQDLKQAVAQLE 1pmmA 420 :VMRIMCRRGFEMDFAELLLEDYKASLKYLS Number of specific fragments extracted= 16 number of extra gaps= 0 total=1983 Will force an alignment to be made, even if fragment is small Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wyuA/T0339-1wyuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wyuA expands to /projects/compbio/data/pdb/1wyu.pdb.gz 1wyuA:# T0339 read from 1wyuA/T0339-1wyuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wyuA read from 1wyuA/T0339-1wyuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wyuA to template set # found chain 1wyuA in template set T0339 6 :MDYNA 1wyuA 68 :FLGGG T0339 11 :TTPLEPEVIQAM 1wyuA 75 :SHHVPPVVQALA T0339 26 :M 1wyuA 91 :F T0339 29 :AWGNPSSPYSAGRKAKDIINAARESLAKMIGG 1wyuA 92 :LTAYTPYQPEVSQGVLQATFEYQTMIAELAGL T0339 63 :Q 1wyuA 124 :E T0339 66 :IFTSG 1wyuA 125 :IANAS T0339 71 :GTESNNLVIHSVVKHF 1wyuA 133 :GATALAEGVLLALRET T0339 93 :KGH 1wyuA 149 :GRM T0339 109 :HFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVS 1wyuA 152 :GVLVSQGVHPEYRAVLRAYLEAVGAKLLTLPLE T0339 144 :SGQTE 1wyuA 185 :GGRTP T0339 156 :VRPTTRLVTIMLA 1wyuA 193 :VGEEVGAVVVQNP T0339 170 :NETGIVMPVPEISQ 1wyuA 206 :NFLGALEDLGPFAE T0339 188 :LNQER 1wyuA 220 :AAHGA T0339 199 :PILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFY 1wyuA 225 :GALFVAVADPLSLGVLKPPGAYGADIAVGDGQSLG T0339 234 :GPRIGALYIR 1wyuA 266 :GPHFGFLATK T0339 244 :GLGEFTPLYPMLFGGG 1wyuA 277 :AFVRQLPGRLVSETVD T0339 260 :QERNFRPGTENTPMIAGLGKAAELVTQ 1wyuA 313 :AKAKSNITTNAQLTALMGAMYLAALGP T0339 287 :NCEAYEAHMRDVRDYLEERLEA 1wyuA 341 :GLREVALKSVEMAHKLHALLLE T0339 312 :QKRIHLNSQFP 1wyuA 363 :VPGVRPFTPKP T0339 327 :LPNTCNFSIR 1wyuA 374 :FFNEFALALP T0339 340 :LQGHVVLAQCRV 1wyuA 384 :KDPEAVRRALAE T0339 352 :LMASVGA 1wyuA 399 :HGATPVP T0339 379 :FDVARNALRLSVGRSTTRAEVDLVVQDLKQA 1wyuA 406 :REYGENLALFAATELHEEEDLLALREALKEV Number of specific fragments extracted= 23 number of extra gaps= 0 total=2006 Will force an alignment to be made, even if fragment is small Number of alignments=97 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wyuA/T0339-1wyuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1wyuA/T0339-1wyuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wyuA read from 1wyuA/T0339-1wyuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wyuA in template set T0339 10 :ATTPLEPEVIQAM 1wyuA 74 :RSHHVPPVVQALA T0339 24 :KAM 1wyuA 90 :EFL T0339 30 :WGNPSSPYSAGRKAKDIINAARESLAKMIGGK 1wyuA 93 :TAYTPYQPEVSQGVLQATFEYQTMIAELAGLE T0339 66 :IFTSG 1wyuA 125 :IANAS T0339 71 :GTESNNLVIHSVVKHF 1wyuA 133 :GATALAEGVLLALRET T0339 106 :AKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVS 1wyuA 149 :GRMGVLVSQGVHPEYRAVLRAYLEAVGAKLLTLPLE T0339 144 :SGQTE 1wyuA 185 :GGRTP T0339 156 :VRPTTRLVTIMLA 1wyuA 193 :VGEEVGAVVVQNP T0339 170 :NETGIVMPVPEISQRIKALNQ 1wyuA 206 :NFLGALEDLGPFAEAAHGAGA T0339 200 :ILVHTDAAQALGKQRVDV 1wyuA 227 :LFVAVADPLSLGVLKPPG T0339 219 :DLGVDFLTIVGHKFY 1wyuA 245 :AYGADIAVGDGQSLG T0339 234 :GP 1wyuA 263 :GF T0339 237 :IGALYIRG 1wyuA 269 :FGFLATKK T0339 246 :GEFTPLYPML 1wyuA 277 :AFVRQLPGRL T0339 261 :ERNFRPGTENTPMIAGLGKAAELVTQ 1wyuA 314 :KAKSNITTNAQLTALMGAMYLAALGP T0339 289 :EAYEAHMRDVRDYLE 1wyuA 340 :EGLREVALKSVEMAH T0339 304 :ERLEAEFG 1wyuA 358 :ALLLEVPG T0339 315 :IHLNSQ 1wyuA 366 :VRPFTP T0339 324 :TQRL 1wyuA 372 :KPFF T0339 329 :NTCNFSIRG 1wyuA 376 :NEFALALPK T0339 341 :QGHVVLAQCRV 1wyuA 385 :DPEAVRRALAE T0339 355 :SV 1wyuA 399 :HG T0339 366 :DQP 1wyuA 401 :ATP T0339 377 :VPFDVARNALRLSVGRSTTRAEVDLVVQDLKQA 1wyuA 404 :VPREYGENLALFAATELHEEEDLLALREALKEV Number of specific fragments extracted= 24 number of extra gaps= 0 total=2030 Will force an alignment to be made, even if fragment is small Number of alignments=98 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wyuA/T0339-1wyuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1wyuA/T0339-1wyuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wyuA read from 1wyuA/T0339-1wyuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wyuA in template set T0339 11 :TTPLEPEVIQAM 1wyuA 75 :SHHVPPVVQALA T0339 29 :AWGNPSSPYSAGRKAKDIINAARESLAKMIGG 1wyuA 92 :LTAYTPYQPEVSQGVLQATFEYQTMIAELAGL T0339 66 :IFTSG 1wyuA 125 :IANAS T0339 71 :GTESNNLVIHSV 1wyuA 133 :GATALAEGVLLA T0339 102 :PVKGAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVS 1wyuA 145 :LRETGRMGVLVSQGVHPEYRAVLRAYLEAVGAKLLTLPLE T0339 144 :SGQTE 1wyuA 185 :GGRTP T0339 156 :VRPTTRLVTIMLA 1wyuA 193 :VGEEVGAVVVQNP T0339 170 :NETGIVMPVPEISQRIKA 1wyuA 206 :NFLGALEDLGPFAEAAHG T0339 198 :PPIL 1wyuA 224 :AGAL T0339 202 :VHTDAAQALGKQRVDVE 1wyuA 229 :VAVADPLSLGVLKPPGA T0339 220 :LGVDFLTIVGHKFYGPR 1wyuA 246 :YGADIAVGDGQSLGLPM T0339 237 :IGALYIRGLGEFTPLYPMLFG 1wyuA 269 :FGFLATKKAFVRQLPGRLVSE T0339 261 :ERNFRPGTENTPMIAGLGKAAELVT 1wyuA 314 :KAKSNITTNAQLTALMGAMYLAALG T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1wyuA 340 :EGLREVALKSVEMAHKLHALLLEVPGVRPFT T0339 324 :TQRLPNTCNFSIRG 1wyuA 371 :PKPFFNEFALALPK T0339 339 :RLQGHVVLAQCRVLMASV 1wyuA 385 :DPEAVRRALAERGFHGAT T0339 376 :GVPFDVARNALRLSVGRSTTRAEVDLVVQDLKQA 1wyuA 403 :PVPREYGENLALFAATELHEEEDLLALREALKEV Number of specific fragments extracted= 17 number of extra gaps= 0 total=2047 Will force an alignment to be made, even if fragment is small Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w7lA/T0339-1w7lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1w7lA expands to /projects/compbio/data/pdb/1w7l.pdb.gz 1w7lA:Bad short name: N1 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: C2' for alphabet: pdb_atoms Bad short name: C3 for alphabet: pdb_atoms Bad short name: O3 for alphabet: pdb_atoms Bad short name: C4 for alphabet: pdb_atoms Bad short name: C4' for alphabet: pdb_atoms Bad short name: C5 for alphabet: pdb_atoms Bad short name: C6 for alphabet: pdb_atoms Bad short name: C5' for alphabet: pdb_atoms Bad short name: OP4 for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms # T0339 read from 1w7lA/T0339-1w7lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w7lA read from 1w7lA/T0339-1w7lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1w7lA to template set # found chain 1w7lA in template set Warning: unaligning (T0339)K3 because of BadResidue code BAD_PEPTIDE in next template residue (1w7lA)V31 Warning: unaligning (T0339)V4 because of BadResidue code BAD_PEPTIDE at template residue (1w7lA)V31 Warning: unaligning (T0339)H117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w7lA)D126 Warning: unaligning (T0339)D118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w7lA)D126 Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w7lA)T248 Warning: unaligning (T0339)N329 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w7lA)F339 Warning: unaligning (T0339)T330 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w7lA)F339 T0339 2 :R 1w7lA 29 :D T0339 5 :YMDYNATT 1w7lA 32 :NLGQGFPD T0339 13 :PLEPEVIQAM 1w7lA 41 :PPPDFAVEAF T0339 27 :WEAWGNPSSPYSAGR 1w7lA 51 :QHAVSGDFMLNQYTK T0339 42 :KAKDIINAARESLAKMIGGKPQ 1w7lA 68 :GYPPLTKILASFFGELLGQEID T0339 64 :DIIFTSGGTESNNLVIHSV 1w7lA 93 :NVLVTVGGYGALFTAFQAL T0339 91 :TSKGH 1w7lA 112 :VDEGD T0339 109 :HFITSSVE 1w7lA 117 :EVIIIEPF T0339 119 :SIRLPLEHL 1w7lA 127 :CYEPMTMMA T0339 132 :VAAVTFVPVSK 1w7lA 136 :GGRPVFVSLKP T0339 143 :VSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1w7lA 158 :SNWQLDPMELAGKFTSRTKALVLNTPNNPLGKVFSREELEL T0339 185 :IKALNQER 1w7lA 199 :VASLCQQH T0339 199 :PILVHTDAAQALGKQR 1w7lA 207 :DVVCITDEVYQWMVYD T0339 215 :VDVEDL 1w7lA 227 :ISIASL T0339 221 :GV 1w7lA 234 :GM T0339 223 :DFLTIVG 1w7lA 239 :TLTIGSA T0339 232 :FY 1w7lA 249 :FS T0339 234 :GPRIGALYIR 1w7lA 253 :GWKVGWVLGP T0339 244 :GLGEFTPLYPMLF 1w7lA 264 :HIMKHLRTVHQNS T0339 266 :PGTENTPMIAGLGKAAELVTQ 1w7lA 277 :VFHCPTQSQAAVAESFEREQL T0339 288 :CEAYEAHMRDVRDYLEERLEAE 1w7lA 306 :FVQFPQAMQRCRDHMIRSLQSV T0339 314 :RIHLNSQFP 1w7lA 328 :GLKPLIPQG T0339 328 :P 1w7lA 337 :S T0339 331 :CNFSI 1w7lA 340 :LITDI T0339 336 :RGPR 1w7lA 355 :PGAV T0339 340 :LQ 1w7lA 360 :EP T0339 342 :GHVVLAQCRV 1w7lA 363 :DRRFVKWMIK T0339 352 :LMASVGAACH 1w7lA 376 :LVAIPVSIFY T0339 363 :DHG 1w7lA 391 :KHF T0339 383 :RNALRLSVGR 1w7lA 394 :DHYIRFCFVK T0339 395 :TRAEVD 1w7lA 404 :DEATLQ T0339 405 :DLKQAVAQLEDQ 1w7lA 410 :AMDEKLRKWKVE Number of specific fragments extracted= 32 number of extra gaps= 3 total=2079 Will force an alignment to be made, even if fragment is small Number of alignments=100 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w7lA/T0339-1w7lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1w7lA/T0339-1w7lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w7lA read from 1w7lA/T0339-1w7lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w7lA in template set Warning: unaligning (T0339)K3 because of BadResidue code BAD_PEPTIDE in next template residue (1w7lA)V31 Warning: unaligning (T0339)V4 because of BadResidue code BAD_PEPTIDE at template residue (1w7lA)V31 Warning: unaligning (T0339)H117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w7lA)D126 Warning: unaligning (T0339)D118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w7lA)D126 Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w7lA)T248 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w7lA)T248 Warning: unaligning (T0339)N329 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w7lA)F339 Warning: unaligning (T0339)T330 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w7lA)F339 T0339 2 :R 1w7lA 29 :D T0339 5 :YMDYNATT 1w7lA 32 :NLGQGFPD T0339 13 :PLEPEVIQAMTKA 1w7lA 41 :PPPDFAVEAFQHA T0339 30 :WGNPSSPYSA 1w7lA 54 :VSGDFMLNQY T0339 40 :G 1w7lA 68 :G T0339 43 :AKDIINAARESLAKMIGGKPQD 1w7lA 69 :YPPLTKILASFFGELLGQEIDP T0339 65 :IIFTSGGTESNNLVIHSVV 1w7lA 94 :VLVTVGGYGALFTAFQALV T0339 105 :GAKPHFITSSVE 1w7lA 113 :DEGDEVIIIEPF T0339 119 :SIRLPLEHL 1w7lA 127 :CYEPMTMMA T0339 132 :VAAVTFVPVS 1w7lA 136 :GGRPVFVSLK T0339 142 :KVSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMP 1w7lA 157 :SSNWQLDPMELAGKFTSRTKALVLNTPNNPLGKVFS T0339 178 :VPEISQRIKALN 1w7lA 196 :LELVASLCQQHD T0339 200 :ILVHTDAAQAL 1w7lA 208 :VVCITDEVYQW T0339 211 :GKQRVDVEDLG 1w7lA 223 :GHQHISIASLP T0339 223 :DFLTIVG 1w7lA 239 :TLTIGSA T0339 233 :Y 1w7lA 249 :F T0339 234 :GPR 1w7lA 251 :ATG T0339 237 :IGALYIRG 1w7lA 256 :VGWVLGPD T0339 246 :GE 1w7lA 264 :HI T0339 262 :RNFR 1w7lA 275 :NSVF T0339 268 :TENTPMIAGLGKAAELVTQ 1w7lA 279 :HCPTQSQAAVAESFEREQL T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1w7lA 305 :YFVQFPQAMQRCRDHMIRSLQSV T0339 311 :G 1w7lA 328 :G T0339 315 :IHLNSQ 1w7lA 329 :LKPLIP T0339 326 :RLP 1w7lA 335 :QGS T0339 331 :CNFSI 1w7lA 340 :LITDI T0339 336 :RGPRLQGHVVLAQC 1w7lA 357 :AVDEPYDRRFVKWM T0339 350 :RV 1w7lA 372 :KN T0339 358 :AACHSDH 1w7lA 377 :VAIPVSI T0339 368 :PSPVLLSYGVP 1w7lA 384 :FYSVPHQKHFD T0339 384 :NALRLSVGR 1w7lA 395 :HYIRFCFVK T0339 395 :TRAEVD 1w7lA 404 :DEATLQ T0339 405 :DLKQAVAQLEDQ 1w7lA 410 :AMDEKLRKWKVE Number of specific fragments extracted= 33 number of extra gaps= 3 total=2112 Will force an alignment to be made, even if fragment is small Number of alignments=101 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w7lA/T0339-1w7lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1w7lA/T0339-1w7lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w7lA read from 1w7lA/T0339-1w7lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w7lA in template set Warning: unaligning (T0339)K3 because of BadResidue code BAD_PEPTIDE in next template residue (1w7lA)V31 Warning: unaligning (T0339)V4 because of BadResidue code BAD_PEPTIDE at template residue (1w7lA)V31 Warning: unaligning (T0339)H117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w7lA)D126 Warning: unaligning (T0339)D118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w7lA)D126 Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w7lA)T248 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w7lA)T248 Warning: unaligning (T0339)N329 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w7lA)F339 Warning: unaligning (T0339)T330 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w7lA)F339 T0339 2 :R 1w7lA 29 :D T0339 5 :YMDYNATT 1w7lA 32 :NLGQGFPD T0339 13 :PLEPEVIQAMTKAM 1w7lA 41 :PPPDFAVEAFQHAV T0339 34 :SSPYSAGRK 1w7lA 55 :SGDFMLNQY T0339 43 :AKDIINAARESLAKMIGGKPQD 1w7lA 69 :YPPLTKILASFFGELLGQEIDP T0339 65 :IIFTSGGTESNNLVIHSV 1w7lA 94 :VLVTVGGYGALFTAFQAL T0339 104 :KGAKPHFITSSVE 1w7lA 112 :VDEGDEVIIIEPF T0339 119 :SIRLPLEHL 1w7lA 127 :CYEPMTMMA T0339 132 :VAAVTFVPVS 1w7lA 136 :GGRPVFVSLK T0339 142 :KVSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMP 1w7lA 157 :SSNWQLDPMELAGKFTSRTKALVLNTPNNPLGKVFS T0339 178 :VPEISQRIKA 1w7lA 196 :LELVASLCQQ T0339 198 :PPILVHTDAAQALGKQRVD 1w7lA 206 :HDVVCITDEVYQWMVYDGH T0339 217 :VEDLGV 1w7lA 230 :ASLPGM T0339 223 :DFLTIVG 1w7lA 239 :TLTIGSA T0339 233 :YGPR 1w7lA 249 :FSAT T0339 237 :IGALYIRGLGEFTPLYPMLFG 1w7lA 256 :VGWVLGPDHIMKHLRTVHQNS T0339 266 :PGTENTPMIAGLGKAAELVTQNCE 1w7lA 277 :VFHCPTQSQAAVAESFEREQLLFR T0339 290 :AYEAHMRDVRDYLEERLEAEFGQKRIH 1w7lA 308 :QFPQAMQRCRDHMIRSLQSVGLKPLIP T0339 326 :RLP 1w7lA 335 :QGS T0339 331 :CNFSI 1w7lA 340 :LITDI T0339 340 :LQGHVVLAQCRVLMASVGAACHSDHG 1w7lA 364 :RRFVKWMIKNKGLVAIPVSIFYSVPH T0339 379 :FDVARNALRLSVG 1w7lA 390 :QKHFDHYIRFCFV T0339 394 :TTRAEVDLVVQDLKQA 1w7lA 403 :KDEATLQAMDEKLRKW T0339 414 :E 1w7lA 419 :K Number of specific fragments extracted= 24 number of extra gaps= 3 total=2136 Will force an alignment to be made, even if fragment is small Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bs0A/T0339-1bs0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bs0A expands to /projects/compbio/data/pdb/1bs0.pdb.gz 1bs0A:Skipped atom 2738, because occupancy 0.460 <= existing 0.540 in 1bs0A Skipped atom 2740, because occupancy 0.460 <= existing 0.540 in 1bs0A Skipped atom 2742, because occupancy 0.460 <= existing 0.540 in 1bs0A Skipped atom 2744, because occupancy 0.460 <= existing 0.540 in 1bs0A Skipped atom 2746, because occupancy 0.460 <= existing 0.540 in 1bs0A Skipped atom 2748, because occupancy 0.460 <= existing 0.540 in 1bs0A Skipped atom 2750, because occupancy 0.460 <= existing 0.540 in 1bs0A Skipped atom 2752, because occupancy 0.460 <= existing 0.540 in 1bs0A Skipped atom 2754, because occupancy 0.460 <= existing 0.540 in 1bs0A Skipped atom 2756, because occupancy 0.460 <= existing 0.540 in 1bs0A Skipped atom 2758, because occupancy 0.460 <= existing 0.540 in 1bs0A # T0339 read from 1bs0A/T0339-1bs0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bs0A read from 1bs0A/T0339-1bs0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1bs0A to template set # found chain 1bs0A in template set Warning: unaligning (T0339)N9 because of BadResidue code BAD_PEPTIDE in next template residue (1bs0A)S46 Warning: unaligning (T0339)A10 because of BadResidue code BAD_PEPTIDE at template residue (1bs0A)S46 Warning: unaligning (T0339)E171 because of BadResidue code BAD_PEPTIDE in next template residue (1bs0A)D181 Warning: unaligning (T0339)T172 because of BadResidue code BAD_PEPTIDE at template residue (1bs0A)D181 Warning: unaligning (T0339)R192 because of BadResidue code BAD_PEPTIDE in next template residue (1bs0A)N198 Warning: unaligning (T0339)P199 because of BadResidue code BAD_PEPTIDE at template residue (1bs0A)N198 T0339 1 :ERKVYMDY 1bs0A 37 :DDRQYLNF T0339 11 :TT 1bs0A 50 :LG T0339 13 :PLEPEVIQAM 1bs0A 53 :SHHPQIIRAW T0339 24 :KAMWEAWGNPSSPYSAGRKAKDIINAARESLAKMIGG 1bs0A 63 :QQGAEQFGIGSGGSGHVSGYSVVHQALEEELAEWLGY T0339 63 :QDIIFTSGGTESNNLVIHSV 1bs0A 100 :SRALLFISGFAANQAVIAAM T0339 91 :TSKGH 1bs0A 120 :MAKED T0339 109 :HFITSSVEHDSIRLPLEHL 1bs0A 125 :RIAADRLSHASLLEAASLS T0339 132 :VAAVTFVPVS 1bs0A 144 :PSQLRRFAHN T0339 148 :EVDDILAAVR 1bs0A 154 :DVTHLARLLA T0339 158 :PTTRLVTIMLANN 1bs0A 167 :PGQQMVVTEGVFS T0339 173 :GIVMPVPEISQ 1bs0A 182 :GDSAPLAEIQQ T0339 188 :LNQE 1bs0A 193 :VTQQ T0339 200 :ILVHTDAAQALGKQR 1bs0A 199 :GWLMVDDAHGTGVIG T0339 219 :DL 1bs0A 215 :QG T0339 221 :GVDFLTIVGHK 1bs0A 226 :KPELLVVTFGK T0339 232 :FYGP 1bs0A 238 :FGVS T0339 237 :IGALYIR 1bs0A 242 :GAAVLCS T0339 244 :GLGEFT 1bs0A 250 :TVADYL T0339 250 :PLYPMLFG 1bs0A 257 :QFARHLIY T0339 266 :PGTENTPMIAGLGKAAELVTQ 1bs0A 265 :STSMPPAQAQALRASLAVIRS T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1bs0A 287 :EGDARREKLAALITRFRAGVQDL T0339 314 :RIHLNSQ 1bs0A 310 :PFTLADS T0339 322 :P 1bs0A 317 :C T0339 328 :PNTCNFSIRG 1bs0A 318 :SAIQPLIVGD T0339 340 :LQ 1bs0A 328 :NS T0339 342 :GHVVLAQCRV 1bs0A 331 :ALQLAEKLRQ T0339 352 :LMASVGAACHSDHG 1bs0A 343 :CWVTAIRPPTVPAG T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQA 1bs0A 357 :TARLRLTLTAAHEMQDIDRLLEVLHGN Number of specific fragments extracted= 28 number of extra gaps= 3 total=2164 Will force an alignment to be made, even if fragment is small Number of alignments=103 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bs0A/T0339-1bs0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1bs0A/T0339-1bs0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bs0A read from 1bs0A/T0339-1bs0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bs0A in template set Warning: unaligning (T0339)N9 because of BadResidue code BAD_PEPTIDE in next template residue (1bs0A)S46 Warning: unaligning (T0339)A10 because of BadResidue code BAD_PEPTIDE at template residue (1bs0A)S46 Warning: unaligning (T0339)E171 because of BadResidue code BAD_PEPTIDE in next template residue (1bs0A)D181 Warning: unaligning (T0339)T172 because of BadResidue code BAD_PEPTIDE at template residue (1bs0A)D181 Warning: unaligning (T0339)L188 because of BadResidue code BAD_PEPTIDE in next template residue (1bs0A)N198 Warning: unaligning (T0339)N189 because of BadResidue code BAD_PEPTIDE at template residue (1bs0A)N198 T0339 5 :YMDY 1bs0A 41 :YLNF T0339 11 :TTPL 1bs0A 47 :NDYL T0339 15 :EPEVIQA 1bs0A 55 :HPQIIRA T0339 23 :TKAMWEAWGN 1bs0A 62 :WQQGAEQFGI T0339 33 :PSSPYS 1bs0A 74 :GGSGHV T0339 39 :AGR 1bs0A 82 :YSV T0339 46 :IINAARESLAKMIGG 1bs0A 85 :VHQALEEELAEWLGY T0339 63 :QDIIFTSGGTESNNLVIHSVV 1bs0A 100 :SRALLFISGFAANQAVIAAMM T0339 105 :GAKPHFITSSVEHDS 1bs0A 121 :AKEDRIAADRLSHAS T0339 124 :LEHLVEEQVAAVTFVPVS 1bs0A 136 :LLEAASLSPSQLRRFAHN T0339 148 :EVDDILAAVRPTT 1bs0A 154 :DVTHLARLLASPC T0339 161 :RLVTIMLANN 1bs0A 170 :QMVVTEGVFS T0339 173 :GIVMPVPEISQRIKA 1bs0A 182 :GDSAPLAEIQQVTQQ T0339 200 :ILVHTDAAQALGKQ 1bs0A 199 :GWLMVDDAHGTGVI T0339 217 :VEDLGVDFLTIVGHKFYGPRIGALYIRG 1bs0A 222 :LQKVKPELLVVTFGKGFGVSGAAVLCSS T0339 246 :G 1bs0A 250 :T T0339 265 :RPGTENTPMIAGLGKAAELVTQ 1bs0A 264 :YSTSMPPAQAQALRASLAVIRS T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1bs0A 287 :EGDARREKLAALITRFRAGVQDL T0339 311 :G 1bs0A 310 :P T0339 315 :IHLNSQ 1bs0A 311 :FTLADS T0339 323 :G 1bs0A 317 :C T0339 328 :PNTCNFSIRGP 1bs0A 318 :SAIQPLIVGDN T0339 340 :LQGHVVLAQCRV 1bs0A 329 :SRALQLAEKLRQ T0339 352 :LMASV 1bs0A 343 :CWVTA T0339 360 :CHSDH 1bs0A 348 :IRPPT T0339 377 :VPFD 1bs0A 353 :VPAG T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQA 1bs0A 357 :TARLRLTLTAAHEMQDIDRLLEVLHGN Number of specific fragments extracted= 27 number of extra gaps= 3 total=2191 Will force an alignment to be made, even if fragment is small Number of alignments=104 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bs0A/T0339-1bs0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1bs0A/T0339-1bs0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bs0A read from 1bs0A/T0339-1bs0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bs0A in template set Warning: unaligning (T0339)E171 because of BadResidue code BAD_PEPTIDE in next template residue (1bs0A)D181 Warning: unaligning (T0339)T172 because of BadResidue code BAD_PEPTIDE at template residue (1bs0A)D181 Warning: unaligning (T0339)P198 because of BadResidue code BAD_PEPTIDE in next template residue (1bs0A)N198 Warning: unaligning (T0339)P199 because of BadResidue code BAD_PEPTIDE at template residue (1bs0A)N198 T0339 13 :PLEPEVIQAMTKAMWEAWGNPS 1bs0A 53 :SHHPQIIRAWQQGAEQFGIGSG T0339 35 :SPYSAG 1bs0A 76 :SGHVSG T0339 45 :DIINAARESLAKMIGG 1bs0A 84 :VVHQALEEELAEWLGY T0339 64 :DIIFTSGGTESNNLVIHSV 1bs0A 101 :RALLFISGFAANQAVIAAM T0339 104 :KGAKPHFITSSVEHDSIRLPL 1bs0A 120 :MAKEDRIAADRLSHASLLEAA T0339 129 :EEQVAAVTFVPVS 1bs0A 141 :SLSPSQLRRFAHN T0339 148 :EVDDILAAV 1bs0A 154 :DVTHLARLL T0339 157 :RPTTRLVTIMLANN 1bs0A 166 :CPGQQMVVTEGVFS T0339 173 :GIVMPVPEISQRIKA 1bs0A 182 :GDSAPLAEIQQVTQQ T0339 200 :ILVHTDAAQALGKQRVD 1bs0A 199 :GWLMVDDAHGTGVIGEQ T0339 217 :VEDLGVDFLTIVGHKFYGPRIGALYIRGLGEFTPLYPMLFG 1bs0A 222 :LQKVKPELLVVTFGKGFGVSGAAVLCSSTVADYLLQFARHL T0339 264 :FRPGTENTPMIAGLGKAAELVT 1bs0A 263 :IYSTSMPPAQAQALRASLAVIR T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFG 1bs0A 286 :DEGDARREKLAALITRFRAGVQDLPF T0339 313 :KRI 1bs0A 312 :TLA T0339 325 :QRLPNTCNFSIRG 1bs0A 315 :DSCSAIQPLIVGD T0339 338 :PRLQGHVVLAQCRVLMASVGAACHSDHG 1bs0A 329 :SRALQLAEKLRQQGCWVTAIRPPTVPAG T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQA 1bs0A 357 :TARLRLTLTAAHEMQDIDRLLEVLHGN Number of specific fragments extracted= 17 number of extra gaps= 2 total=2208 Will force an alignment to be made, even if fragment is small Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lc5A/T0339-1lc5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lc5A expands to /projects/compbio/data/pdb/1lc5.pdb.gz 1lc5A:# T0339 read from 1lc5A/T0339-1lc5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lc5A read from 1lc5A/T0339-1lc5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lc5A to template set # found chain 1lc5A in template set Warning: unaligning (T0339)V410 because last residue in template chain is (1lc5A)L357 T0339 3 :KVYMD 1lc5A 26 :LLDFS T0339 8 :YNATTPLEPEVI 1lc5A 32 :NINPLGMPVSVK T0339 24 :KAMWEAWGNPSSPYS 1lc5A 44 :RALIDNLDCIERYPD T0339 41 :RKAKD 1lc5A 59 :ADYFH T0339 50 :ARESLAKMIGGKPQDIIFTSGGTESNNLVIHSV 1lc5A 64 :LHQALARHHQVPASWILAGNGETESIFTVASGL T0339 91 :TSK 1lc5A 97 :KPR T0339 109 :HFITSSVEHDSIRLPLEHL 1lc5A 100 :RAMIVTPGFAEYGRALAQS T0339 132 :VAAVTFVPVSKV 1lc5A 119 :GCEIRRWSLREA T0339 144 :SGQTE 1lc5A 132 :GWQLT T0339 149 :VDD 1lc5A 140 :LEA T0339 156 :VRPTTRLVTIMLANNETGIVMPVPEISQ 1lc5A 143 :LTPDLDCLFLCTPNNPTGLLPERPLLQA T0339 185 :IKALNQER 1lc5A 171 :IADRCKSL T0339 199 :PILVHTDAAQALGKQRVD 1lc5A 179 :NINLILDEAFIDFIPHET T0339 217 :VEDL 1lc5A 199 :IPAL T0339 221 :GV 1lc5A 204 :DN T0339 223 :DFLTIVGHK 1lc5A 208 :IWVLRSLTK T0339 232 :FY 1lc5A 218 :YA T0339 234 :GPRIGALYIR 1lc5A 222 :GLRLGYLVNS T0339 244 :G 1lc5A 233 :D T0339 245 :LGEFT 1lc5A 235 :AMARM T0339 252 :YPM 1lc5A 240 :RRQ T0339 256 :FG 1lc5A 243 :QM T0339 266 :PGTENTPMIAGLGKAAE 1lc5A 245 :PWSVNALAALAGEVALQ T0339 285 :TQ 1lc5A 262 :DS T0339 287 :NCEAYEAHMRDVRDYLEERLEA 1lc5A 265 :WQQATWHWLREEGARFYQALCQ T0339 312 :QKRIHLNSQF 1lc5A 287 :LPLLTVYPGR T0339 328 :PNTCNFSIRGPRLQ 1lc5A 297 :ANYLLLRCEREDID T0339 345 :VLAQCRV 1lc5A 311 :LQRRLLT T0339 352 :LMA 1lc5A 320 :ILI T0339 355 :SVGAACHSD 1lc5A 324 :SCANYPGLD T0339 383 :RNALRLSVG 1lc5A 333 :SRYYRVAIR T0339 395 :TRAEVDLVVQDLKQA 1lc5A 342 :SAAQNERLLAALRNV Number of specific fragments extracted= 32 number of extra gaps= 0 total=2240 Will force an alignment to be made, even if fragment is small Number of alignments=106 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lc5A/T0339-1lc5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1lc5A/T0339-1lc5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lc5A read from 1lc5A/T0339-1lc5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lc5A in template set T0339 8 :Y 1lc5A 29 :F T0339 31 :GNPSSPYSAGRKAKDIINA 1lc5A 30 :SANINPLGMPVSVKRALID T0339 50 :ARESLAKMIGGKPQDIIFTSGGTESNNLVIHSV 1lc5A 64 :LHQALARHHQVPASWILAGNGETESIFTVASGL T0339 105 :GAKPHFITSSV 1lc5A 97 :KPRRAMIVTPG T0339 120 :IRL 1lc5A 108 :FAE T0339 124 :LEHLVEEQVAAVTFVPVSKVSG 1lc5A 111 :YGRALAQSGCEIRRWSLREADG T0339 146 :QTE 1lc5A 134 :QLT T0339 152 :ILAAVRPTTRLVTIMLANNETGIVMP 1lc5A 139 :ILEALTPDLDCLFLCTPNNPTGLLPE T0339 178 :VPEISQRIKALN 1lc5A 168 :LQAIADRCKSLN T0339 200 :ILVHTDAAQ 1lc5A 180 :INLILDEAF T0339 209 :ALGKQRVDVEDLG 1lc5A 191 :FIPHETGFIPALK T0339 224 :FLTIVGHKFY 1lc5A 209 :WVLRSLTKFY T0339 234 :GPR 1lc5A 220 :IPG T0339 237 :IGALYIRG 1lc5A 225 :LGYLVNSD T0339 246 :G 1lc5A 233 :D T0339 250 :PLYPMLFGGGQERNFR 1lc5A 234 :AAMARMRRQQMPWSVN T0339 275 :AGLGKAAELVTQ 1lc5A 250 :ALAALAGEVALQ T0339 287 :NC 1lc5A 264 :AW T0339 289 :EAYEAHMRDVRDYLEERLEAEFG 1lc5A 267 :QATWHWLREEGARFYQALCQLPL T0339 315 :IHLNSQ 1lc5A 290 :LTVYPG T0339 326 :R 1lc5A 296 :R T0339 328 :PNTCNFSIRGPRLQ 1lc5A 297 :ANYLLLRCEREDID T0339 345 :VLAQCRV 1lc5A 311 :LQRRLLT T0339 352 :LMASV 1lc5A 320 :ILIRS T0339 359 :ACHSDH 1lc5A 325 :CANYPG T0339 377 :VPF 1lc5A 331 :LDS T0339 384 :NALRLSVGR 1lc5A 334 :RYYRVAIRS T0339 396 :RAEVDLVVQDLKQA 1lc5A 343 :AAQNERLLAALRNV Number of specific fragments extracted= 28 number of extra gaps= 0 total=2268 Will force an alignment to be made, even if fragment is small Number of alignments=107 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lc5A/T0339-1lc5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1lc5A/T0339-1lc5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lc5A read from 1lc5A/T0339-1lc5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lc5A in template set T0339 9 :NATTPLEPEVIQAM 1lc5A 33 :INPLGMPVSVKRAL T0339 48 :NA 1lc5A 47 :ID T0339 50 :ARESLAKMIGGKPQDIIFTSGGTESNNLVIHSV 1lc5A 64 :LHQALARHHQVPASWILAGNGETESIFTVASGL T0339 106 :AKPHFITSSVEHDSIRLPLEHL 1lc5A 97 :KPRRAMIVTPGFAEYGRALAQS T0339 132 :VAAVTFVPVS 1lc5A 119 :GCEIRRWSLR T0339 142 :KVSGQTE 1lc5A 130 :ADGWQLT T0339 150 :DDILAAVRPTTRLVTIMLANNETGIVMP 1lc5A 137 :DAILEALTPDLDCLFLCTPNNPTGLLPE T0339 178 :VPEISQRIKA 1lc5A 168 :LQAIADRCKS T0339 198 :PPILVHTDAAQALGKQRVD 1lc5A 178 :LNINLILDEAFIDFIPHET T0339 217 :VEDLGVDFLTIVGHKFYGPR 1lc5A 202 :LKDNPHIWVLRSLTKFYAIP T0339 237 :IGALYIRGLGEFTPLYPMLFGGGQ 1lc5A 225 :LGYLVNSDDAAMARMRRQQMPWSV T0339 270 :NTP 1lc5A 249 :NAL T0339 277 :LGKAAELVT 1lc5A 252 :AALAGEVAL T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1lc5A 264 :AWQQATWHWLREEGARFYQALCQLPLLTVYP T0339 324 :TQRLPNTCNFSIRGPR 1lc5A 295 :GRANYLLLRCEREDID T0339 343 :HVVLAQCRVLMASV 1lc5A 311 :LQRRLLTQRILIRS T0339 359 :ACHSDHG 1lc5A 325 :CANYPGL T0339 382 :ARNALRLSVG 1lc5A 332 :DSRYYRVAIR T0339 395 :TRAEVDLVVQDLKQA 1lc5A 342 :SAAQNERLLAALRNV Number of specific fragments extracted= 19 number of extra gaps= 0 total=2287 Will force an alignment to be made, even if fragment is small Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yizA/T0339-1yizA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yizA expands to /projects/compbio/data/pdb/1yiz.pdb.gz 1yizA:Bad short name: N1 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: C2' for alphabet: pdb_atoms Bad short name: C3 for alphabet: pdb_atoms Bad short name: O3 for alphabet: pdb_atoms Bad short name: C4 for alphabet: pdb_atoms Bad short name: C4' for alphabet: pdb_atoms Bad short name: C5 for alphabet: pdb_atoms Bad short name: C6 for alphabet: pdb_atoms Bad short name: C5' for alphabet: pdb_atoms Bad short name: OP4 for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms # T0339 read from 1yizA/T0339-1yizA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yizA read from 1yizA/T0339-1yizA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yizA to template set # found chain 1yizA in template set Warning: unaligning (T0339)G40 because of BadResidue code BAD_PEPTIDE in next template residue (1yizA)R75 Warning: unaligning (T0339)R41 because of BadResidue code BAD_PEPTIDE at template residue (1yizA)R75 Warning: unaligning (T0339)P139 because of BadResidue code BAD_PEPTIDE in next template residue (1yizA)L154 Warning: unaligning (T0339)V140 because of BadResidue code BAD_PEPTIDE at template residue (1yizA)L154 Warning: unaligning (T0339)Q213 because of BadResidue code BAD_PEPTIDE in next template residue (1yizA)E230 Warning: unaligning (T0339)R214 because of BadResidue code BAD_PEPTIDE at template residue (1yizA)E230 Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yizA)T256 T0339 2 :RKVYMDYNATT 1yizA 38 :KPLNLGQGFPD T0339 13 :PLEPEVIQAMTKA 1yizA 50 :HAPKYALNALAAA T0339 30 :WGNPSSP 1yizA 63 :ANSPDPL T0339 37 :YSA 1yizA 71 :NQY T0339 42 :KAKDIINAARESLAKMIGGKPQ 1yizA 78 :GHPRLVQALSKLYSQLVDRTIN T0339 64 :DIIFTSGGTESNNLVIHSV 1yizA 103 :EVLVTVGAYEALYATIQGH T0339 91 :TSKGH 1yizA 122 :VDEGD T0339 109 :HFITSSVEHDSIRLPLEHL 1yizA 127 :EVIIIEPFFDCYEPMVKAA T0339 132 :VAAVTFV 1yizA 146 :GGIPRFI T0339 141 :SKV 1yizA 155 :KPN T0339 144 :SGQT 1yizA 160 :GGTI T0339 148 :EVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1yizA 171 :DNNELEALFNEKTKMIIINTPHNPLGKVMDRAELEV T0339 185 :IKALNQER 1yizA 207 :VANLCKKW T0339 199 :PILVHTDAAQALGK 1yizA 215 :NVLCVSDEVYEHMV T0339 217 :VEDL 1yizA 237 :ICTL T0339 221 :GV 1yizA 242 :GM T0339 223 :DFLTIVG 1yizA 247 :TITIGSA T0339 232 :FY 1yizA 257 :FS T0339 234 :GPRIGALYIR 1yizA 261 :GWKIGWAYGP T0339 244 :GLGEFTPLYPMLF 1yizA 272 :ALLKNLQMVHQNC T0339 266 :PGTENTPMIAGLGKAAELVTQ 1yizA 285 :VYTCATPIQEAIAVGFETELK T0339 288 :CEAYEAHMRDVRDYLEERLEAE 1yizA 314 :FNSISGELMAKRDYMASFLAEV T0339 314 :RIHLNSQFP 1yizA 336 :GMNPTVPQG T0339 328 :PNTCNFSIRGPR 1yizA 345 :GYFMVADWSSLD T0339 340 :LQGHVVLAQCRV 1yizA 368 :RKDYRFTKWMTK T0339 352 :LMASVGAACHSDH 1yizA 383 :LQGIPPSAFYSEP T0339 378 :PFDVARNALRLSVGR 1yizA 396 :NKHLGEDFVRYCFFK T0339 395 :TRAEVDLVVQDLKQA 1yizA 411 :KDENLQKAAEILRKW Number of specific fragments extracted= 28 number of extra gaps= 3 total=2315 Will force an alignment to be made, even if fragment is small Number of alignments=109 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yizA/T0339-1yizA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1yizA/T0339-1yizA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yizA read from 1yizA/T0339-1yizA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yizA in template set Warning: unaligning (T0339)P33 because of BadResidue code BAD_PEPTIDE in next template residue (1yizA)R75 Warning: unaligning (T0339)S34 because of BadResidue code BAD_PEPTIDE at template residue (1yizA)R75 Warning: unaligning (T0339)P139 because of BadResidue code BAD_PEPTIDE in next template residue (1yizA)L154 Warning: unaligning (T0339)V140 because of BadResidue code BAD_PEPTIDE at template residue (1yizA)L154 Warning: unaligning (T0339)Q213 because of BadResidue code BAD_PEPTIDE in next template residue (1yizA)E230 Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yizA)T256 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yizA)T256 T0339 2 :RKVYMDYNATT 1yizA 38 :KPLNLGQGFPD T0339 13 :PLEPEVIQAMTKA 1yizA 50 :HAPKYALNALAAA T0339 27 :WE 1yizA 63 :AN T0339 29 :AWGN 1yizA 70 :ANQY T0339 35 :SP 1yizA 76 :GF T0339 37 :Y 1yizA 79 :H T0339 44 :KDIINAARESLAKMIGG 1yizA 80 :PRLVQALSKLYSQLVDR T0339 61 :KPQ 1yizA 99 :NPM T0339 64 :DIIFTSGGTESNNLVIHSVV 1yizA 103 :EVLVTVGAYEALYATIQGHV T0339 105 :GAKPHFITSSVEHDSIRLPL 1yizA 123 :DEGDEVIIIEPFFDCYEPMV T0339 129 :EEQVAAVTFV 1yizA 143 :KAAGGIPRFI T0339 141 :S 1yizA 155 :K T0339 142 :KVSG 1yizA 158 :KTGG T0339 146 :QTEVDDILAAVRPTTRLVTIMLANNETGIVMP 1yizA 169 :VLDNNELEALFNEKTKMIIINTPHNPLGKVMD T0339 178 :VPEISQRIKALN 1yizA 204 :LEVVANLCKKWN T0339 200 :ILVHTDAAQALGK 1yizA 216 :VLCVSDEVYEHMV T0339 214 :RVDV 1yizA 234 :HIRI T0339 219 :DLG 1yizA 239 :TLP T0339 223 :DFLTIVG 1yizA 247 :TITIGSA T0339 233 :YGP 1yizA 257 :FSL T0339 236 :R 1yizA 261 :G T0339 237 :IGALYIRG 1yizA 264 :IGWAYGPE T0339 246 :G 1yizA 272 :A T0339 266 :PGTENTPMIAGLGKAAELVTQ 1yizA 285 :VYTCATPIQEAIAVGFETELK T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1yizA 313 :YFNSISGELMAKRDYMASFLAEV T0339 311 :G 1yizA 336 :G T0339 315 :IHLNSQ 1yizA 337 :MNPTVP T0339 326 :RLPNTCNFSI 1yizA 343 :QGGYFMVADW T0339 336 :RGPRLQGHVVLAQCRVLMASVG 1yizA 364 :ETDARKDYRFTKWMTKSVGLQG T0339 358 :AACHSDH 1yizA 389 :SAFYSEP T0339 378 :PFDVARNALRLSVGR 1yizA 396 :NKHLGEDFVRYCFFK T0339 395 :TRAEVDLVVQDLKQA 1yizA 411 :KDENLQKAAEILRKW Number of specific fragments extracted= 32 number of extra gaps= 3 total=2347 Will force an alignment to be made, even if fragment is small Number of alignments=110 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yizA/T0339-1yizA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1yizA/T0339-1yizA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yizA read from 1yizA/T0339-1yizA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yizA in template set Warning: unaligning (T0339)S38 because of BadResidue code BAD_PEPTIDE in next template residue (1yizA)R75 Warning: unaligning (T0339)A39 because of BadResidue code BAD_PEPTIDE at template residue (1yizA)R75 Warning: unaligning (T0339)P139 because of BadResidue code BAD_PEPTIDE in next template residue (1yizA)L154 Warning: unaligning (T0339)V140 because of BadResidue code BAD_PEPTIDE at template residue (1yizA)L154 Warning: unaligning (T0339)K212 because of BadResidue code BAD_PEPTIDE in next template residue (1yizA)E230 Warning: unaligning (T0339)Q213 because of BadResidue code BAD_PEPTIDE at template residue (1yizA)E230 Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yizA)T256 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yizA)T256 T0339 2 :RKVYMDYNATT 1yizA 38 :KPLNLGQGFPD T0339 13 :PLEPEVIQAMTKAMW 1yizA 50 :HAPKYALNALAAAAN T0339 34 :S 1yizA 69 :L T0339 35 :SPY 1yizA 71 :NQY T0339 40 :GRKAKDIINAARESLAKMIGG 1yizA 76 :GFGHPRLVQALSKLYSQLVDR T0339 61 :KP 1yizA 99 :NP T0339 63 :QDIIFTSGGTESNNLVIHSV 1yizA 102 :TEVLVTVGAYEALYATIQGH T0339 104 :KGAKPHFITSSVEHDSIRLPLEHL 1yizA 122 :VDEGDEVIIIEPFFDCYEPMVKAA T0339 132 :VAAVTFV 1yizA 146 :GGIPRFI T0339 141 :S 1yizA 155 :K T0339 142 :KVSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMP 1yizA 165 :SADWVLDNNELEALFNEKTKMIIINTPHNPLGKVMD T0339 178 :VPEISQRIKA 1yizA 204 :LEVVANLCKK T0339 198 :PPILVHTDAAQ 1yizA 214 :WNVLCVSDEVY T0339 209 :ALG 1yizA 226 :HMV T0339 214 :RVD 1yizA 231 :PFE T0339 223 :DFLTIVG 1yizA 247 :TITIGSA T0339 233 :YGPR 1yizA 257 :FSLT T0339 237 :IGALYIRGLGEFTPLYPMLFG 1yizA 264 :IGWAYGPEALLKNLQMVHQNC T0339 266 :PGTENTPMIAGLGKAAELVTQNCE 1yizA 285 :VYTCATPIQEAIAVGFETELKRLK T0339 290 :AYEAHMRDVRDYLEERLEAEFGQKRIH 1yizA 316 :SISGELMAKRDYMASFLAEVGMNPTVP T0339 326 :RLPNTCNFSIRGPR 1yizA 343 :QGGYFMVADWSSLD T0339 340 :LQGHVVLAQCRVLMASVGAACHSDHG 1yizA 371 :YRFTKWMTKSVGLQGIPPSAFYSEPN T0339 379 :FDVARNALRLSVG 1yizA 397 :KHLGEDFVRYCFF T0339 394 :TTRAEVDLVVQDLKQA 1yizA 410 :KKDENLQKAAEILRKW Number of specific fragments extracted= 24 number of extra gaps= 3 total=2371 Will force an alignment to be made, even if fragment is small Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2oatA/T0339-2oatA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2oatA expands to /projects/compbio/data/pdb/2oat.pdb.gz 2oatA:# T0339 read from 2oatA/T0339-2oatA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2oatA read from 2oatA/T0339-2oatA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2oatA to template set # found chain 2oatA in template set Warning: unaligning (T0339)K93 because of BadResidue code BAD_PEPTIDE in next template residue (2oatA)Y166 Warning: unaligning (T0339)G94 because of BadResidue code BAD_PEPTIDE at template residue (2oatA)Y166 T0339 1 :ERKVYMDYNA 2oatA 74 :EGRKYFDFLS T0339 11 :TTPLEPEVIQAMTKAMWEAW 2oatA 90 :QGHCHPKIVNALKSQVDKLT T0339 33 :PSSPYSAGRKAK 2oatA 110 :LTSRAFYNNVLG T0339 49 :AARESLAKMIGG 2oatA 122 :EYEEYITKLFNY T0339 63 :QDIIFTSGGTESNNLVIHSVVKHFH 2oatA 134 :HKVLPMNTGVEAGETACKLARKWGY T0339 88 :ANQTS 2oatA 160 :VKGIQ T0339 95 :H 2oatA 167 :K T0339 108 :PHFITSSVEHDSIRLPLE 2oatA 168 :AKIVFAAGNFWGRTLSAI T0339 126 :HLVEEQV 2oatA 192 :TSYDGFG T0339 135 :VTFVPVS 2oatA 204 :FDIIPYN T0339 148 :EVDDILAAVR 2oatA 211 :DLPALERALQ T0339 158 :PTTRLVTIMLANNETGIVMP 2oatA 222 :PNVAAFMVEPIQGEAGVVVP T0339 179 :PEISQ 2oatA 244 :GYLMG T0339 185 :IKALNQER 2oatA 249 :VRELCTRH T0339 199 :PILVHTDAAQ 2oatA 257 :QVLFIADEIQ T0339 209 :ALGKQRVD 2oatA 268 :GLARTGRW T0339 217 :VEDLGV 2oatA 278 :VDYENV T0339 223 :DFLTIV 2oatA 286 :DIVLLG T0339 231 :K 2oatA 292 :K T0339 232 :FY 2oatA 294 :LS T0339 234 :GPR 2oatA 297 :GLY T0339 237 :IGALYIR 2oatA 301 :VSAVLCD T0339 244 :GLGEFT 2oatA 309 :DIMLTI T0339 251 :LYPMLFG 2oatA 315 :KPGEHGS T0339 266 :PGTENTPMIAGLGKAAELVTQ 2oatA 322 :TYGGNPLGCRVAIAALEVLEE T0339 289 :EAYEAHMRDVRDYLEERLEAE 2oatA 343 :ENLAENADKLGIILRNELMKL T0339 311 :GQKRIHLNSQF 2oatA 364 :PSDVVTAVRGK T0339 328 :PNTCNFSIRGPR 2oatA 375 :GLLNAIVIKETK T0339 340 :LQGHVVLAQCRV 2oatA 388 :WDAWKVCLRLRD T0339 352 :LMASVGA 2oatA 402 :LLAKPTH T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQAV 2oatA 409 :GDIIRFAPPLVIKEDELRESIEIINKTI Number of specific fragments extracted= 31 number of extra gaps= 1 total=2402 Will force an alignment to be made, even if fragment is small Number of alignments=112 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2oatA/T0339-2oatA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 2oatA/T0339-2oatA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2oatA read from 2oatA/T0339-2oatA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2oatA in template set Warning: unaligning (T0339)G105 because of BadResidue code BAD_PEPTIDE in next template residue (2oatA)Y166 Warning: unaligning (T0339)A106 because of BadResidue code BAD_PEPTIDE at template residue (2oatA)Y166 T0339 2 :RKVYMDYNA 2oatA 75 :GRKYFDFLS T0339 11 :TTPLEPEVIQA 2oatA 90 :QGHCHPKIVNA T0339 23 :TKAMWEAWGNPSSP 2oatA 101 :LKSQVDKLTLTSRA T0339 47 :INAARESLAKMIGG 2oatA 120 :LGEYEEYITKLFNY T0339 63 :QDIIFTSGGTESNNLVIHSVVKHFHANQTSK 2oatA 134 :HKVLPMNTGVEAGETACKLARKWGYTVKGIQ T0339 107 :KPHFITSSVEHDSIRLPLE 2oatA 167 :KAKIVFAAGNFWGRTLSAI T0339 126 :HLVEEQV 2oatA 192 :TSYDGFG T0339 135 :VTFVPVS 2oatA 204 :FDIIPYN T0339 148 :EVDDILAAV 2oatA 211 :DLPALERAL T0339 157 :RPTTRLVTIMLANNETGIVMP 2oatA 221 :DPNVAAFMVEPIQGEAGVVVP T0339 178 :VPEISQRIKALN 2oatA 246 :LMGVRELCTRHQ T0339 200 :ILVHTDAAQ 2oatA 258 :VLFIADEIQ T0339 209 :ALGKQRVDVEDLGV 2oatA 270 :ARTGRWLAVDYENV T0339 223 :DFLTIVGHKFYGP 2oatA 286 :DIVLLGKALSGGL T0339 236 :RIGALYIRG 2oatA 300 :PVSAVLCDD T0339 246 :G 2oatA 309 :D T0339 251 :LYPMLFGGGQERNF 2oatA 310 :IMLTIKPGEHGSTY T0339 268 :TENTPMIAGLGKAAELVTQ 2oatA 324 :GGNPLGCRVAIAALEVLEE T0339 287 :NC 2oatA 344 :NL T0339 292 :EAHMRDVRDYLEERLEAEFGQKRIHLNSQ 2oatA 346 :AENADKLGIILRNELMKLPSDVVTAVRGK T0339 328 :PNTCNFSIRG 2oatA 375 :GLLNAIVIKE T0339 338 :PRLQGHVVLAQCRV 2oatA 386 :KDWDAWKVCLRLRD T0339 352 :LMASV 2oatA 402 :LLAKP T0339 381 :VARNALRLSVGRSTTRAEVDLVVQDLKQAV 2oatA 407 :THGDIIRFAPPLVIKEDELRESIEIINKTI Number of specific fragments extracted= 24 number of extra gaps= 1 total=2426 Will force an alignment to be made, even if fragment is small Number of alignments=113 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2oatA/T0339-2oatA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 2oatA/T0339-2oatA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2oatA read from 2oatA/T0339-2oatA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2oatA in template set Warning: unaligning (T0339)G105 because of BadResidue code BAD_PEPTIDE in next template residue (2oatA)Y166 Warning: unaligning (T0339)A106 because of BadResidue code BAD_PEPTIDE at template residue (2oatA)Y166 T0339 5 :YMDYNAT 2oatA 78 :YFDFLSS T0339 32 :NPS 2oatA 85 :YSA T0339 35 :SPYSAGRKAKDIIN 2oatA 89 :NQGHCHPKIVNALK T0339 49 :AARESLAKMIGG 2oatA 122 :EYEEYITKLFNY T0339 64 :DIIFTSGGTESNNLVIHSVVKHFHANQ 2oatA 135 :KVLPMNTGVEAGETACKLARKWGYTVK T0339 102 :PVK 2oatA 162 :GIQ T0339 107 :KPHFITSSVEHDSIRLPLEHL 2oatA 167 :KAKIVFAAGNFWGRTLSAISS T0339 129 :EEQVAA 2oatA 193 :SYDGFG T0339 135 :VTFVPVS 2oatA 204 :FDIIPYN T0339 148 :EVDDILAAV 2oatA 211 :DLPALERAL T0339 157 :RPTTRLVTIMLANNETGIVMP 2oatA 221 :DPNVAAFMVEPIQGEAGVVVP T0339 178 :VPEISQRIKA 2oatA 246 :LMGVRELCTR T0339 198 :PPILVHTDAAQALGKQRVD 2oatA 256 :HQVLFIADEIQTGLARTGR T0339 217 :VEDLGV 2oatA 278 :VDYENV T0339 223 :DFLTIVGHKFYGPR 2oatA 286 :DIVLLGKALSGGLY T0339 237 :IGALYIRGLGEFTPLYPMLFGG 2oatA 301 :VSAVLCDDDIMLTIKPGEHGST T0339 267 :GTENTPMIAGLGKAAELVT 2oatA 323 :YGGNPLGCRVAIAALEVLE T0339 290 :AYEAHMRDVRDYLEERLEAEFGQKRIH 2oatA 344 :NLAENADKLGIILRNELMKLPSDVVTA T0339 324 :TQRLPNTCNFSIR 2oatA 371 :VRGKGLLNAIVIK T0339 337 :GPRLQGHVVLAQCRVLMASVG 2oatA 387 :DWDAWKVCLRLRDNGLLAKPT T0339 382 :ARNALRLSVGRSTTRAEVDLVVQDLKQAV 2oatA 408 :HGDIIRFAPPLVIKEDELRESIEIINKTI Number of specific fragments extracted= 21 number of extra gaps= 1 total=2447 Will force an alignment to be made, even if fragment is small Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1svvA/T0339-1svvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1svvA expands to /projects/compbio/data/pdb/1svv.pdb.gz 1svvA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0339 read from 1svvA/T0339-1svvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1svvA read from 1svvA/T0339-1svvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1svvA to template set # found chain 1svvA in template set Warning: unaligning (T0339)K3 because first residue in template chain is (1svvA)P15 Warning: unaligning (T0339)I120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1svvA)H104 Warning: unaligning (T0339)R121 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1svvA)H104 Warning: unaligning (T0339)L167 because of BadResidue code BAD_PEPTIDE in next template residue (1svvA)T154 Warning: unaligning (T0339)A168 because of BadResidue code BAD_PEPTIDE at template residue (1svvA)T154 T0339 4 :VYMDYNATTPLEPEVIQ 1svvA 16 :YSFVNDYSVGMHPKILD T0339 25 :AMWEAWGNPSSPYSAGR 1svvA 33 :LMARDNMTQHAGYGQDS T0339 46 :IINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSV 1svvA 50 :HCAKAARLIGELLERPDADVHFISGGTQTNLIACSLA T0339 91 :TSKGH 1svvA 87 :LRPWE T0339 109 :HFITSSVEHDS 1svvA 92 :AVIATQLGHIS T0339 122 :LPLEHL 1svvA 107 :GAIEAT T0339 132 :VAAVTFVPVS 1svvA 113 :GHKVVTAPCP T0339 144 :SGQTEVDDILAAVR 1svvA 123 :DGKLRVADIESALH T0339 158 :PT 1svvA 141 :EH T0339 160 :TRLVTIM 1svvA 146 :PKLVYIS T0339 170 :NETGIVMPVPEISQ 1svvA 155 :TEVGTQYTKQELED T0339 185 :IKALNQER 1svvA 169 :ISASCKEH T0339 199 :PILVHTDAAQ 1svvA 177 :GLYLFLDGAR T0339 211 :GKQR 1svvA 189 :SALS T0339 215 :VDVEDL 1svvA 198 :LTLADI T0339 222 :VDFLTIVGHKFYGPR 1svvA 207 :TDMFYIGATKAGGMF T0339 237 :IGALYIR 1svvA 223 :EALIILN T0339 244 :GLGEFTPLYPMLFGG 1svvA 231 :ALKPNARHLIKQRGA T0339 266 :PGTENTP 1svvA 246 :LMAKGWL T0339 277 :LGKAAELVTQ 1svvA 253 :LGIQFEVLMK T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1svvA 265 :LFFELGAHSNKMAAILKAGLEAC T0339 314 :RIHLNSQFP 1svvA 288 :GIRLAWPSA T0339 328 :PNTCNFSIR 1svvA 297 :SNQLFPILE T0339 343 :HVVLAQCRV 1svvA 306 :NTMIAELNN T0339 352 :LMASVGAACHSD 1svvA 316 :FDMYTVEPLKDG T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQ 1svvA 328 :TCIMRLCTSWATEEKECHRFVEVLKR Number of specific fragments extracted= 26 number of extra gaps= 2 total=2473 Will force an alignment to be made, even if fragment is small Number of alignments=115 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1svvA/T0339-1svvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1svvA/T0339-1svvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1svvA read from 1svvA/T0339-1svvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1svvA in template set Warning: unaligning (T0339)K3 because first residue in template chain is (1svvA)P15 Warning: unaligning (T0339)I120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1svvA)H104 Warning: unaligning (T0339)R121 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1svvA)H104 Warning: unaligning (T0339)A168 because of BadResidue code BAD_PEPTIDE in next template residue (1svvA)T154 Warning: unaligning (T0339)N169 because of BadResidue code BAD_PEPTIDE at template residue (1svvA)T154 T0339 4 :VYMDYNATTPLEPEVIQAMTK 1svvA 16 :YSFVNDYSVGMHPKILDLMAR T0339 29 :AWGNPSSPYSAGR 1svvA 37 :DNMTQHAGYGQDS T0339 46 :IINAARESLAKMIGG 1svvA 50 :HCAKAARLIGELLER T0339 62 :PQ 1svvA 65 :PD T0339 64 :DIIFTSGGTESNNLVIHSVV 1svvA 68 :DVHFISGGTQTNLIACSLAL T0339 105 :GAKPHFITSSVEHDS 1svvA 88 :RPWEAVIATQLGHIS T0339 126 :H 1svvA 108 :A T0339 128 :VEEQVAAVTFVPVS 1svvA 109 :IEATGHKVVTAPCP T0339 144 :SGQTEVDDILAAV 1svvA 123 :DGKLRVADIESAL T0339 157 :RPT 1svvA 140 :SEH T0339 160 :TRLVTI 1svvA 146 :PKLVYI T0339 167 :L 1svvA 152 :S T0339 170 :NETGIVMP 1svvA 155 :TEVGTQYT T0339 178 :VPEISQRIKALN 1svvA 166 :LEDISASCKEHG T0339 200 :ILVHTDA 1svvA 178 :LYLFLDG T0339 207 :AQALGKQRVDVEDL 1svvA 190 :ALSSPVNDLTLADI T0339 222 :VDFLTIVGHKFYGPRIGALYIRGLGEFTPLYPMLFGGGQERNF 1svvA 207 :TDMFYIGATKAGGMFGEALIILNDALKPNARHLIKQRGALMAK T0339 267 :G 1svvA 250 :G T0339 275 :AGLGKAAELVTQ 1svvA 251 :WLLGIQFEVLMK T0339 287 :NC 1svvA 264 :NL T0339 289 :EAYEAHMRDVRDYLEERLEAE 1svvA 267 :FELGAHSNKMAAILKAGLEAC T0339 311 :G 1svvA 288 :G T0339 315 :IHLNSQF 1svvA 289 :IRLAWPS T0339 327 :LPNTCNFSIRG 1svvA 296 :ASNQLFPILEN T0339 340 :LQGHVV 1svvA 307 :TMIAEL T0339 377 :VPFD 1svvA 324 :LKDG T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQ 1svvA 328 :TCIMRLCTSWATEEKECHRFVEVLKR Number of specific fragments extracted= 27 number of extra gaps= 2 total=2500 Will force an alignment to be made, even if fragment is small Number of alignments=116 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1svvA/T0339-1svvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1svvA/T0339-1svvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1svvA read from 1svvA/T0339-1svvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1svvA in template set Warning: unaligning (T0339)K3 because first residue in template chain is (1svvA)P15 Warning: unaligning (T0339)I120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1svvA)H104 Warning: unaligning (T0339)R121 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1svvA)H104 Warning: unaligning (T0339)A168 because of BadResidue code BAD_PEPTIDE in next template residue (1svvA)T154 Warning: unaligning (T0339)N169 because of BadResidue code BAD_PEPTIDE at template residue (1svvA)T154 T0339 4 :VYMDYNATTPLEPEVIQAMTKA 1svvA 16 :YSFVNDYSVGMHPKILDLMARD T0339 30 :WGNPSSPYSAG 1svvA 38 :NMTQHAGYGQD T0339 45 :DIINAARESLAKMIGG 1svvA 49 :SHCAKAARLIGELLER T0339 62 :PQDIIFTSGGTESNNLVIHSV 1svvA 66 :DADVHFISGGTQTNLIACSLA T0339 104 :KGAKPHFITSSVEHDS 1svvA 87 :LRPWEAVIATQLGHIS T0339 126 :HL 1svvA 108 :AI T0339 129 :EEQVAAVTFVPV 1svvA 110 :EATGHKVVTAPC T0339 143 :VSGQTEVDDILAAV 1svvA 122 :PDGKLRVADIESAL T0339 157 :RPT 1svvA 140 :SEH T0339 160 :TRLVT 1svvA 146 :PKLVY T0339 166 :ML 1svvA 151 :IS T0339 170 :NETGIVMP 1svvA 155 :TEVGTQYT T0339 178 :VPEISQRIKA 1svvA 166 :LEDISASCKE T0339 198 :PPILVHTDAAQ 1svvA 176 :HGLYLFLDGAR T0339 209 :ALGKQRVDVEDL 1svvA 192 :SSPVNDLTLADI T0339 222 :VDFLTIVGHKFYGPR 1svvA 207 :TDMFYIGATKAGGMF T0339 237 :IGALYIRGLGEFTPLYPMLFGGGQERNF 1svvA 223 :EALIILNDALKPNARHLIKQRGALMAKG T0339 275 :AGLGKAAELVT 1svvA 251 :WLLGIQFEVLM T0339 286 :QNCEAYEAHMRDVRDYLEERLEAE 1svvA 264 :NLFFELGAHSNKMAAILKAGLEAC T0339 311 :GQKRIH 1svvA 288 :GIRLAW T0339 325 :QRLPNTCNFSIR 1svvA 294 :PSASNQLFPILE T0339 341 :QGHVVLAQ 1svvA 306 :NTMIAELN T0339 350 :RVLMASVG 1svvA 314 :NDFDMYTV T0339 377 :VPFDVARNALRLSVGRSTTRAEVDLVVQDLKQ 1svvA 322 :EPLKDGTCIMRLCTSWATEEKECHRFVEVLKR Number of specific fragments extracted= 24 number of extra gaps= 2 total=2524 Will force an alignment to be made, even if fragment is small Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yiyA/T0339-1yiyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yiyA expands to /projects/compbio/data/pdb/1yiy.pdb.gz 1yiyA:# T0339 read from 1yiyA/T0339-1yiyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yiyA read from 1yiyA/T0339-1yiyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yiyA to template set # found chain 1yiyA in template set Warning: unaligning (T0339)G40 because of BadResidue code BAD_PEPTIDE in next template residue (1yiyA)R75 Warning: unaligning (T0339)R41 because of BadResidue code BAD_PEPTIDE at template residue (1yiyA)R75 Warning: unaligning (T0339)S92 because of BadResidue code BAD_PEPTIDE in next template residue (1yiyA)E124 Warning: unaligning (T0339)K93 because of BadResidue code BAD_PEPTIDE at template residue (1yiyA)E124 Warning: unaligning (T0339)Q213 because of BadResidue code BAD_PEPTIDE in next template residue (1yiyA)E230 Warning: unaligning (T0339)R214 because of BadResidue code BAD_PEPTIDE at template residue (1yiyA)E230 T0339 2 :RKVYMDYNATT 1yiyA 38 :KPLNLGQGFPD T0339 13 :PLEPEVIQAMTKA 1yiyA 50 :HAPKYALNALAAA T0339 30 :WGNPSSP 1yiyA 63 :ANSPDPL T0339 37 :YSA 1yiyA 71 :NQY T0339 42 :KAKDIINAARESLAKMIGGKPQ 1yiyA 78 :GHPRLVQALSKLYSQLVDRTIN T0339 64 :DIIFTSGGTESNNLVIHSV 1yiyA 103 :EVLVTVGAYEALYATIQGH T0339 91 :T 1yiyA 122 :V T0339 94 :GH 1yiyA 125 :GD T0339 109 :HFITSSVEHDSIRLPLEHL 1yiyA 127 :EVIIIEPFFDCYEPMVKAA T0339 132 :VAAVTFVPVSKV 1yiyA 146 :GGIPRFIPLKPN T0339 144 :SGQT 1yiyA 160 :GGTI T0339 148 :EVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1yiyA 171 :DNNELEALFNEKTKMIIINTPHNPLGKVMDRAELEV T0339 185 :IKALNQER 1yiyA 207 :VANLCKKW T0339 199 :PILVHTDAAQALGK 1yiyA 215 :NVLCVSDEVYEHMV T0339 215 :V 1yiyA 235 :I T0339 217 :VEDL 1yiyA 237 :ICTL T0339 221 :GV 1yiyA 242 :GM T0339 223 :DFLTIVGHK 1yiyA 247 :TITIGSAGK T0339 232 :FY 1yiyA 257 :FS T0339 234 :GPRIGALYIR 1yiyA 261 :GWKIGWAYGP T0339 244 :GLGEFTPLYPMLF 1yiyA 272 :ALLKNLQMVHQNC T0339 266 :PGTENTPMIAGLGKAAELVTQ 1yiyA 285 :VYTCATPIQEAIAVGFETELK T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1yiyA 313 :YFNSISGELMAKRDYMASFLAEV T0339 314 :RIHLNSQFP 1yiyA 336 :GMNPTVPQG T0339 328 :PNTCNFSIRGPR 1yiyA 345 :GYFMVADWSSLD T0339 340 :LQGHVVLAQCRV 1yiyA 368 :RKDYRFTKWMTK T0339 352 :LMASVGAACHSDH 1yiyA 383 :LQGIPPSAFYSEP T0339 378 :PFDVARNALRLSVGR 1yiyA 396 :NKHLGEDFVRYCFFK T0339 395 :TRAEVDLVVQDLKQAV 1yiyA 411 :KDENLQKAAEILRKWK Number of specific fragments extracted= 29 number of extra gaps= 3 total=2553 Will force an alignment to be made, even if fragment is small Number of alignments=118 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yiyA/T0339-1yiyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1yiyA/T0339-1yiyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yiyA read from 1yiyA/T0339-1yiyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yiyA in template set Warning: unaligning (T0339)P33 because of BadResidue code BAD_PEPTIDE in next template residue (1yiyA)R75 Warning: unaligning (T0339)S34 because of BadResidue code BAD_PEPTIDE at template residue (1yiyA)R75 Warning: unaligning (T0339)G105 because of BadResidue code BAD_PEPTIDE in next template residue (1yiyA)E124 Warning: unaligning (T0339)A106 because of BadResidue code BAD_PEPTIDE at template residue (1yiyA)E124 Warning: unaligning (T0339)Q213 because of BadResidue code BAD_PEPTIDE in next template residue (1yiyA)E230 T0339 2 :RKVYMDYNATT 1yiyA 38 :KPLNLGQGFPD T0339 13 :PLEPEVIQAMTKAM 1yiyA 50 :HAPKYALNALAAAA T0339 29 :AWGN 1yiyA 70 :ANQY T0339 35 :SP 1yiyA 76 :GF T0339 39 :A 1yiyA 78 :G T0339 43 :AKDIINAARESLAKMIGG 1yiyA 79 :HPRLVQALSKLYSQLVDR T0339 61 :KPQ 1yiyA 99 :NPM T0339 64 :DIIFTSGGTESNNLVIHSVV 1yiyA 103 :EVLVTVGAYEALYATIQGHV T0339 107 :KPHFITSSVEHDSIRLPL 1yiyA 125 :GDEVIIIEPFFDCYEPMV T0339 129 :EEQVAAVTFVPV 1yiyA 143 :KAAGGIPRFIPL T0339 141 :SKVSGQ 1yiyA 157 :NKTGGT T0339 147 :TEVDDILAAVRPTTRLVTIMLANNETGIVMP 1yiyA 170 :LDNNELEALFNEKTKMIIINTPHNPLGKVMD T0339 178 :VPEISQRIKALN 1yiyA 204 :LEVVANLCKKWN T0339 200 :ILVHTDAAQALGK 1yiyA 216 :VLCVSDEVYEHMV T0339 214 :RVD 1yiyA 234 :HIR T0339 217 :V 1yiyA 238 :C T0339 219 :DLG 1yiyA 239 :TLP T0339 223 :DFLTIVGHKFYGP 1yiyA 247 :TITIGSAGKTFSL T0339 236 :R 1yiyA 261 :G T0339 237 :IGALYIRG 1yiyA 264 :IGWAYGPE T0339 246 :GEF 1yiyA 272 :ALL T0339 266 :PGTENTPMIAGLGKAAELVTQ 1yiyA 285 :VYTCATPIQEAIAVGFETELK T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1yiyA 313 :YFNSISGELMAKRDYMASFLAEV T0339 311 :G 1yiyA 336 :G T0339 315 :IHLNSQ 1yiyA 337 :MNPTVP T0339 326 :RLPNTCNFSI 1yiyA 343 :QGGYFMVADW T0339 336 :RGPRLQGHVVLAQCRVLMASVG 1yiyA 364 :ETDARKDYRFTKWMTKSVGLQG T0339 358 :AACHSDH 1yiyA 389 :SAFYSEP T0339 378 :PFDVARNALRLSVGR 1yiyA 396 :NKHLGEDFVRYCFFK T0339 395 :TRAEVDLVVQDLKQAV 1yiyA 411 :KDENLQKAAEILRKWK Number of specific fragments extracted= 30 number of extra gaps= 3 total=2583 Will force an alignment to be made, even if fragment is small Number of alignments=119 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yiyA/T0339-1yiyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1yiyA/T0339-1yiyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yiyA read from 1yiyA/T0339-1yiyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yiyA in template set Warning: unaligning (T0339)S38 because of BadResidue code BAD_PEPTIDE in next template residue (1yiyA)R75 Warning: unaligning (T0339)A39 because of BadResidue code BAD_PEPTIDE at template residue (1yiyA)R75 Warning: unaligning (T0339)G105 because of BadResidue code BAD_PEPTIDE in next template residue (1yiyA)E124 Warning: unaligning (T0339)A106 because of BadResidue code BAD_PEPTIDE at template residue (1yiyA)E124 Warning: unaligning (T0339)K212 because of BadResidue code BAD_PEPTIDE in next template residue (1yiyA)E230 Warning: unaligning (T0339)Q213 because of BadResidue code BAD_PEPTIDE at template residue (1yiyA)E230 T0339 2 :RKVYMDYNATT 1yiyA 38 :KPLNLGQGFPD T0339 13 :PLEPEVIQAMTKA 1yiyA 50 :HAPKYALNALAAA T0339 28 :EAWGNPS 1yiyA 63 :ANSPDPL T0339 35 :SPY 1yiyA 71 :NQY T0339 40 :GRKAKDIINAARESLAKMIGG 1yiyA 76 :GFGHPRLVQALSKLYSQLVDR T0339 61 :KP 1yiyA 99 :NP T0339 63 :QDIIFTSGGTESNNLVIHSV 1yiyA 102 :TEVLVTVGAYEALYATIQGH T0339 104 :K 1yiyA 122 :V T0339 107 :KPHFITSSVEHDSIRLPLEHL 1yiyA 125 :GDEVIIIEPFFDCYEPMVKAA T0339 132 :VAAVTFVPVS 1yiyA 146 :GGIPRFIPLK T0339 142 :KVSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMP 1yiyA 165 :SADWVLDNNELEALFNEKTKMIIINTPHNPLGKVMD T0339 178 :VPEISQRIKA 1yiyA 204 :LEVVANLCKK T0339 198 :PPILVHTDAAQ 1yiyA 214 :WNVLCVSDEVY T0339 209 :ALG 1yiyA 226 :HMV T0339 214 :RVD 1yiyA 231 :PFE T0339 217 :VEDLGV 1yiyA 238 :CTLPGM T0339 223 :DFLTIVGHKFYGPR 1yiyA 247 :TITIGSAGKTFSLT T0339 237 :IGALYIRGLGEFTPLYPMLFG 1yiyA 264 :IGWAYGPEALLKNLQMVHQNC T0339 266 :PGTENTPMIAGLGKAAELVTQNCE 1yiyA 285 :VYTCATPIQEAIAVGFETELKRLK T0339 290 :AYEAHMRDVRDYLEERLEAEFGQKRIH 1yiyA 316 :SISGELMAKRDYMASFLAEVGMNPTVP T0339 326 :RLPNTCNFSIRGPRLQ 1yiyA 343 :QGGYFMVADWSSLDSK T0339 342 :GHVVLAQCRVLMASVGAACHSDHG 1yiyA 373 :FTKWMTKSVGLQGIPPSAFYSEPN T0339 379 :FDVARNALRLSVG 1yiyA 397 :KHLGEDFVRYCFF T0339 394 :TTRAEVDLVVQDLKQAV 1yiyA 410 :KKDENLQKAAEILRKWK Number of specific fragments extracted= 24 number of extra gaps= 3 total=2607 Will force an alignment to be made, even if fragment is small Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eluB/T0339-1eluB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1eluB expands to /projects/compbio/data/pdb/1elu.pdb.gz 1eluB:# T0339 read from 1eluB/T0339-1eluB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eluB read from 1eluB/T0339-1eluB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1eluB to template set # found chain 1eluB in template set T0339 2 :RKVYMDYNATTPLEPEVIQAMTKAMWEAWGNPSSPYSAGRKAKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSV 1eluB 19 :NKTYFNFGGQGILPTVALEAITAMYGYLQENGPFSIAANQHIQQLIAQLRQALAETFNVDPNTITITDNVTTGCDIVLWGL T0339 90 :QTSKGH 1eluB 100 :DWHQGD T0339 109 :HFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSKV 1eluB 106 :EILLTDCEHPGIIAIVQAIAARFGITYRFFPVAAT T0339 144 :SGQ 1eluB 142 :NQG T0339 148 :E 1eluB 145 :D T0339 149 :VDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1eluB 147 :AAVLANHLGPKTRLVILSHLLWNTGQVLPLAEIMA T0339 188 :LNQER 1eluB 182 :VCRRH T0339 196 :GLP 1eluB 187 :QGN T0339 199 :PILVHTDAAQALGKQRVDVEDLGVDFLTIVGHK 1eluB 191 :PVRVLVDGAQSAGSLPLDFSRLEVDYYAFTGHK T0339 232 :FY 1eluB 225 :FA T0339 234 :GPRIGALYIR 1eluB 228 :PAGVGGLYIH T0339 244 :GLGEFTP 1eluB 239 :DCLGEIN T0339 251 :LYPM 1eluB 252 :RSIT T0339 260 :QERNFRPGTENTPMIAGLGKAAELVTQ 1eluB 268 :GGKRFEVATSAYPQYAGLLAALQLHQR T0339 287 :NCEAYEAHMRDVRDYLEERLEA 1eluB 297 :TAEERYQAICQRSEFLWRGLNQ T0339 312 :QKRIHLNSQFPGT 1eluB 319 :LPHVHCLATSAPQ T0339 328 :PNTCNFSIRGP 1eluB 332 :AGLVSFTVDSP T0339 340 :LQGHVVLAQCRV 1eluB 343 :LGHRAIVQKLEE T0339 352 :LMASVGAA 1eluB 357 :IYLRTIAD T0339 383 :RNALRLSVGRSTTRAEVDLVVQDL 1eluB 365 :PDCIRACCHYITDEEEINHLLARL Number of specific fragments extracted= 20 number of extra gaps= 0 total=2627 Will force an alignment to be made, even if fragment is small Number of alignments=121 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eluB/T0339-1eluB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1eluB/T0339-1eluB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eluB read from 1eluB/T0339-1eluB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eluB in template set T0339 2 :RKVYMDYNATTPLEPEVIQAMTKAMWEAWGN 1eluB 19 :NKTYFNFGGQGILPTVALEAITAMYGYLQEN T0339 33 :PSS 1eluB 51 :PFS T0339 37 :YSAGRKAKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSV 1eluB 54 :IAANQHIQQLIAQLRQALAETFNVDPNTITITDNVTTGCDIVLWGL T0339 90 :Q 1eluB 101 :W T0339 105 :GAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSKVSGQTE 1eluB 102 :HQGDEILLTDCEHPGIIAIVQAIAARFGITYRFFPVAATLNQGD T0339 149 :VDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKALN 1eluB 147 :AAVLANHLGPKTRLVILSHLLWNTGQVLPLAEIMAVCRRHQ T0339 196 :GLPPILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFY 1eluB 188 :GNYPVRVLVDGAQSAGSLPLDFSRLEVDYYAFTGHKWF T0339 234 :GP 1eluB 227 :GP T0339 236 :RIGALYIRG 1eluB 230 :GVGGLYIHG T0339 246 :GEFTPLYPMLFGGGQ 1eluB 239 :DCLGEINPTYVGWRS T0339 261 :ERNFRPGTENTPMIAGLGKAAELVTQ 1eluB 269 :GKRFEVATSAYPQYAGLLAALQLHQR T0339 287 :NCEAYEAHMRDVRDYLEERLEAEFG 1eluB 297 :TAEERYQAICQRSEFLWRGLNQLPH T0339 315 :IHLNSQ 1eluB 322 :VHCLAT T0339 323 :GTQRLP 1eluB 328 :SAPQAG T0339 330 :TCNFSIRGP 1eluB 334 :LVSFTVDSP T0339 340 :LQGHVVLAQCRV 1eluB 343 :LGHRAIVQKLEE T0339 352 :LMASV 1eluB 357 :IYLRT T0339 377 :VPF 1eluB 362 :IAD T0339 383 :RNALRLSVGRSTTRAEVDLVVQDL 1eluB 365 :PDCIRACCHYITDEEEINHLLARL Number of specific fragments extracted= 19 number of extra gaps= 0 total=2646 Will force an alignment to be made, even if fragment is small Number of alignments=122 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eluB/T0339-1eluB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1eluB/T0339-1eluB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eluB read from 1eluB/T0339-1eluB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eluB in template set T0339 3 :KVYMDYNATTPLEPEVIQAMTKAMWEAWGNPSSPYSAGRKAKDIINAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSV 1eluB 20 :KTYFNFGGQGILPTVALEAITAMYGYLQENGPFSIAANQHIQQLIAQLRQALAETFNVDPNTITITDNVTTGCDIVLWGL T0339 103 :VKGAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSKVSGQTE 1eluB 100 :DWHQGDEILLTDCEHPGIIAIVQAIAARFGITYRFFPVAATLNQGD T0339 149 :VDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKA 1eluB 147 :AAVLANHLGPKTRLVILSHLLWNTGQVLPLAEIMAVCRR T0339 197 :LPPILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFYGPR 1eluB 189 :NYPVRVLVDGAQSAGSLPLDFSRLEVDYYAFTGHKWFAGP T0339 237 :IGALYIRGLGEFTPLYPMLFGGGQ 1eluB 231 :VGGLYIHGDCLGEINPTYVGWRSI T0339 261 :ERNFRPGTENTPMIAGLGKAAELVT 1eluB 269 :GKRFEVATSAYPQYAGLLAALQLHQ T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1eluB 296 :GTAEERYQAICQRSEFLWRGLNQLPHVHCLA T0339 323 :GTQRLPNTCNFSIRG 1eluB 327 :TSAPQAGLVSFTVDS T0339 338 :PRLQGHVVLAQCRVLMASV 1eluB 343 :LGHRAIVQKLEEQRIYLRT T0339 377 :VP 1eluB 362 :IA T0339 382 :ARNALRLSVGRSTTRAEVDLVVQDL 1eluB 364 :DPDCIRACCHYITDEEEINHLLARL Number of specific fragments extracted= 11 number of extra gaps= 0 total=2657 Will force an alignment to be made, even if fragment is small Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uu1A/T0339-1uu1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1uu1A expands to /projects/compbio/data/pdb/1uu1.pdb.gz 1uu1A:# T0339 read from 1uu1A/T0339-1uu1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uu1A read from 1uu1A/T0339-1uu1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1uu1A to template set # found chain 1uu1A in template set Warning: unaligning (T0339)G40 because of BadResidue code BAD_PEPTIDE in next template residue (1uu1A)P57 Warning: unaligning (T0339)K42 because of BadResidue code BAD_PEPTIDE at template residue (1uu1A)P57 T0339 1 :ERK 1uu1A 17 :EKR T0339 4 :VYMD 1uu1A 22 :TYLA T0339 8 :YNATTPLEPEVIQAMTK 1uu1A 27 :NENPFPFPEDLVDEVFR T0339 30 :WGNPSSP 1uu1A 44 :RLNSDAL T0339 37 :YSA 1uu1A 53 :YYD T0339 43 :AK 1uu1A 58 :DE T0339 49 :AARESLAKMIG 1uu1A 60 :ELIEKILSYLD T0339 60 :GKPQDIIFTSGGTESNNLVIHSV 1uu1A 74 :LSKNNVSVGNGADEIIYVMMLMF T0339 95 :H 1uu1A 97 :D T0339 109 :HFITSSVEHDSIRLPLEHL 1uu1A 98 :RSVFFPPTYSCYRIFAKAV T0339 132 :VAAVTFVPVSK 1uu1A 117 :GAKFLEVPLTK T0339 144 :SGQTE 1uu1A 128 :DLRIP T0339 156 :VRPT 1uu1A 136 :VGEG T0339 161 :RLVTIMLANNETGIVMPVPEISQ 1uu1A 140 :DVVFIPNPNNPTGHVFEREEIER T0339 188 :LNQE 1uu1A 163 :ILKT T0339 199 :PILVHTDAAQALGKQRVDVEDL 1uu1A 167 :GAFVALDEAYYEFHGESYVDFL T0339 221 :GVDFLTIVGHK 1uu1A 192 :ENLAVIRTFSK T0339 232 :FY 1uu1A 204 :FS T0339 234 :GPRIGALYIR 1uu1A 208 :AQRVGYVVAS T0339 244 :GLGEFTPLYPM 1uu1A 219 :KFIDAYNRVRL T0339 266 :PGTENTPMIAGLGKAAEL 1uu1A 230 :PFNVSYVSQMFAKVALDH T0339 285 :TQNCEAYEAHMRDVRDYLEERLEAE 1uu1A 248 :REIFEERTKFIVEERERMKSALREM T0339 314 :RIHLNSQF 1uu1A 273 :GYRITDSR T0339 328 :PNTCNFSIRG 1uu1A 281 :GNFVFVFMEK T0339 340 :LQGHVVLAQCRV 1uu1A 291 :EEKERLLEHLRT T0339 352 :LMASVG 1uu1A 305 :VAVRSF T0339 383 :RNALRLSVG 1uu1A 311 :REGVRITIG T0339 395 :TRAEVDLVVQDLK 1uu1A 320 :KREENDMILRELE Number of specific fragments extracted= 28 number of extra gaps= 1 total=2685 Will force an alignment to be made, even if fragment is small Number of alignments=124 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uu1A/T0339-1uu1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1uu1A/T0339-1uu1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uu1A read from 1uu1A/T0339-1uu1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1uu1A in template set Warning: unaligning (T0339)S35 because of BadResidue code BAD_PEPTIDE in next template residue (1uu1A)P57 Warning: unaligning (T0339)P36 because of BadResidue code BAD_PEPTIDE at template residue (1uu1A)P57 T0339 2 :RKVYMD 1uu1A 20 :DKTYLA T0339 8 :YNATTPLEPEVIQAMTK 1uu1A 27 :NENPFPFPEDLVDEVFR T0339 28 :EAWGNPS 1uu1A 49 :ALRIYYD T0339 37 :Y 1uu1A 58 :D T0339 48 :NAARESLAKMIGG 1uu1A 59 :EELIEKILSYLDT T0339 61 :KPQDIIFTSGGTESNNLVIHSV 1uu1A 75 :SKNNVSVGNGADEIIYVMMLMF T0339 108 :PHFITSSVE 1uu1A 97 :DRSVFFPPT T0339 121 :RLPLEHLVEEQVAAVTFVPVSK 1uu1A 106 :YSCYRIFAKAVGAKFLEVPLTK T0339 144 :SGQTE 1uu1A 128 :DLRIP T0339 156 :VRPT 1uu1A 136 :VGEG T0339 161 :RLVTIMLANNETGIVMPVPEI 1uu1A 140 :DVVFIPNPNNPTGHVFEREEI T0339 183 :QRIKALN 1uu1A 161 :ERILKTG T0339 200 :ILVHTDAAQALGKQRVDVEDLG 1uu1A 168 :AFVALDEAYYEFHGESYVDFLK T0339 223 :DFLTIV 1uu1A 193 :NLAVIR T0339 229 :GHKFY 1uu1A 200 :FSKAF T0339 234 :GP 1uu1A 207 :AA T0339 236 :RIGALYIRG 1uu1A 210 :RVGYVVASE T0339 246 :GEFT 1uu1A 219 :KFID T0339 264 :FRPGTENTPMIAGLGKAAE 1uu1A 228 :RLPFNVSYVSQMFAKVALD T0339 283 :LVTQNCEAYEAHMRDVRDYLEER 1uu1A 250 :IFEERTKFIVEERERMKSALREM T0339 311 :G 1uu1A 273 :G T0339 315 :IHLN 1uu1A 274 :YRIT T0339 325 :QRLPNTCNFSIRG 1uu1A 278 :DSRGNFVFVFMEK T0339 340 :LQGHVVLAQCRV 1uu1A 291 :EEKERLLEHLRT T0339 352 :LMASV 1uu1A 305 :VAVRS T0339 382 :ARNALRLSVGR 1uu1A 310 :FREGVRITIGK T0339 396 :RAEVDLVVQDLK 1uu1A 321 :REENDMILRELE Number of specific fragments extracted= 27 number of extra gaps= 1 total=2712 Will force an alignment to be made, even if fragment is small Number of alignments=125 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uu1A/T0339-1uu1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1uu1A/T0339-1uu1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uu1A read from 1uu1A/T0339-1uu1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1uu1A in template set Warning: unaligning (T0339)G40 because of BadResidue code BAD_PEPTIDE in next template residue (1uu1A)P57 T0339 1 :ERKVYMD 1uu1A 19 :RDKTYLA T0339 8 :YNATTPLEPEVIQAMTK 1uu1A 27 :NENPFPFPEDLVDEVFR T0339 30 :WGNPS 1uu1A 44 :RLNSD T0339 35 :SPYSA 1uu1A 51 :RIYYD T0339 48 :NAARESLAKMIGG 1uu1A 59 :EELIEKILSYLDT T0339 61 :KPQDIIFTSGGTESNNLVIHSV 1uu1A 75 :SKNNVSVGNGADEIIYVMMLMF T0339 108 :PHFITSSVEHDSIRLPLEHL 1uu1A 97 :DRSVFFPPTYSCYRIFAKAV T0339 132 :VAAVTFVPVS 1uu1A 117 :GAKFLEVPLT T0339 143 :VSGQTE 1uu1A 127 :KDLRIP T0339 156 :VRPT 1uu1A 136 :VGEG T0339 161 :RLVTIMLANNETGIVMPVPEISQRIK 1uu1A 140 :DVVFIPNPNNPTGHVFEREEIERILK T0339 198 :PPILVHTDAAQALGKQRVD 1uu1A 166 :TGAFVALDEAYYEFHGESY T0339 217 :VEDLGVDFLTIVGHKFYGPR 1uu1A 188 :LKKYENLAVIRTFSKAFSLA T0339 237 :IGALYIRGLGEFTPLYP 1uu1A 211 :VGYVVASEKFIDAYNRV T0339 264 :FRPGTENTPMIAGLGKAAELVT 1uu1A 228 :RLPFNVSYVSQMFAKVALDHRE T0339 286 :QNCEAYEAHMRDVRDYLEER 1uu1A 253 :ERTKFIVEERERMKSALREM T0339 320 :QFPGTQRLPNTCNFSIRGPRLQGHVVLAQCRVLMASV 1uu1A 273 :GYRITDSRGNFVFVFMEKEEKERLLEHLRTKNVAVRS T0339 382 :ARNALRLSVG 1uu1A 310 :FREGVRITIG T0339 395 :TRAEVDLVVQDLK 1uu1A 320 :KREENDMILRELE Number of specific fragments extracted= 19 number of extra gaps= 1 total=2731 Will force an alignment to be made, even if fragment is small Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bjwA/T0339-1bjwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bjwA expands to /projects/compbio/data/pdb/1bjw.pdb.gz 1bjwA:Bad short name: N1 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: C2' for alphabet: pdb_atoms Bad short name: C3 for alphabet: pdb_atoms Bad short name: O3 for alphabet: pdb_atoms Bad short name: C4 for alphabet: pdb_atoms Bad short name: C4' for alphabet: pdb_atoms Bad short name: C5 for alphabet: pdb_atoms Bad short name: C6 for alphabet: pdb_atoms Bad short name: C5' for alphabet: pdb_atoms Bad short name: OP4 for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms # T0339 read from 1bjwA/T0339-1bjwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bjwA read from 1bjwA/T0339-1bjwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1bjwA to template set # found chain 1bjwA in template set Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bjwA)A235 T0339 2 :RKVYMDYNATTP 1bjwA 32 :DLVALTAGEPDF T0339 14 :LEPEVIQAMTKAMWE 1bjwA 45 :TPEHVKEAARRALAQ T0339 33 :PSSPYSAGRKAKDIINAARESLAKMIG 1bjwA 60 :GKTKYAPPAGIPELREALAEKFRRENG T0339 60 :GKPQDIIFTSGGTESNNLVIHSV 1bjwA 89 :VTPEETIVTVGGKQALFNLFQAI T0339 91 :TSKGH 1bjwA 112 :LDPGD T0339 109 :HFITSSVEHDSIRLPLEHL 1bjwA 117 :EVIVLSPYWVSYPEMVRFA T0339 132 :VAAVTFVPVSKV 1bjwA 136 :GGVVVEVETLPE T0339 144 :SGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1bjwA 149 :GFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEA T0339 185 :IKALNQER 1bjwA 189 :LARLAVEH T0339 199 :PILVHTDAAQALGKQR 1bjwA 197 :DFYLVSDEIYEHLLYE T0339 215 :VDVEDL 1bjwA 216 :FSPGRV T0339 223 :DFLTIVG 1bjwA 226 :TLTVNGA T0339 232 :FY 1bjwA 236 :FA T0339 234 :GPRIGALYIR 1bjwA 240 :GWRIGYACGP T0339 244 :GLGEFT 1bjwA 251 :EVIKAM T0339 251 :LYPMLFG 1bjwA 257 :ASVSSQS T0339 266 :PGTENTPMIAGLGKAAE 1bjwA 264 :TTSPDTIAQWATLEALT T0339 283 :LVTQNCEAYEAHMRDVRDYLEERLEAE 1bjwA 284 :ASRAFVEMAREAYRRRRDLLLEGLTAL T0339 314 :RIHLNSQFP 1bjwA 311 :GLKAVRPSG T0339 328 :PNTCNFSIRGPRLQGHVVLAQCRV 1bjwA 320 :AFYVLMDTSPIAPDEVRAAERLLE T0339 352 :LMASVGAACHS 1bjwA 346 :VAVVPGTDFAA T0339 383 :RNALRLS 1bjwA 357 :FGHVRLS T0339 392 :RSTTRAEVDLVVQDL 1bjwA 364 :YATSEENLRKALERF Number of specific fragments extracted= 23 number of extra gaps= 0 total=2754 Will force an alignment to be made, even if fragment is small Number of alignments=127 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bjwA/T0339-1bjwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1bjwA/T0339-1bjwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bjwA read from 1bjwA/T0339-1bjwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bjwA in template set Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bjwA)A235 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bjwA)A235 T0339 2 :RKVYMDYNATT 1bjwA 32 :DLVALTAGEPD T0339 13 :PLEPEVIQAMTKAMWEAWGN 1bjwA 44 :DTPEHVKEAARRALAQGKTK T0339 33 :PSSP 1bjwA 67 :PAGI T0339 44 :KDIINAARESLAKMIGG 1bjwA 71 :PELREALAEKFRRENGL T0339 61 :KPQDIIFTSGGTESNNLVIHSVV 1bjwA 90 :TPEETIVTVGGKQALFNLFQAIL T0339 105 :GAKPHFITSSVE 1bjwA 113 :DPGDEVIVLSPY T0339 121 :RLPLEHLVEEQVAAVTFVPVSKVSG 1bjwA 125 :WVSYPEMVRFAGGVVVEVETLPEEG T0339 146 :QTEVDDILAAVRPTTRLVTIMLANNETGIVMP 1bjwA 151 :VPDPERVRRAITPRTKALVVNSPNNPTGAVYP T0339 178 :VPEISQRIKALN 1bjwA 186 :LEALARLAVEHD T0339 200 :ILVHTDAAQALGKQRVD 1bjwA 198 :FYLVSDEIYEHLLYEGE T0339 217 :V 1bjwA 218 :P T0339 219 :DLGV 1bjwA 219 :GRVA T0339 223 :DFLTIVG 1bjwA 226 :TLTVNGA T0339 233 :YGP 1bjwA 236 :FAM T0339 236 :R 1bjwA 240 :G T0339 237 :IGALYIRG 1bjwA 243 :IGYACGPK T0339 246 :G 1bjwA 251 :E T0339 261 :ER 1bjwA 264 :TT T0339 268 :TENTPMIAGLGKAAE 1bjwA 266 :SPDTIAQWATLEALT T0339 283 :LVTQNCEAYEAHMRDVRDYLEERLEAE 1bjwA 284 :ASRAFVEMAREAYRRRRDLLLEGLTAL T0339 311 :G 1bjwA 311 :G T0339 315 :IHLNSQ 1bjwA 312 :LKAVRP T0339 326 :RLPNTCNFSIRGPRLQGHVVLAQCRV 1bjwA 318 :SGAFYVLMDTSPIAPDEVRAAERLLE T0339 352 :LMASVGA 1bjwA 346 :VAVVPGT T0339 379 :FDVARNALRLSVGR 1bjwA 353 :DFAAFGHVRLSYAT T0339 395 :TRAEVDLVVQDL 1bjwA 367 :SEENLRKALERF Number of specific fragments extracted= 26 number of extra gaps= 0 total=2780 Will force an alignment to be made, even if fragment is small Number of alignments=128 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bjwA/T0339-1bjwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1bjwA/T0339-1bjwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bjwA read from 1bjwA/T0339-1bjwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bjwA in template set Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bjwA)A235 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bjwA)A235 T0339 2 :RKVYMDYNATT 1bjwA 32 :DLVALTAGEPD T0339 13 :PLEPEVIQAMTKAMWEAW 1bjwA 44 :DTPEHVKEAARRALAQGK T0339 31 :GNPSSP 1bjwA 65 :APPAGI T0339 44 :KDIINAARESLAKMIGG 1bjwA 71 :PELREALAEKFRRENGL T0339 61 :KPQDIIFTSGGTESNNLVIHSV 1bjwA 90 :TPEETIVTVGGKQALFNLFQAI T0339 104 :KGAKPHFITSSVEHDSIRLPLEHL 1bjwA 112 :LDPGDEVIVLSPYWVSYPEMVRFA T0339 132 :VAAVTFVPVS 1bjwA 136 :GGVVVEVETL T0339 142 :KVSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMP 1bjwA 147 :EEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYP T0339 178 :VPEISQRIKA 1bjwA 186 :LEALARLAVE T0339 198 :PPILVHTDAAQALGKQRVD 1bjwA 196 :HDFYLVSDEIYEHLLYEGE T0339 217 :VEDLGVDFLTIVG 1bjwA 220 :RVAPEHTLTVNGA T0339 233 :YGPR 1bjwA 236 :FAMT T0339 237 :IGALYIRGLGEFTPLYPM 1bjwA 243 :IGYACGPKEVIKAMASVS T0339 264 :FRPGTENTPMIAGLGKAAELVT 1bjwA 262 :QSTTSPDTIAQWATLEALTNQE T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1bjwA 287 :AFVEMAREAYRRRRDLLLEGLTALGLKAVRP T0339 326 :RLPNTCNFSIRG 1bjwA 318 :SGAFYVLMDTSP T0339 338 :PRLQGHVVLAQCRVLMASVG 1bjwA 332 :PDEVRAAERLLEAGVAVVPG T0339 378 :PFDVARNALRLSVG 1bjwA 352 :TDFAAFGHVRLSYA T0339 394 :TTRAEVDLVVQDL 1bjwA 366 :TSEENLRKALERF Number of specific fragments extracted= 19 number of extra gaps= 0 total=2799 Will force an alignment to be made, even if fragment is small Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jg8A/T0339-1jg8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jg8A expands to /projects/compbio/data/pdb/1jg8.pdb.gz 1jg8A:Bad short name: N1 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: C2' for alphabet: pdb_atoms Bad short name: C3 for alphabet: pdb_atoms Bad short name: O3 for alphabet: pdb_atoms Bad short name: C4 for alphabet: pdb_atoms Bad short name: C4' for alphabet: pdb_atoms Bad short name: C5 for alphabet: pdb_atoms Bad short name: C6 for alphabet: pdb_atoms Bad short name: C5' for alphabet: pdb_atoms Bad short name: OP4 for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms # T0339 read from 1jg8A/T0339-1jg8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jg8A read from 1jg8A/T0339-1jg8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jg8A to template set # found chain 1jg8A in template set Warning: unaligning (T0339)K3 because first residue in template chain is (1jg8A)M5 Warning: unaligning (T0339)L167 because of BadResidue code BAD_PEPTIDE in next template residue (1jg8A)T141 Warning: unaligning (T0339)A168 because of BadResidue code BAD_PEPTIDE at template residue (1jg8A)T141 Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jg8A)G204 T0339 4 :VYMDYNATTPLEPEVIQAMT 1jg8A 6 :IDLRSDTVTKPTEEMRKAMA T0339 33 :PSSPYSAGRKAKDIINAARESLAKMIGG 1jg8A 26 :QAEVGDDVYGEDPTINELERLAAETFGK T0339 63 :QDIIFTSGGTESNNLVIHSV 1jg8A 54 :EAALFVPSGTMGNQVSIMAH T0339 91 :TSKGH 1jg8A 74 :TQRGD T0339 109 :HFITSSVEHDSIR 1jg8A 79 :EVILEADSHIFWY T0339 122 :LPLEHL 1jg8A 95 :AMAVLS T0339 132 :VAAVTFVPVS 1jg8A 101 :GVMPHPVPGK T0339 144 :SGQTEVDDILAAVRPT 1jg8A 111 :NGAMDPDDVRKAIRPR T0339 160 :TRLVTIM 1jg8A 133 :TSLIAIE T0339 169 :NNE 1jg8A 142 :HNR T0339 172 :TGIVMPVPEISQ 1jg8A 146 :GGRVVPLENIKE T0339 185 :IKALNQER 1jg8A 158 :ICTIAKEH T0339 199 :PILVHTDAAQ 1jg8A 166 :GINVHIDGAR T0339 209 :ALGKQRVDVEDL 1jg8A 179 :ASIASGVPVKEY T0339 221 :GVDFLTIVG 1jg8A 193 :YADSVMFCL T0339 232 :FYGPRIGALYIR 1jg8A 205 :LCAPVGSVVVGD T0339 244 :GLGEFTPLYPMLFGG 1jg8A 218 :DFIERARKARKMLGG T0339 266 :PGTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEER 1jg8A 233 :GMRQAGVLAAAGIIALTKMVDRLKEDHENARFLALKLKEI T0339 314 :RIHLNSQ 1jg8A 273 :GYSVNPE T0339 325 :QRLPNTCNFSIRGPRLQGHVVLAQCRV 1jg8A 280 :DVKTNMVILRTDNLKVNAHGFIEALRN T0339 352 :LMASVGA 1jg8A 309 :VLANAVS T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQAVAQL 1jg8A 316 :DTEIRLVTHKDVSRNDIEEALNIFEKLFRKF Number of specific fragments extracted= 22 number of extra gaps= 1 total=2821 Will force an alignment to be made, even if fragment is small Number of alignments=130 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jg8A/T0339-1jg8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1jg8A/T0339-1jg8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jg8A read from 1jg8A/T0339-1jg8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jg8A in template set Warning: unaligning (T0339)K3 because first residue in template chain is (1jg8A)M5 Warning: unaligning (T0339)L167 because of BadResidue code BAD_PEPTIDE in next template residue (1jg8A)T141 Warning: unaligning (T0339)A168 because of BadResidue code BAD_PEPTIDE at template residue (1jg8A)T141 Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jg8A)G204 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jg8A)G204 T0339 4 :VYMDYNATTPLEPEVIQA 1jg8A 6 :IDLRSDTVTKPTEEMRKA T0339 27 :WEAWGNPSSPYSAG 1jg8A 24 :MAQAEVGDDVYGED T0339 45 :DIINAARESLAKMIGGKP 1jg8A 38 :PTINELERLAAETFGKEA T0339 65 :IIFTSGGTESNNLVIHSVV 1jg8A 56 :ALFVPSGTMGNQVSIMAHT T0339 105 :GAKPHFITSSVEH 1jg8A 75 :QRGDEVILEADSH T0339 120 :IRL 1jg8A 88 :IFW T0339 123 :PLEHL 1jg8A 95 :AMAVL T0339 131 :QVAAVTFVPVS 1jg8A 100 :SGVMPHPVPGK T0339 144 :SGQTEVDDILAAVRP 1jg8A 111 :NGAMDPDDVRKAIRP T0339 160 :TRLVTIM 1jg8A 133 :TSLIAIE T0339 169 :NNET 1jg8A 142 :HNRS T0339 173 :GIVMP 1jg8A 147 :GRVVP T0339 178 :VPEISQRIKALN 1jg8A 155 :IKEICTIAKEHG T0339 200 :ILVHTDAAQALG 1jg8A 167 :INVHIDGARIFN T0339 214 :RVDVEDL 1jg8A 184 :GVPVKEY T0339 221 :GVDFLTIVG 1jg8A 193 :YADSVMFCL T0339 233 :Y 1jg8A 205 :L T0339 234 :GPR 1jg8A 207 :APV T0339 238 :GALYIRGLGEF 1jg8A 210 :GSVVVGDRDFI T0339 256 :FGGGQ 1jg8A 230 :LGGGM T0339 268 :TENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEER 1jg8A 235 :RQAGVLAAAGIIALTKMVDRLKEDHENARFLALKLKEI T0339 311 :G 1jg8A 273 :G T0339 315 :IHL 1jg8A 274 :YSV T0339 322 :PGTQRLPNTCNFSIRGPRLQGHVVLAQCRV 1jg8A 277 :NPEDVKTNMVILRTDNLKVNAHGFIEALRN T0339 352 :LMASV 1jg8A 309 :VLANA T0339 381 :VARNALRLSVGRSTTRAEVDLVVQDLKQAVAQL 1jg8A 314 :VSDTEIRLVTHKDVSRNDIEEALNIFEKLFRKF Number of specific fragments extracted= 26 number of extra gaps= 1 total=2847 Will force an alignment to be made, even if fragment is small Number of alignments=131 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jg8A/T0339-1jg8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1jg8A/T0339-1jg8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jg8A read from 1jg8A/T0339-1jg8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jg8A in template set Warning: unaligning (T0339)K3 because first residue in template chain is (1jg8A)M5 Warning: unaligning (T0339)L167 because of BadResidue code BAD_PEPTIDE in next template residue (1jg8A)T141 Warning: unaligning (T0339)A168 because of BadResidue code BAD_PEPTIDE at template residue (1jg8A)T141 Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jg8A)G204 Warning: unaligning (T0339)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jg8A)G204 T0339 4 :VYMDYNATTPLEPEVIQAMT 1jg8A 6 :IDLRSDTVTKPTEEMRKAMA T0339 29 :AWGNPSSPYSAG 1jg8A 26 :QAEVGDDVYGED T0339 45 :DIINAARESLAKMIGG 1jg8A 38 :PTINELERLAAETFGK T0339 64 :DIIFTSGGTESNNLVIHSV 1jg8A 55 :AALFVPSGTMGNQVSIMAH T0339 104 :KGAKPHFITSSVEHDSIR 1jg8A 74 :TQRGDEVILEADSHIFWY T0339 123 :PLEHL 1jg8A 95 :AMAVL T0339 131 :QVAAVTFVPVS 1jg8A 100 :SGVMPHPVPGK T0339 144 :SGQTEVDDILAAV 1jg8A 111 :NGAMDPDDVRKAI T0339 157 :RPT 1jg8A 127 :NIH T0339 160 :TRLVTIM 1jg8A 133 :TSLIAIE T0339 169 :NNET 1jg8A 142 :HNRS T0339 173 :GIVMP 1jg8A 147 :GRVVP T0339 178 :VPEISQRIKA 1jg8A 155 :IKEICTIAKE T0339 198 :PPILVHTDAAQ 1jg8A 165 :HGINVHIDGAR T0339 209 :ALG 1jg8A 181 :IAS T0339 214 :RVDVEDL 1jg8A 184 :GVPVKEY T0339 221 :GVDFLTIVG 1jg8A 193 :YADSVMFCL T0339 233 :YGPR 1jg8A 205 :LCAP T0339 237 :IGALYIRGLGEFTPLYPMLFGGG 1jg8A 210 :GSVVVGDRDFIERARKARKMLGG T0339 266 :PGTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEER 1jg8A 233 :GMRQAGVLAAAGIIALTKMVDRLKEDHENARFLALKLKEI T0339 311 :G 1jg8A 273 :G T0339 315 :IH 1jg8A 274 :YS T0339 321 :FPGTQRLPNTCNFSIRG 1jg8A 276 :VNPEDVKTNMVILRTDN T0339 338 :PRLQGHVVLAQCRVLMASVG 1jg8A 295 :VNAHGFIEALRNSGVLANAV T0339 382 :ARNALRLSVGRSTTRAEVDLVVQDLKQAVAQL 1jg8A 315 :SDTEIRLVTHKDVSRNDIEEALNIFEKLFRKF Number of specific fragments extracted= 25 number of extra gaps= 1 total=2872 Will force an alignment to be made, even if fragment is small Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dfoA/T0339-1dfoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dfoA expands to /projects/compbio/data/pdb/1dfo.pdb.gz 1dfoA:# T0339 read from 1dfoA/T0339-1dfoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dfoA read from 1dfoA/T0339-1dfoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dfoA to template set # found chain 1dfoA in template set T0339 5 :YM 1dfoA 31 :EL T0339 8 :YNATTPLEPEVIQA 1dfoA 33 :IASENYTSPRVMQA T0339 31 :GNPSSP 1dfoA 58 :GYPGKR T0339 37 :YSAGRKAKDIINAARESLAKMIGG 1dfoA 65 :YGGCEYVDIVEQLAIDRAKELFGA T0339 63 :QDIIFTS 1dfoA 89 :DYANVQP T0339 70 :GGTESNNLVIHSV 1dfoA 97 :SGSQANFAVYTAL T0339 91 :TSKGH 1dfoA 110 :LEPGD T0339 109 :HFITSSVEHDSIR 1dfoA 115 :TVLGMNLAHGGHL T0339 122 :LPLEHL 1dfoA 135 :FSGKLY T0339 134 :AVTFVPVSK 1dfoA 141 :NIVPYGIDA T0339 144 :SGQTEVDDILAAVR 1dfoA 150 :TGHIDYADLEKQAK T0339 158 :PTTRLVT 1dfoA 165 :HKPKMII T0339 167 :LANNETGIVMPVPEISQ 1dfoA 172 :GGFSAYSGVVDWAKMRE T0339 188 :LNQER 1dfoA 189 :IADSI T0339 199 :PILVHTDAAQ 1dfoA 194 :GAYLFVDMAH T0339 209 :ALGKQRVDVED 1dfoA 209 :AAGVYPNPVPH T0339 222 :VDFLTIVGHK 1dfoA 220 :AHVVTTTTHK T0339 232 :FYGPRIGALYIR 1dfoA 231 :LAGPRGGLILAK T0339 245 :LGEFT 1dfoA 248 :LYKKL T0339 251 :LYPMLFGG 1dfoA 253 :NSAVFPGG T0339 266 :PGTENTPMIAGLGKAAELVTQ 1dfoA 261 :QGGPLMHVIAGKAVALKEAME T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1dfoA 283 :EFKTYQQQVAKNAKAMVEVFLER T0339 314 :RIHLNS 1dfoA 306 :GYKVVS T0339 322 :PGTQ 1dfoA 312 :GGTD T0339 328 :PNTCNFSIRGPRLQGHVVLAQCRV 1dfoA 316 :NHLFLVDLVDKNLTGKEADAALGR T0339 352 :LMASVGAACHSDHGDQP 1dfoA 342 :ITVNKNSVPNDPKSPFV T0339 383 :RNALRLSV 1dfoA 359 :TSGIRVGT T0339 391 :GRSTTRAEVDLVVQDLKQAVAQLE 1dfoA 371 :RRGFKEAEAKELAGWMCDVLDSIN Number of specific fragments extracted= 28 number of extra gaps= 0 total=2900 Will force an alignment to be made, even if fragment is small Number of alignments=133 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dfoA/T0339-1dfoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1dfoA/T0339-1dfoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dfoA read from 1dfoA/T0339-1dfoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dfoA in template set T0339 4 :VYM 1dfoA 30 :IEL T0339 8 :YNATTPLEPEVIQAM 1dfoA 33 :IASENYTSPRVMQAQ T0339 26 :MWEAWGN 1dfoA 51 :LTNKYAE T0339 33 :P 1dfoA 60 :P T0339 34 :SSPYSA 1dfoA 65 :YGGCEY T0339 43 :AKDIINAARESLAKMIGGKP 1dfoA 71 :VDIVEQLAIDRAKELFGADY T0339 65 :IIF 1dfoA 91 :ANV T0339 68 :TSGGTESNNLVIHSVV 1dfoA 95 :PHSGSQANFAVYTALL T0339 105 :GAKPHFITSSVEHDSIR 1dfoA 111 :EPGDTVLGMNLAHGGHL T0339 126 :HLVEE 1dfoA 135 :FSGKL T0339 133 :AAVTFVPVSK 1dfoA 140 :YNIVPYGIDA T0339 144 :SGQTEVDDILAAV 1dfoA 150 :TGHIDYADLEKQA T0339 159 :TTRLV 1dfoA 166 :KPKMI T0339 165 :IMLANNETGI 1dfoA 171 :IGGFSAYSGV T0339 176 :MPVPEISQRIKALN 1dfoA 181 :VDWAKMREIADSIG T0339 200 :ILVHTDAAQ 1dfoA 195 :AYLFVDMAH T0339 209 :ALGKQRVDV 1dfoA 209 :AAGVYPNPV T0339 219 :D 1dfoA 218 :P T0339 221 :GVDFLTIVGHKFY 1dfoA 219 :HAHVVTTTTHKTL T0339 234 :GPRIGALYIRGLG 1dfoA 233 :GPRGGLILAKGGS T0339 250 :P 1dfoA 246 :E T0339 251 :LYPMLFGGGQ 1dfoA 252 :LNSAVFPGGQ T0339 267 :GTENTPMIAGLGKAAELVTQ 1dfoA 262 :GGPLMHVIAGKAVALKEAME T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1dfoA 283 :EFKTYQQQVAKNAKAMVEVFLER T0339 311 :G 1dfoA 306 :G T0339 315 :IHLNSQ 1dfoA 307 :YKVVSG T0339 323 :GTQ 1dfoA 313 :GTD T0339 328 :PNTCNFSIRGPRLQGHVVLAQCRV 1dfoA 316 :NHLFLVDLVDKNLTGKEADAALGR T0339 352 :LMASVGAACHSD 1dfoA 342 :ITVNKNSVPNDP T0339 377 :VPFDVA 1dfoA 354 :KSPFVT T0339 384 :NALRLSV 1dfoA 360 :SGIRVGT T0339 391 :GRSTTRAEVDLVVQDLKQAVAQL 1dfoA 371 :RRGFKEAEAKELAGWMCDVLDSI Number of specific fragments extracted= 32 number of extra gaps= 0 total=2932 Will force an alignment to be made, even if fragment is small Number of alignments=134 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dfoA/T0339-1dfoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1dfoA/T0339-1dfoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dfoA read from 1dfoA/T0339-1dfoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dfoA in template set T0339 9 :NATTPLEPEVIQAMTKAMWEAW 1dfoA 34 :ASENYTSPRVMQAQGSQLTNKY T0339 31 :GNPS 1dfoA 58 :GYPG T0339 35 :SPYSAGRKAKDIINAARESLAKMIGG 1dfoA 63 :RYYGGCEYVDIVEQLAIDRAKELFGA T0339 65 :IIFTSGGTESNNLVIHSV 1dfoA 92 :NVQPHSGSQANFAVYTAL T0339 104 :KGAKPHFITSSVEHDSIRLP 1dfoA 110 :LEPGDTVLGMNLAHGGHLTH T0339 124 :LEHL 1dfoA 136 :SGKL T0339 133 :AAVTFVPVS 1dfoA 140 :YNIVPYGID T0339 143 :VSGQTEVDDILAAV 1dfoA 149 :ATGHIDYADLEKQA T0339 163 :VTIMLANNETGI 1dfoA 169 :MIIGGFSAYSGV T0339 176 :MPVPEISQRIKA 1dfoA 181 :VDWAKMREIADS T0339 198 :PPILVHTDAAQ 1dfoA 193 :IGAYLFVDMAH T0339 209 :ALGKQRVDVE 1dfoA 209 :AAGVYPNPVP T0339 221 :GVDFLTIVGHKFYGPR 1dfoA 219 :HAHVVTTTTHKTLAGP T0339 237 :IGALYIRG 1dfoA 236 :GGLILAKG T0339 245 :LGEFTPLYPMLFGG 1dfoA 247 :ELYKKLNSAVFPGG T0339 266 :PGTENTPMIAGLGKAAELVT 1dfoA 261 :QGGPLMHVIAGKAVALKEAM T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1dfoA 282 :PEFKTYQQQVAKNAKAMVEVFLERGYKVVSG T0339 323 :GTQRLPNTCNFSIRGPRLQGHVVLAQCRVLMASVGAACHSDHG 1dfoA 313 :GTDNHLFLVDLVDKNLTGKEADAALGRANITVNKNSVPNDPKS T0339 380 :DVARNALRLSVG 1dfoA 356 :PFVTSGIRVGTP T0339 392 :RSTTRAEVDLVVQDLKQA 1dfoA 372 :RGFKEAEAKELAGWMCDV T0339 410 :VAQLED 1dfoA 399 :IERIKG Number of specific fragments extracted= 21 number of extra gaps= 0 total=2953 Will force an alignment to be made, even if fragment is small Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h0cA/T0339-1h0cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1h0cA expands to /projects/compbio/data/pdb/1h0c.pdb.gz 1h0cA:# T0339 read from 1h0cA/T0339-1h0cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h0cA read from 1h0cA/T0339-1h0cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1h0cA to template set # found chain 1h0cA in template set Warning: unaligning (T0339)V132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h0cA)V123 Warning: unaligning (T0339)V135 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h0cA)V123 T0339 2 :RKVYMDYNATTPLEPEVIQA 1h0cA 21 :PNQLLLGPGPSNLPPRIMAA T0339 30 :WG 1h0cA 41 :GG T0339 33 :PSSPYSAGRKAKDIINAARESLAKMIGGKPQDIIFTSG 1h0cA 43 :LQMIGSMSKDMYQIMDEIKEGIQYVFQTRNPLTLVISG T0339 71 :GTESNNLVIHSV 1h0cA 82 :GHCALEAALVNV T0339 91 :TSKGH 1h0cA 94 :LEPGD T0339 109 :HFITSSVEHDS 1h0cA 99 :SFLVGANGIWG T0339 121 :RLPLEHL 1h0cA 110 :QRAVDIG T0339 129 :EEQ 1h0cA 117 :ERI T0339 136 :TFVPVSK 1h0cA 124 :HPMTKDP T0339 144 :SGQTEVDDILAAVR 1h0cA 131 :GGHYTLQEVEEGLA T0339 158 :PTTRLVTIMLANNETGIVMPVPEISQ 1h0cA 146 :HKPVLLFLTHGESSTGVLQPLDGFGE T0339 188 :LNQER 1h0cA 172 :LCHRY T0339 199 :PILVHTDAAQALGKQRVDVEDLGVDFLTIVGHK 1h0cA 177 :KCLLLVDSVASLGGTPLYMDRQGIDILYSGSQK T0339 232 :FY 1h0cA 211 :LN T0339 234 :GPRIGALYIR 1h0cA 214 :PPGTSLISFS T0339 244 :GLGEFT 1h0cA 225 :KAKKKM T0339 250 :PLYPMLFGGG 1h0cA 232 :SRKTKPFSFY T0339 260 :QERNFRPGTENTPMIAGLGKAAELVTQ 1h0cA 255 :DQPRMYHHTIPVISLYSLRESLALIAE T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1h0cA 283 :GLENSWRQHREAAAYLHGRLQAL T0339 314 :RIHLNSQ 1h0cA 306 :GLQLFVK T0339 322 :PGTQRLPNTCNFSIR 1h0cA 313 :DPALRLPTVTTVAVP T0339 337 :G 1h0cA 329 :G T0339 340 :LQGHVVLAQCRV 1h0cA 330 :YDWRDIVSYVID T0339 352 :LMASVGAACHS 1h0cA 345 :IEIMGGLGPST T0339 383 :RNALRLSV 1h0cA 356 :GKVLRIGL T0339 391 :GRSTTRAEVDLVVQDLKQAVAQL 1h0cA 365 :GCNATRENVDRVTEALRAALQHC Number of specific fragments extracted= 26 number of extra gaps= 0 total=2979 Will force an alignment to be made, even if fragment is small Number of alignments=136 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h0cA/T0339-1h0cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1h0cA/T0339-1h0cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h0cA read from 1h0cA/T0339-1h0cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1h0cA in template set Warning: unaligning (T0339)V132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h0cA)V123 Warning: unaligning (T0339)V135 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h0cA)V123 T0339 1 :ERKVYM 1h0cA 21 :PNQLLL T0339 8 :YNATTPLEPEVIQA 1h0cA 27 :GPGPSNLPPRIMAA T0339 30 :WGN 1h0cA 41 :GGL T0339 34 :SSPYSAGRKAKDIINAARESLAKMIGGKPQDIIFTSG 1h0cA 44 :QMIGSMSKDMYQIMDEIKEGIQYVFQTRNPLTLVISG T0339 71 :GTESNNLVIHSVV 1h0cA 82 :GHCALEAALVNVL T0339 105 :GAKPHFITSSV 1h0cA 95 :EPGDSFLVGAN T0339 118 :DSIRLPLEHLVEEQ 1h0cA 106 :GIWGQRAVDIGERI T0339 136 :TFVPVSK 1h0cA 124 :HPMTKDP T0339 144 :SGQTEVDDILAAV 1h0cA 131 :GGHYTLQEVEEGL T0339 159 :TTRLVTIMLANNETGIVMPVPEISQRIKALN 1h0cA 147 :KPVLLFLTHGESSTGVLQPLDGFGELCHRYK T0339 200 :ILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFY 1h0cA 178 :CLLLVDSVASLGGTPLYMDRQGIDILYSGSQKAL T0339 234 :GP 1h0cA 213 :AP T0339 236 :RIGALYIRG 1h0cA 216 :GTSLISFSD T0339 245 :LG 1h0cA 231 :YS T0339 249 :TPLYPMLFGGGQ 1h0cA 233 :RKTKPFSFYLDI T0339 261 :ERNFRPGTENTPMIAGLGKAAELVTQ 1h0cA 256 :QPRMYHHTIPVISLYSLRESLALIAE T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1h0cA 283 :GLENSWRQHREAAAYLHGRLQAL T0339 311 :G 1h0cA 306 :G T0339 315 :IHLNSQ 1h0cA 307 :LQLFVK T0339 322 :PGTQRLPNTCNFSIRGP 1h0cA 313 :DPALRLPTVTTVAVPAG T0339 340 :LQGHVVLAQCRV 1h0cA 330 :YDWRDIVSYVID T0339 352 :LMASV 1h0cA 343 :FDIEI T0339 376 :GVPFDVARNALRLSV 1h0cA 349 :GGLGPSTGKVLRIGL T0339 391 :GRSTTRAEVDLVVQDLKQAVAQ 1h0cA 365 :GCNATRENVDRVTEALRAALQH Number of specific fragments extracted= 24 number of extra gaps= 0 total=3003 Will force an alignment to be made, even if fragment is small Number of alignments=137 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h0cA/T0339-1h0cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1h0cA/T0339-1h0cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h0cA read from 1h0cA/T0339-1h0cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1h0cA in template set Warning: unaligning (T0339)V132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h0cA)V123 Warning: unaligning (T0339)V135 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h0cA)V123 T0339 6 :MDYNATTPLEPEVIQA 1h0cA 25 :LLGPGPSNLPPRIMAA T0339 36 :PYSAGRKAKDIINAARESLAKMIGGKPQD 1h0cA 46 :IGSMSKDMYQIMDEIKEGIQYVFQTRNPL T0339 65 :IIFTSGGTESNNLVIHSV 1h0cA 76 :LVISGSGHCALEAALVNV T0339 104 :KGAKPHFITSSV 1h0cA 94 :LEPGDSFLVGAN T0339 117 :HDSIRLPLEHL 1h0cA 106 :GIWGQRAVDIG T0339 129 :EEQ 1h0cA 117 :ERI T0339 136 :TFVPVS 1h0cA 124 :HPMTKD T0339 143 :VSGQTEVDDILAAV 1h0cA 130 :PGGHYTLQEVEEGL T0339 159 :TTRLVTIMLANNETGIVMPVPEISQRIKA 1h0cA 147 :KPVLLFLTHGESSTGVLQPLDGFGELCHR T0339 198 :PPILVHTDAAQALGKQRVDVEDLGVDFLTIVGHKFYGPR 1h0cA 176 :YKCLLLVDSVASLGGTPLYMDRQGIDILYSGSQKALNAP T0339 237 :IGALYIRGLGEF 1h0cA 217 :TSLISFSDKAKK T0339 249 :TPLYPMLFGGGQ 1h0cA 232 :SRKTKPFSFYLD T0339 261 :ERNFRPGTENTPMIAGLGKAAELVT 1h0cA 256 :QPRMYHHTIPVISLYSLRESLALIA T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1h0cA 282 :QGLENSWRQHREAAAYLHGRLQALGLQLFVK T0339 322 :PGTQRLPNTCNFSIRG 1h0cA 313 :DPALRLPTVTTVAVPA T0339 338 :PRLQGHVVLAQ 1h0cA 330 :YDWRDIVSYVI T0339 349 :CRVLMASVGAACHSDH 1h0cA 342 :HFDIEIMGGLGPSTGK T0339 385 :ALRLS 1h0cA 358 :VLRIG T0339 390 :VGRSTTRAEVDLVVQDLKQAVAQ 1h0cA 364 :LGCNATRENVDRVTEALRAALQH Number of specific fragments extracted= 19 number of extra gaps= 0 total=3022 Will force an alignment to be made, even if fragment is small Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u08A/T0339-1u08A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u08A expands to /projects/compbio/data/pdb/1u08.pdb.gz 1u08A:# T0339 read from 1u08A/T0339-1u08A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u08A read from 1u08A/T0339-1u08A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u08A to template set # found chain 1u08A in template set T0339 3 :KVYMDYNATTP 1u08A 32 :AINLSQGFPDF T0339 14 :LEPEVIQAMTKAMWE 1u08A 44 :GPRYLQERLAHHVAQ T0339 33 :PSSPYSAGRKAKDIINAARESLAKMIG 1u08A 59 :GANQYAPMTGVQALREAIAQKTERLYG T0339 60 :GKPQ 1u08A 88 :PDAD T0339 64 :DIIFTSGGTESNNLVIHSV 1u08A 93 :DITVTAGATEALYAAITAL T0339 91 :TSKGH 1u08A 112 :VRNGD T0339 109 :HFITSSVEHDSIRLPLEHL 1u08A 117 :EVICFDPSYDSYAPAIALS T0339 132 :VAAVTFVPVSKVSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1u08A 136 :GGIVKRMALQPPHFRVDWQEFAALLSERTRLVILNTPHNPSATVWQQADFAA T0339 185 :IKALNQER 1u08A 188 :LWQAIAGH T0339 199 :PILVHTDAAQALGKQR 1u08A 196 :EIFVISDEVYEHINFS T0339 215 :VD 1u08A 215 :HA T0339 217 :VEDL 1u08A 218 :VLAH T0339 221 :GV 1u08A 227 :RA T0339 224 :FLTIVGHK 1u08A 229 :VAVSSFGK T0339 232 :FY 1u08A 238 :YH T0339 234 :GPRIGALYIR 1u08A 242 :GWKVGYCVAP T0339 244 :GLGEFTPLYPMLF 1u08A 253 :PISAEIRKVHQYL T0339 266 :PGTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEERLEAE 1u08A 266 :TFSVNTPAQLALADMLRAEPEHYLALPDFYRQKRDILVNALNES T0339 314 :RIHLNSQFP 1u08A 310 :RLEILPCEG T0339 328 :PNTCNFSIR 1u08A 319 :TYFLLVDYS T0339 337 :GPRLQGHVVLAQCRV 1u08A 329 :VSTLDDVEFCQWLTQ T0339 352 :LMASVGAACH 1u08A 347 :VAAIPLSVFC T0339 362 :SDHG 1u08A 358 :DPFP T0339 383 :RNALRLSVGR 1u08A 362 :HKLIRLCFAK T0339 395 :TRAEVDLVVQDL 1u08A 372 :KESTLLAAAERL Number of specific fragments extracted= 25 number of extra gaps= 0 total=3047 Will force an alignment to be made, even if fragment is small Number of alignments=139 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u08A/T0339-1u08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1u08A/T0339-1u08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u08A read from 1u08A/T0339-1u08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u08A in template set T0339 4 :VYMDYNATT 1u08A 33 :INLSQGFPD T0339 13 :PLEPEVIQAMTKAMWEAWGN 1u08A 43 :DGPRYLQERLAHHVAQGANQ T0339 33 :PSS 1u08A 66 :MTG T0339 43 :AKDIINAARESLAKMIGG 1u08A 69 :VQALREAIAQKTERLYGY T0339 61 :KPQ 1u08A 89 :DAD T0339 64 :DIIFTSGGTESNNLVIHSVV 1u08A 93 :DITVTAGATEALYAAITALV T0339 105 :GAKPHFITSSVEHDSIRLPLEHL 1u08A 113 :RNGDEVICFDPSYDSYAPAIALS T0339 132 :VAAVTFVPVSKVSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMP 1u08A 136 :GGIVKRMALQPPHFRVDWQEFAALLSERTRLVILNTPHNPSATVWQ T0339 178 :VPEISQRIKALN 1u08A 185 :FAALWQAIAGHE T0339 200 :ILVHTDAAQALGKQR 1u08A 197 :IFVISDEVYEHINFS T0339 217 :V 1u08A 219 :L T0339 219 :DL 1u08A 220 :AH T0339 224 :FLTIVGHKFY 1u08A 229 :VAVSSFGKTY T0339 234 :GPRIGALYIRG 1u08A 242 :GWKVGYCVAPA T0339 246 :G 1u08A 253 :P T0339 261 :ER 1u08A 266 :TF T0339 268 :TENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEERLEAE 1u08A 268 :SVNTPAQLALADMLRAEPEHYLALPDFYRQKRDILVNALNES T0339 311 :G 1u08A 310 :R T0339 315 :IHLN 1u08A 311 :LEIL T0339 323 :GTQRLP 1u08A 315 :PCEGTY T0339 330 :TCNFSI 1u08A 321 :FLLVDY T0339 336 :RGPRLQGHVVLAQCRV 1u08A 328 :AVSTLDDVEFCQWLTQ T0339 352 :LMASVGAACHSDH 1u08A 348 :AAIPLSVFCADPF T0339 382 :ARNALRLSVGR 1u08A 361 :PHKLIRLCFAK T0339 395 :TRAEVDLVVQDL 1u08A 372 :KESTLLAAAERL Number of specific fragments extracted= 25 number of extra gaps= 0 total=3072 Will force an alignment to be made, even if fragment is small Number of alignments=140 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u08A/T0339-1u08A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1u08A/T0339-1u08A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u08A read from 1u08A/T0339-1u08A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u08A in template set T0339 4 :VYMDYNATT 1u08A 33 :INLSQGFPD T0339 13 :PLEPEVIQAMTKAMWEAWGNPS 1u08A 43 :DGPRYLQERLAHHVAQGANQYA T0339 37 :YS 1u08A 67 :TG T0339 43 :AKDIINAARESLAKMIGG 1u08A 69 :VQALREAIAQKTERLYGY T0339 61 :KPQD 1u08A 89 :DADS T0339 65 :IIFTSGGTESNNLVIHSV 1u08A 94 :ITVTAGATEALYAAITAL T0339 104 :KGAKPHFITSSVEHDSIRLPLEHL 1u08A 112 :VRNGDEVICFDPSYDSYAPAIALS T0339 132 :VAAVTFVPVSKVSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMP 1u08A 136 :GGIVKRMALQPPHFRVDWQEFAALLSERTRLVILNTPHNPSATVWQ T0339 178 :VPEISQRIKA 1u08A 185 :FAALWQAIAG T0339 198 :PPILVHTDAAQALGKQRVD 1u08A 195 :HEIFVISDEVYEHINFSQQ T0339 219 :DLGVDFLTIVGHKFYGPR 1u08A 224 :LRERAVAVSSFGKTYHMT T0339 237 :IGALYIRGLGEFTPLYPM 1u08A 245 :VGYCVAPAPISAEIRKVH T0339 265 :RPGTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEERLEAEFG 1u08A 265 :LTFSVNTPAQLALADMLRAEPEHYLALPDFYRQKRDILVNALNESRL T0339 313 :KRIH 1u08A 312 :EILP T0339 325 :QRLPNTCNFSIRG 1u08A 316 :CEGTYFLLVDYSA T0339 338 :PRLQGHVV 1u08A 332 :LDDVEFCQ T0339 346 :LAQCRVLMASVGAACHSDHG 1u08A 341 :LTQEHGVAAIPLSVFCADPF T0339 382 :ARNALRLSVG 1u08A 361 :PHKLIRLCFA T0339 394 :TTRAEVDLVVQDL 1u08A 371 :KKESTLLAAAERL Number of specific fragments extracted= 19 number of extra gaps= 0 total=3091 Will force an alignment to be made, even if fragment is small Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gewA/T0339-1gewA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gewA expands to /projects/compbio/data/pdb/1gew.pdb.gz 1gewA:# T0339 read from 1gewA/T0339-1gewA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gewA read from 1gewA/T0339-1gewA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gewA to template set # found chain 1gewA in template set Warning: unaligning (T0339)L406 because last residue in template chain is (1gewA)L351 T0339 30 :WGNPSSPYS 1gewA 53 :NRYPECQPK T0339 49 :AARESLAKMIGGKPQDIIFTSGGTESNNLVIHSV 1gewA 62 :AVIENYAQYAGVKPEQVLVSRGADEGIELLIRAF T0339 91 :TSKG 1gewA 96 :CEPG T0339 95 :H 1gewA 101 :D T0339 109 :HFITSSVEHDSIRLPLEHL 1gewA 102 :AILYCPPTYGMYSVSAETI T0339 132 :VAAVTFVPVSK 1gewA 121 :GVECRTVPTLD T0339 144 :SGQTEVDDILA 1gewA 132 :NWQLDLQGISD T0339 158 :PTTRLVTIMLANNETGIVMPVPEISQ 1gewA 145 :DGVKVVYVCSPNNPTGQLINPQDFRT T0339 185 :IKALNQE 1gewA 171 :LLELTRG T0339 199 :PILVHTDAAQALGKQR 1gewA 178 :KAIVVADEAYIEFCPQ T0339 215 :VDVEDL 1gewA 195 :SLAGWL T0339 221 :GV 1gewA 202 :EY T0339 223 :DFLTIVGHK 1gewA 206 :LAILRTLSK T0339 232 :FY 1gewA 216 :FA T0339 234 :GPRIGALYIR 1gewA 220 :GLRCGFTLAN T0339 244 :GLGEFT 1gewA 231 :EVINLL T0339 250 :PLYP 1gewA 238 :KVIA T0339 266 :PGTENTPMIAGLGKAA 1gewA 242 :PYPLSTPVADIAAQAL T0339 283 :L 1gewA 261 :G T0339 285 :TQNCEAYEAHMRDVRDYLEERLEA 1gewA 262 :IVAMRERVAQIIAEREYLIAALKE T0339 312 :QKRIHLNSQFP 1gewA 286 :IPCVEQVFDSE T0339 328 :PNTCNFSIR 1gewA 297 :TNYILARFK T0339 341 :QGHVVLAQCRV 1gewA 306 :ASSAVFKSLWD T0339 352 :LMA 1gewA 319 :IIL T0339 357 :GAACHSDHG 1gewA 322 :RDQNKQPSL T0339 383 :RNALRLSVG 1gewA 331 :SGCLRITVG T0339 395 :TRAEVDLVVQD 1gewA 340 :TREESQRVIDA Number of specific fragments extracted= 27 number of extra gaps= 0 total=3118 Will force an alignment to be made, even if fragment is small Number of alignments=142 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gewA/T0339-1gewA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1gewA/T0339-1gewA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gewA read from 1gewA/T0339-1gewA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gewA in template set Warning: unaligning (T0339)L406 because last residue in template chain is (1gewA)L351 T0339 49 :AARESLAKMIGGKPQDIIFTSGGTESNNLVIHSVV 1gewA 62 :AVIENYAQYAGVKPEQVLVSRGADEGIELLIRAFC T0339 104 :KGAKPHFITSSVEHDS 1gewA 97 :EPGKDAILYCPPTYGM T0339 124 :LEHLVEEQVAAVTFVPVSK 1gewA 113 :YSVSAETIGVECRTVPTLD T0339 144 :SGQTEVDDILAAV 1gewA 132 :NWQLDLQGISDKL T0339 158 :PTTRLVTIMLANNETGIVMP 1gewA 145 :DGVKVVYVCSPNNPTGQLIN T0339 178 :VPEISQRIKALN 1gewA 168 :FRTLLELTRGKA T0339 200 :ILVHTDAAQALGKQRVDVEDLG 1gewA 180 :IVVADEAYIEFCPQASLAGWLA T0339 224 :FLTIVGHKFYGP 1gewA 207 :AILRTLSKAFAL T0339 236 :R 1gewA 220 :G T0339 237 :IGALYIR 1gewA 223 :CGFTLAN T0339 246 :GEFTPL 1gewA 238 :KVIAPY T0339 264 :FRP 1gewA 244 :PLS T0339 271 :T 1gewA 247 :T T0339 275 :AGLGKAAELVTQ 1gewA 248 :PVADIAAQALSP T0339 287 :NCEAYEAHMRDVRD 1gewA 261 :GIVAMRERVAQIIA T0339 301 :YLEERLEAEFG 1gewA 278 :YLIAALKEIPC T0339 315 :IHLNSQFP 1gewA 289 :VEQVFDSE T0339 328 :PNTCNFSIRG 1gewA 297 :TNYILARFKA T0339 342 :GHVVLAQCRV 1gewA 307 :SSAVFKSLWD T0339 352 :LMASV 1gewA 319 :IILRD T0339 362 :S 1gewA 324 :Q T0339 377 :VPFDVARNALRLSVGR 1gewA 325 :NKQPSLSGCLRITVGT T0339 396 :RAEVDLVVQD 1gewA 341 :REESQRVIDA Number of specific fragments extracted= 23 number of extra gaps= 0 total=3141 Will force an alignment to be made, even if fragment is small Number of alignments=143 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gewA/T0339-1gewA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1gewA/T0339-1gewA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gewA read from 1gewA/T0339-1gewA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gewA in template set Warning: unaligning (T0339)L406 because last residue in template chain is (1gewA)L351 T0339 14 :LEPEVIQAMTKAM 1gewA 59 :QPKAVIENYAQYA T0339 59 :GGKPQDIIFTSGGTESNNLVIHSV 1gewA 72 :GVKPEQVLVSRGADEGIELLIRAF T0339 103 :VKGAKPHFITSSVEHDSIRLPLEHL 1gewA 96 :CEPGKDAILYCPPTYGMYSVSAETI T0339 132 :VAAVTFVPVS 1gewA 121 :GVECRTVPTL T0339 143 :VSGQTEVDDILAAV 1gewA 131 :DNWQLDLQGISDKL T0339 158 :PTTRLVTIMLANNETGIVMP 1gewA 145 :DGVKVVYVCSPNNPTGQLIN T0339 178 :VPEISQRIK 1gewA 168 :FRTLLELTR T0339 198 :PPILVHTDAAQALGKQRVD 1gewA 177 :GKAIVVADEAYIEFCPQAS T0339 217 :VEDLGVDFLTIVGHKFYGPR 1gewA 200 :LAEYPHLAILRTLSKAFALA T0339 237 :IGALYIRGLGEFTPLYPMLFGGG 1gewA 223 :CGFTLANEEVINLLMKVIAPYPL T0339 270 :NTP 1gewA 246 :STP T0339 276 :GLGKAAELVT 1gewA 249 :VADIAAQALS T0339 286 :QNCEAYEAHMRDV 1gewA 260 :QGIVAMRERVAQI T0339 299 :RDYLEERLEAEFGQKRIH 1gewA 276 :REYLIAALKEIPCVEQVF T0339 325 :QRLPNTCNFSIRG 1gewA 294 :DSETNYILARFKA T0339 340 :LQGHVVLAQCRVLMASVG 1gewA 307 :SSAVFKSLWDQGIILRDQ T0339 377 :VPFDVARNALRLSVG 1gewA 325 :NKQPSLSGCLRITVG T0339 395 :TRAEVDLVVQD 1gewA 340 :TREESQRVIDA Number of specific fragments extracted= 18 number of extra gaps= 0 total=3159 Will force an alignment to be made, even if fragment is small Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ibjA/T0339-1ibjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ibjA expands to /projects/compbio/data/pdb/1ibj.pdb.gz 1ibjA:# T0339 read from 1ibjA/T0339-1ibjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ibjA read from 1ibjA/T0339-1ibjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ibjA to template set # found chain 1ibjA in template set Warning: unaligning (T0339)Q312 because of BadResidue code BAD_PEPTIDE in next template residue (1ibjA)P350 Warning: unaligning (T0339)K313 because of BadResidue code BAD_PEPTIDE at template residue (1ibjA)P350 T0339 31 :GNPSSP 1ibjA 118 :SAIENG T0339 37 :YSAGRKAKDIINAARESLAKMIGG 1ibjA 125 :YDYTRSGNPTRDALESLLAKLDKA T0339 63 :QDIIFTSGGTESNNLVIHS 1ibjA 149 :DRAFCFTSGMAALSAVTHL T0339 91 :TSKGH 1ibjA 168 :IKNGE T0339 109 :HFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSK 1ibjA 173 :EIVAGDDVYGGSDRLLSQVVPRSGVVVKRVNTTK T0339 149 :VDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1ibjA 207 :LDEVAAAIGPQTKLVWLESPTNPRQQISDIRKISE T0339 188 :LNQER 1ibjA 242 :MAHAQ T0339 199 :PILVHTDAAQALGKQRVDV 1ibjA 247 :GALVLVDNSIMSPVLSRPL T0339 219 :DLGVDFLTIVGHK 1ibjA 266 :ELGADIVMHSATK T0339 232 :FYGPR 1ibjA 280 :IAGHS T0339 237 :IGALYIR 1ibjA 288 :AGVLAVK T0339 244 :G 1ibjA 296 :E T0339 245 :LGEFTPLYPMLFG 1ibjA 298 :LAKEVYFLQNSEG T0339 267 :GTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLE 1ibjA 311 :SGLAPFDCWLCLRGIKTMALRIEKQQENARKIAMYLS T0339 308 :A 1ibjA 348 :S T0339 314 :RIHLNS 1ibjA 351 :RVKKVY T0339 323 :GTQRLPNTCNFSIRG 1ibjA 372 :QAKGAGSVFSFITGS T0339 340 :LQ 1ibjA 387 :VA T0339 342 :GHVVLAQCRV 1ibjA 390 :SKHLVETTKY T0339 352 :LMASVGAACH 1ibjA 402 :IAVSFGSVKS T0339 362 :SDHGDQPSPVLLSYGVPFDVARNALRLSVGRS 1ibjA 415 :MPCFMSHASIPAEVREARGLTEDLVRISAGIE T0339 398 :EVDLVVQDLKQAVA 1ibjA 447 :DVDDLISDLDIAFK Number of specific fragments extracted= 22 number of extra gaps= 1 total=3181 Will force an alignment to be made, even if fragment is small Number of alignments=145 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ibjA/T0339-1ibjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1ibjA/T0339-1ibjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ibjA read from 1ibjA/T0339-1ibjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ibjA in template set Warning: unaligning (T0339)E309 because of BadResidue code BAD_PEPTIDE in next template residue (1ibjA)P350 Warning: unaligning (T0339)F310 because of BadResidue code BAD_PEPTIDE at template residue (1ibjA)P350 T0339 34 :SSPYSAGRKAKDIINAARESLAKMIGG 1ibjA 122 :NGPYDYTRSGNPTRDALESLLAKLDKA T0339 63 :QDIIFTSGGTESNNLVIHSV 1ibjA 149 :DRAFCFTSGMAALSAVTHLI T0339 105 :GAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSK 1ibjA 169 :KNGEEIVAGDDVYGGSDRLLSQVVPRSGVVVKRVNTTK T0339 149 :VDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKALN 1ibjA 207 :LDEVAAAIGPQTKLVWLESPTNPRQQISDIRKISEMAHAQG T0339 200 :ILVHTDAAQALGKQRVDV 1ibjA 248 :ALVLVDNSIMSPVLSRPL T0339 219 :DLGVDFLTIVGHKFY 1ibjA 266 :ELGADIVMHSATKFI T0339 234 :GP 1ibjA 282 :GH T0339 236 :R 1ibjA 285 :D T0339 237 :IGALYIRGLGEFTPLYPMLFGGGQERNFRPGTENTPMIAGLGKAAELVTQ 1ibjA 288 :AGVLAVKGEKLAKEVYFLQNSEGSGLAPFDCWLCLRGIKTMALRIEKQQE T0339 294 :HMRDVRD 1ibjA 338 :NARKIAM T0339 305 :RLEA 1ibjA 345 :YLSS T0339 311 :GQKRIHLNSQFP 1ibjA 351 :RVKKVYYAGLPD T0339 323 :GTQRLPNTCNFSIRG 1ibjA 372 :QAKGAGSVFSFITGS T0339 342 :GHVVLAQCRV 1ibjA 387 :VALSKHLVET T0339 352 :LMASVG 1ibjA 402 :IAVSFG T0339 358 :AACHSDHGDQPSPVLLSYGVPFDVARNALRLSVGR 1ibjA 411 :SLISMPCFMSHASIPAEVREARGLTEDLVRISAGI T0339 397 :AEVDLVVQDLKQAVA 1ibjA 446 :EDVDDLISDLDIAFK Number of specific fragments extracted= 17 number of extra gaps= 1 total=3198 Will force an alignment to be made, even if fragment is small Number of alignments=146 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ibjA/T0339-1ibjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1ibjA/T0339-1ibjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ibjA read from 1ibjA/T0339-1ibjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ibjA in template set Warning: unaligning (T0339)E309 because of BadResidue code BAD_PEPTIDE in next template residue (1ibjA)P350 Warning: unaligning (T0339)F310 because of BadResidue code BAD_PEPTIDE at template residue (1ibjA)P350 T0339 45 :DIINAARESLAKMIGG 1ibjA 133 :PTRDALESLLAKLDKA T0339 63 :QDIIFTSGGTESNNLVIHSV 1ibjA 149 :DRAFCFTSGMAALSAVTHLI T0339 105 :GAKPHFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVS 1ibjA 169 :KNGEEIVAGDDVYGGSDRLLSQVVPRSGVVVKRVNTT T0339 148 :EVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQRIKA 1ibjA 206 :KLDEVAAAIGPQTKLVWLESPTNPRQQISDIRKISEMAHA T0339 198 :PPILVHTDAAQALGKQRVDV 1ibjA 246 :QGALVLVDNSIMSPVLSRPL T0339 219 :DLGVDFLTIVGHKFYGPR 1ibjA 266 :ELGADIVMHSATKFIAGH T0339 237 :IGALYIRGLGEFTP 1ibjA 288 :AGVLAVKGEKLAKE T0339 262 :RNFRPGTENTP 1ibjA 307 :NSEGSGLAPFD T0339 277 :LGKAAELVT 1ibjA 318 :CWLCLRGIK T0339 286 :QNCEAYEA 1ibjA 330 :LRIEKQQE T0339 298 :VRDYLEERLEA 1ibjA 338 :NARKIAMYLSS T0339 311 :GQKRIHL 1ibjA 351 :RVKKVYY T0339 318 :NSQFP 1ibjA 360 :LPDHP T0339 323 :GTQRLPNTCNFSIR 1ibjA 372 :QAKGAGSVFSFITG T0339 339 :RLQGHVVLAQ 1ibjA 386 :SVALSKHLVE T0339 350 :RVLMASVGAACHSDHG 1ibjA 409 :VKSLISMPCFMSHASI T0339 378 :PFDVAR 1ibjA 425 :PAEVRE T0339 384 :NALRLSVGRSTTR 1ibjA 437 :DLVRISAGIEDVD T0339 401 :LVVQDLKQAVA 1ibjA 450 :DLISDLDIAFK Number of specific fragments extracted= 19 number of extra gaps= 1 total=3217 Will force an alignment to be made, even if fragment is small Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kkjA/T0339-1kkjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kkjA expands to /projects/compbio/data/pdb/1kkj.pdb.gz 1kkjA:# T0339 read from 1kkjA/T0339-1kkjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kkjA read from 1kkjA/T0339-1kkjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kkjA to template set # found chain 1kkjA in template set Warning: unaligning (T0339)L167 because of BadResidue code BAD_PEPTIDE in next template residue (1kkjA)A170 Warning: unaligning (T0339)A168 because of BadResidue code BAD_PEPTIDE at template residue (1kkjA)A170 Warning: unaligning (T0339)L255 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1kkjA)P252 Warning: unaligning (T0339)F256 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1kkjA)P252 T0339 4 :VYM 1kkjA 26 :IEL T0339 8 :YNATTPLEPEVIQA 1kkjA 29 :IASENFVSRAVMEA T0339 31 :GNPSSP 1kkjA 54 :GYPGRR T0339 37 :YSAGRKAKDIINAARESLAKMIGG 1kkjA 61 :YGGCEYVDIVEELARERAKQLFGA T0339 63 :QDIIFTS 1kkjA 85 :EHANVQP T0339 70 :GGTESNNLVIHSV 1kkjA 93 :SGAQANMAVYFTV T0339 91 :TSKGH 1kkjA 106 :LEHGD T0339 109 :HFITSSVEHDSIR 1kkjA 111 :TVLGMNLSHGGHL T0339 122 :LPLEHL 1kkjA 131 :FSGVQY T0339 134 :AVTFVPVSKVSGQTEVDDILAAVR 1kkjA 137 :NFVAYGVDPETHVIDYDDVREKAR T0339 158 :PTTRLVT 1kkjA 162 :HRPKLIV T0339 169 :NNETGIVMPVPEISQ 1kkjA 171 :ASAYPRIIDFAKFRE T0339 188 :LNQER 1kkjA 186 :IADEV T0339 199 :PILVHTDAAQ 1kkjA 191 :GAYLMVDMAH T0339 209 :ALGKQ 1kkjA 203 :GLVAA T0339 215 :VD 1kkjA 210 :HP T0339 217 :VED 1kkjA 214 :VPY T0339 222 :VDFLTIVGHK 1kkjA 217 :AHFVTTTTHK T0339 232 :FYGPRIGALYIR 1kkjA 228 :LRGPRGGMILCQ T0339 244 :GLGEFT 1kkjA 241 :QFAKQI T0339 251 :LYPM 1kkjA 247 :DKAI T0339 257 :G 1kkjA 253 :G T0339 266 :PGTENTPMIAGLGK 1kkjA 254 :IQGGPLMHVIAAKA T0339 280 :AAELVTQ 1kkjA 269 :AFGEALQ T0339 287 :NCEAYEAHMRDVRDYLEERLEAE 1kkjA 277 :DFKAYAKRVVDNAKRLASALQNE T0339 314 :RIHLNS 1kkjA 300 :GFTLVS T0339 322 :PGTQ 1kkjA 306 :GGTD T0339 328 :PNTCNFSIRGPRLQGHVVLAQCRV 1kkjA 310 :NHLLLVDLRPQQLTGKTAEKVLDE T0339 352 :LMASVGAACHSDHGDQP 1kkjA 336 :ITVNKNTIPYDPESPFV T0339 383 :RNALRLSV 1kkjA 353 :TSGIRIGT T0339 391 :GRSTTRAEVDLVVQDLKQA 1kkjA 365 :TRGFGLEEMDEIAAIIGLV T0339 410 :VAQLED 1kkjA 393 :LEEARQ Number of specific fragments extracted= 32 number of extra gaps= 2 total=3249 Will force an alignment to be made, even if fragment is small Number of alignments=148 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kkjA/T0339-1kkjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1kkjA/T0339-1kkjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kkjA read from 1kkjA/T0339-1kkjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kkjA in template set Warning: unaligning (T0339)I165 because of BadResidue code BAD_PEPTIDE in next template residue (1kkjA)A170 Warning: unaligning (T0339)M166 because of BadResidue code BAD_PEPTIDE at template residue (1kkjA)A170 Warning: unaligning (T0339)F256 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1kkjA)P252 Warning: unaligning (T0339)G257 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1kkjA)P252 T0339 4 :VYM 1kkjA 26 :IEL T0339 8 :YNATTPLEPEVIQAM 1kkjA 29 :IASENFVSRAVMEAQ T0339 27 :WEAWGN 1kkjA 48 :TNKYAE T0339 33 :P 1kkjA 56 :P T0339 34 :SSPYSA 1kkjA 61 :YGGCEY T0339 43 :AKDIINAARESLAKMIGG 1kkjA 67 :VDIVEELARERAKQLFGA T0339 63 :QDIIFTS 1kkjA 85 :EHANVQP T0339 70 :GGTESNNLVIHSVV 1kkjA 93 :SGAQANMAVYFTVL T0339 105 :GAKPHFITSSVEHDSI 1kkjA 107 :EHGDTVLGMNLSHGGH T0339 123 :PLEHL 1kkjA 131 :FSGVQ T0339 133 :AAVTFVPVSKVSGQTEVDDILAAV 1kkjA 136 :YNFVAYGVDPETHVIDYDDVREKA T0339 159 :TTRLVT 1kkjA 163 :RPKLIV T0339 167 :LAN 1kkjA 171 :ASA T0339 172 :TGIVMPVPEISQRIKALN 1kkjA 174 :YPRIIDFAKFREIADEVG T0339 200 :ILVHTDAAQ 1kkjA 192 :AYLMVDMAH T0339 209 :ALGKQRVDVE 1kkjA 206 :AAGLHPNPVP T0339 221 :GVDFLTIVGHKFY 1kkjA 216 :YAHFVTTTTHKTL T0339 234 :GPRIGALYIRG 1kkjA 230 :GPRGGMILCQE T0339 246 :GEFTPLYPML 1kkjA 241 :QFAKQIDKAI T0339 258 :G 1kkjA 253 :G T0339 265 :RPGTENTPMIAGLGKAAELVTQ 1kkjA 254 :IQGGPLMHVIAAKAVAFGEALQ T0339 287 :NCEAYEAHMRDVRDYLEERLEA 1kkjA 277 :DFKAYAKRVVDNAKRLASALQN T0339 310 :FG 1kkjA 299 :EG T0339 315 :IHLNSQ 1kkjA 301 :FTLVSG T0339 323 :GTQ 1kkjA 307 :GTD T0339 328 :PNTCNFSIRGPRLQGHVVLAQCRVLMASVG 1kkjA 310 :NHLLLVDLRPQQLTGKTAEKVLDEVGITVN T0339 360 :CHSDHG 1kkjA 341 :NTIPYD T0339 376 :GVPFDVA 1kkjA 347 :PESPFVT T0339 384 :NALRLSV 1kkjA 354 :SGIRIGT T0339 391 :GRSTTRAEVDLVVQDLKQA 1kkjA 365 :TRGFGLEEMDEIAAIIGLV T0339 410 :VAQLED 1kkjA 393 :LEEARQ Number of specific fragments extracted= 31 number of extra gaps= 2 total=3280 Will force an alignment to be made, even if fragment is small Number of alignments=149 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kkjA/T0339-1kkjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1kkjA/T0339-1kkjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kkjA read from 1kkjA/T0339-1kkjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kkjA in template set Warning: unaligning (T0339)L167 because of BadResidue code BAD_PEPTIDE in next template residue (1kkjA)A170 Warning: unaligning (T0339)A168 because of BadResidue code BAD_PEPTIDE at template residue (1kkjA)A170 Warning: unaligning (T0339)L255 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1kkjA)P252 Warning: unaligning (T0339)F256 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1kkjA)P252 T0339 9 :NATTPLEPEVIQAM 1kkjA 30 :ASENFVSRAVMEAQ T0339 29 :AWGNPS 1kkjA 52 :AEGYPG T0339 35 :SPYSAGRKAKDIINAARESLAKMIGG 1kkjA 59 :RYYGGCEYVDIVEELARERAKQLFGA T0339 65 :IIFTSGGTESNNLVIHSV 1kkjA 88 :NVQPHSGAQANMAVYFTV T0339 104 :KGAKPHFITSSVEHDSIRLP 1kkjA 106 :LEHGDTVLGMNLSHGGHLTH T0339 124 :LEHL 1kkjA 132 :SGVQ T0339 133 :AAVTFVPVSKVSGQTEVDDILAAV 1kkjA 136 :YNFVAYGVDPETHVIDYDDVREKA T0339 161 :R 1kkjA 165 :K T0339 164 :TIM 1kkjA 166 :LIV T0339 169 :NNETGIVMPVPEISQRIKA 1kkjA 171 :ASAYPRIIDFAKFREIADE T0339 198 :PPILVHTDAAQ 1kkjA 190 :VGAYLMVDMAH T0339 209 :ALGKQRVDVE 1kkjA 206 :AAGLHPNPVP T0339 221 :GVDFLTIVGHKFYGPR 1kkjA 216 :YAHFVTTTTHKTLRGP T0339 237 :IGALYIRGLGEFTPLYPM 1kkjA 233 :GGMILCQEQFAKQIDKAI T0339 257 :GG 1kkjA 253 :GI T0339 266 :PGTENTPMIAGLGKAAELVT 1kkjA 255 :QGGPLMHVIAAKAVAFGEAL T0339 286 :QNCEAYEAHMRDVRDYLEERLEA 1kkjA 276 :DDFKAYAKRVVDNAKRLASALQN T0339 310 :FGQKRIH 1kkjA 299 :EGFTLVS T0339 322 :PGTQRLPNTCNFSIRGPRLQGHVVLAQCRVLMASVGAACHSDHG 1kkjA 306 :GGTDNHLLLVDLRPQQLTGKTAEKVLDEVGITVNKNTIPYDPES T0339 380 :DVARNALRLSVG 1kkjA 350 :PFVTSGIRIGTA T0339 392 :RSTTRAEVDLVVQDLK 1kkjA 366 :RGFGLEEMDEIAAIIG T0339 408 :QAVAQLED 1kkjA 391 :QALEEARQ Number of specific fragments extracted= 22 number of extra gaps= 2 total=3302 Will force an alignment to be made, even if fragment is small Number of alignments=150 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gd9A/T0339-1gd9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gd9A expands to /projects/compbio/data/pdb/1gd9.pdb.gz 1gd9A:# T0339 read from 1gd9A/T0339-1gd9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gd9A read from 1gd9A/T0339-1gd9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gd9A to template set # found chain 1gd9A in template set Warning: unaligning (T0339)E1 because of BadResidue code BAD_PEPTIDE in next template residue (1gd9A)D27 Warning: unaligning (T0339)R2 because of BadResidue code BAD_PEPTIDE at template residue (1gd9A)D27 T0339 3 :KVYMDYNATTP 1gd9A 28 :VISLGIGEPDF T0339 14 :LEPEVIQAMTKAMWE 1gd9A 40 :TPQHIKEYAKEALDK T0339 33 :PSSPYSAGRKAKDIINAARESLAKMIG 1gd9A 55 :GLTHYGPNIGLLELREAIAEKLKKQNG T0339 60 :GKPQ 1gd9A 84 :ADPK T0339 64 :DIIFTSGGTESNNLVIHSV 1gd9A 89 :EIMVLLGANQAFLMGLSAF T0339 91 :TSKGH 1gd9A 108 :LKDGE T0339 109 :HFITSSVEHDSIRLPLEHL 1gd9A 113 :EVLIPTPAFVSYAPAVILA T0339 132 :VAAVTFVPVSKV 1gd9A 132 :GGKPVEVPTYEE T0339 144 :SGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1gd9A 145 :EFRLNVDELKKYVTDKTRALIINSPCNPTGAVLTKKDLEE T0339 185 :IKALNQER 1gd9A 185 :IADFVVEH T0339 199 :PILVHTDAAQALGKQR 1gd9A 193 :DLIVISDEVYEHFIYD T0339 215 :VD 1gd9A 212 :HY T0339 217 :VEDL 1gd9A 215 :IASL T0339 221 :GV 1gd9A 220 :GM T0339 223 :DFLTIVGHK 1gd9A 225 :TITVNGFSK T0339 232 :FY 1gd9A 235 :FA T0339 234 :GPRIGALYIR 1gd9A 239 :GWRLGFVAAP T0339 244 :GLGEFTPLYPMLF 1gd9A 250 :WIIERMVKFQMYN T0339 266 :PGTENTPMIAGLGKAAE 1gd9A 263 :ATCPVTFIQYAAAKALK T0339 283 :LVTQNCEAYEAHMRDVRDYLEERLEAE 1gd9A 282 :RSWKAVEEMRKEYDRRRKLVWKRLNEM T0339 314 :RIHLNSQFP 1gd9A 309 :GLPTVKPKG T0339 328 :PNTCNFSIRGPRLQGHVVLAQCRV 1gd9A 318 :AFYIFPRIRDTGLTSKKFSELMLK T0339 352 :LMASVGAACH 1gd9A 345 :VAVVPGSAFG T0339 380 :DVARNALRLS 1gd9A 355 :KAGEGYVRIS T0339 392 :RSTTRAEVDLVVQDLKQAVAQL 1gd9A 365 :YATAYEKLEEAMDRMERVLKER Number of specific fragments extracted= 25 number of extra gaps= 1 total=3327 Will force an alignment to be made, even if fragment is small Number of alignments=151 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gd9A/T0339-1gd9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1gd9A/T0339-1gd9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gd9A read from 1gd9A/T0339-1gd9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gd9A in template set Warning: unaligning (T0339)E1 because of BadResidue code BAD_PEPTIDE in next template residue (1gd9A)D27 Warning: unaligning (T0339)R2 because of BadResidue code BAD_PEPTIDE at template residue (1gd9A)D27 T0339 3 :KVYMDYNATT 1gd9A 28 :VISLGIGEPD T0339 13 :PLEPEVIQAMTKAM 1gd9A 39 :DTPQHIKEYAKEAL T0339 28 :EAWGNPSSPYSA 1gd9A 53 :DKGLTHYGPNIG T0339 43 :AKDIINAARESLAKMIGG 1gd9A 65 :LLELREAIAEKLKKQNGI T0339 61 :KPQ 1gd9A 85 :DPK T0339 64 :DIIFTSGGTESNNLVIHSVV 1gd9A 89 :EIMVLLGANQAFLMGLSAFL T0339 105 :GAKPHFITSSVEHDSIRLPLEHL 1gd9A 109 :KDGEEVLIPTPAFVSYAPAVILA T0339 132 :VAAVTFVPVSKVSG 1gd9A 132 :GGKPVEVPTYEEDE T0339 146 :QTEVDDILAAVRPTTRLVTIMLANNETGIVMP 1gd9A 147 :RLNVDELKKYVTDKTRALIINSPCNPTGAVLT T0339 178 :VPEISQRIKALN 1gd9A 182 :LEEIADFVVEHD T0339 200 :ILVHTDAAQALGKQ 1gd9A 194 :LIVISDEVYEHFIY T0339 215 :VDVEDLG 1gd9A 213 :YSIASLD T0339 223 :DFLTIVGHKFYGP 1gd9A 225 :TITVNGFSKTFAM T0339 236 :R 1gd9A 239 :G T0339 237 :IGALYIRG 1gd9A 242 :LGFVAAPS T0339 246 :GEFTPLYPMLFGG 1gd9A 250 :WIIERMVKFQMYN T0339 266 :PGTENTPMIAGLGKAA 1gd9A 263 :ATCPVTFIQYAAAKAL T0339 282 :ELVTQNCEAYEAHMRDVRDYLEERLEAE 1gd9A 281 :ERSWKAVEEMRKEYDRRRKLVWKRLNEM T0339 311 :G 1gd9A 309 :G T0339 315 :IHLNSQ 1gd9A 310 :LPTVKP T0339 326 :RLPNTCNFSIRGPRLQGHVVLAQCRV 1gd9A 316 :KGAFYIFPRIRDTGLTSKKFSELMLK T0339 352 :LMASVGAACH 1gd9A 345 :VAVVPGSAFG T0339 380 :DVARNALRLSVGR 1gd9A 355 :KAGEGYVRISYAT T0339 395 :TRAEVDLVVQDLKQAVAQ 1gd9A 368 :AYEKLEEAMDRMERVLKE Number of specific fragments extracted= 24 number of extra gaps= 1 total=3351 Will force an alignment to be made, even if fragment is small Number of alignments=152 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gd9A/T0339-1gd9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0339 read from 1gd9A/T0339-1gd9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gd9A read from 1gd9A/T0339-1gd9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gd9A in template set Warning: unaligning (T0339)R2 because of BadResidue code BAD_PEPTIDE at template residue (1gd9A)D27 T0339 3 :KVYMDYNATT 1gd9A 28 :VISLGIGEPD T0339 13 :PLEPEVIQAMTKAMWEAWGNPS 1gd9A 39 :DTPQHIKEYAKEALDKGLTHYG T0339 35 :SPY 1gd9A 62 :NIG T0339 43 :AKDIINAARESLAKMIGG 1gd9A 65 :LLELREAIAEKLKKQNGI T0339 61 :KPQD 1gd9A 85 :DPKT T0339 65 :IIFTSGGTESNNLVIHSV 1gd9A 90 :IMVLLGANQAFLMGLSAF T0339 104 :KGAKPHFITSSVEHDSIRLPLEHL 1gd9A 108 :LKDGEEVLIPTPAFVSYAPAVILA T0339 132 :VAAVTFVPVS 1gd9A 132 :GGKPVEVPTY T0339 142 :KVSGQTEVDDILAAVRPTTRLVTIMLANNETGIVMP 1gd9A 143 :EDEFRLNVDELKKYVTDKTRALIINSPCNPTGAVLT T0339 178 :VPEISQRIKA 1gd9A 182 :LEEIADFVVE T0339 198 :PPILVHTDAAQ 1gd9A 192 :HDLIVISDEVY T0339 209 :ALGKQRVD 1gd9A 204 :HFIYDDAR T0339 217 :VEDLGV 1gd9A 216 :ASLDGM T0339 223 :DFLTIVGHKFYGPR 1gd9A 225 :TITVNGFSKTFAMT T0339 237 :IGALYIRGLGEFTPLYPMLFG 1gd9A 242 :LGFVAAPSWIIERMVKFQMYN T0339 266 :PGTENTPMIAGLGKAAELVT 1gd9A 263 :ATCPVTFIQYAAAKALKDER T0339 286 :QNCEAYEAHMRDVRDYLEERLEAEFGQKRIH 1gd9A 285 :KAVEEMRKEYDRRRKLVWKRLNEMGLPTVKP T0339 326 :RLPNTCNFSIR 1gd9A 316 :KGAFYIFPRIR T0339 337 :GPRLQGHVVLAQ 1gd9A 329 :GLTSKKFSELML T0339 349 :CRVLMASVGAACH 1gd9A 342 :EARVAVVPGSAFG T0339 380 :DVARNALRLSVG 1gd9A 355 :KAGEGYVRISYA T0339 394 :TTRAEVDLVVQDLKQAVAQ 1gd9A 367 :TAYEKLEEAMDRMERVLKE Number of specific fragments extracted= 22 number of extra gaps= 1 total=3373 Will force an alignment to be made, even if fragment is small Number of alignments=153 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kmjA/T0339-1kmjA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kmjA expands to /projects/compbio/data/pdb/1kmj.pdb.gz 1kmjA:# T0339 read from 1kmjA/T0339-1kmjA-t06-local-adpstyle5.a2m # 1kmjA read from 1kmjA/T0339-1kmjA-t06-local-adpstyle5.a2m # adding 1kmjA to template set # found chain 1kmjA in template set Warning: unaligning (T0339)P33 because of BadResidue code BAD_PEPTIDE in next template residue (1kmjA)H55 Warning: unaligning (T0339)S34 because of BadResidue code BAD_PEPTIDE at template residue (1kmjA)H55 Warning: unaligning (T0339)L162 because of BadResidue code BAD_PEPTIDE in next template residue (1kmjA)L168 Warning: unaligning (T0339)V163 because of BadResidue code BAD_PEPTIDE at template residue (1kmjA)L168 Warning: unaligning (T0339)Q260 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1kmjA)P271 Warning: unaligning (T0339)E261 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1kmjA)P271 Warning: unaligning (T0339)A359 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kmjA)A365 Warning: unaligning (T0339)H361 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kmjA)A365 T0339 3 :KVYMDYNATTPLEPEVIQAMTKAMWEAWGN 1kmjA 24 :LAYLDSAASAQKPSQVIDAEAEFYRHGYAA T0339 35 :SP 1kmjA 56 :RG T0339 37 :YSAGRKAKDIINAARESLAKMIGGKPQ 1kmjA 59 :HTLSAQATEKMENVRKRASLFINARSA T0339 64 :DIIFTSGGTESNNLVIHSVVKHF 1kmjA 87 :ELVFVRGTTEGINLVANSWGNSN T0339 91 :TSKGH 1kmjA 110 :VRAGD T0339 109 :HFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSK 1kmjA 115 :NIIISQMEHHANIVPWQMLCARVGAELRVIPLNP T0339 144 :SGQTEVDDILAAVRPTTR 1kmjA 149 :DGTLQLETLPTLFDEKTR T0339 164 :TIMLANNETGIVMPVPEISQ 1kmjA 169 :AITHVSNVLGTENPLAEMIT T0339 188 :LNQER 1kmjA 189 :LAHQH T0339 199 :PILVHTDAAQALGKQRVDVEDLGVDFLTIVGHK 1kmjA 194 :GAKVLVDGAQAVMHHPVDVQALDCDFYVFSGHK T0339 232 :FYGPRIGALYIR 1kmjA 228 :YGPTGIGILYVK T0339 244 :GLGEF 1kmjA 241 :ALLQE T0339 251 :LYPMLFGGG 1kmjA 246 :MPPWEGGGS T0339 262 :RNFRPGTENTPMIAGLGKAAELVTQ 1kmjA 272 :WRFEAGTPNTGGIIGLGAALEYVSA T0339 287 :NCEAYEAHMRDVRDYLEERLEA 1kmjA 298 :GLNNIAEYEQNLMHYALSQLES T0339 312 :QKRIHLNSQFPG 1kmjA 320 :VPDLTLYGPQNR T0339 328 :PNTCNFSIRG 1kmjA 332 :LGVIAFNLGK T0339 340 :LQGHVVLAQCRV 1kmjA 342 :HHAYDVGSFLDN T0339 352 :LMASVGA 1kmjA 356 :IAVRTGH T0339 362 :SDHGDQPSP 1kmjA 366 :MPLMAYYNV T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQAV 1kmjA 375 :PAMCRASLAMYNTHEEVDRLVTGLQRIH Number of specific fragments extracted= 21 number of extra gaps= 3 total=3394 Will force an alignment to be made, even if fragment is small Number of alignments=154 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kmkA/T0339-1kmkA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kmkA expands to /projects/compbio/data/pdb/1kmk.pdb.gz 1kmkA:# T0339 read from 1kmkA/T0339-1kmkA-t06-local-adpstyle5.a2m # 1kmkA read from 1kmkA/T0339-1kmkA-t06-local-adpstyle5.a2m # adding 1kmkA to template set # found chain 1kmkA in template set Warning: unaligning (T0339)P33 because of BadResidue code BAD_PEPTIDE in next template residue (1kmkA)H55 Warning: unaligning (T0339)S34 because of BadResidue code BAD_PEPTIDE at template residue (1kmkA)H55 Warning: unaligning (T0339)R121 because of BadResidue code BAD_PEPTIDE in next template residue (1kmkA)V128 Warning: unaligning (T0339)L122 because of BadResidue code BAD_PEPTIDE at template residue (1kmkA)V128 Warning: unaligning (T0339)G258 because of BadResidue code BAD_PEPTIDE in next template residue (1kmkA)S254 Warning: unaligning (T0339)G259 because of BadResidue code BAD_PEPTIDE at template residue (1kmkA)S254 Warning: unaligning (T0339)Q260 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1kmkA)P271 Warning: unaligning (T0339)E261 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1kmkA)P271 Warning: unaligning (T0339)A359 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kmkA)A365 Warning: unaligning (T0339)H361 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kmkA)A365 T0339 3 :KVYMDYNATTPLEPEVIQAMTKAMWEAWGN 1kmkA 24 :LAYLDSAASAQKPSQVIDAEAEFYRHGYAA T0339 35 :SP 1kmkA 56 :RG T0339 37 :YSAGRKAKDIINAARESLAKMIGGKPQ 1kmkA 59 :HTLSAQATEKMENVRKRASLFINARSA T0339 64 :DIIFTSGGTESNNLVIHSVVKHF 1kmkA 87 :ELVFVRGTTEGINLVANSWGNSN T0339 91 :TSKGH 1kmkA 110 :VRAGD T0339 109 :HFITSSVEHDSI 1kmkA 115 :NIIISQMEHHAN T0339 123 :PLEHLVEEQVAAVTFVPVSK 1kmkA 129 :PWQMLCARVGAELRVIPLNP T0339 144 :SGQTEVDDILAAVRPTTRLVTIMLANNETGIVMPVPEISQ 1kmkA 149 :DGTLQLETLPTLFDEKTRLLAITHVSNVLGTENPLAEMIT T0339 188 :LNQER 1kmkA 189 :LAHQH T0339 199 :PILVHTDAAQALGKQRVDVEDLGVDFLTIVGHK 1kmkA 194 :GAKVLVDGAQAVMHHPVDVQALDCDFYVFSGHK T0339 232 :FYGPRIGALYIR 1kmkA 228 :YGPTGIGILYVK T0339 244 :GLGEF 1kmkA 241 :ALLQE T0339 251 :LYPMLFG 1kmkA 246 :MPPWEGG T0339 262 :RNFRPGTENTPMIAGLGKAAELVTQ 1kmkA 272 :WRFEAGTPNTGGIIGLGAALEYVSA T0339 287 :NCEAYEAHMRDVRDYLEERLEA 1kmkA 298 :GLNNIAEYEQNLMHYALSQLES T0339 312 :QKRIHLNSQFPG 1kmkA 320 :VPDLTLYGPQNR T0339 328 :PNTCNFSIRG 1kmkA 332 :LGVIAFNLGK T0339 340 :LQGHVVLAQCRV 1kmkA 342 :HHAYDVGSFLDN T0339 352 :LMASVGA 1kmkA 356 :IAVRTGH T0339 362 :SDHGDQPSP 1kmkA 366 :MPLMAYYNV T0339 383 :RNALRLSVGRSTTRAEVDLVVQDLKQAV 1kmkA 375 :PAMCRASLAMYNTHEEVDRLVTGLQRIH Number of specific fragments extracted= 21 number of extra gaps= 4 total=3415 Will force an alignment to be made, even if fragment is small Number of alignments=155 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y4iA/T0339-1y4iA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1y4iA expands to /projects/compbio/data/pdb/1y4i.pdb.gz 1y4iA:Bad short name: N1 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: C2' for alphabet: pdb_atoms Bad short name: C3 for alphabet: pdb_atoms Bad short name: O3 for alphabet: pdb_atoms Bad short name: C4 for alphabet: pdb_atoms Bad short name: C4' for alphabet: pdb_atoms Bad short name: C5 for alphabet: pdb_atoms Bad short name: C6 for alphabet: pdb_atoms Bad short name: C5' for alphabet: pdb_atoms Bad short name: OP4 for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms # T0339 read from 1y4iA/T0339-1y4iA-t06-local-adpstyle5.a2m # 1y4iA read from 1y4iA/T0339-1y4iA-t06-local-adpstyle5.a2m # adding 1y4iA to template set # found chain 1y4iA in template set Warning: unaligning (T0339)T112 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y4iA)A109 Warning: unaligning (T0339)S113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y4iA)A109 Warning: unaligning (T0339)N169 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y4iA)N160 Warning: unaligning (T0339)N170 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y4iA)N160 Warning: unaligning (T0339)I227 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y4iA)S207 Warning: unaligning (T0339)V228 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y4iA)S207 Warning: unaligning (T0339)H230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1y4iA)Y211 Warning: unaligning (T0339)E289 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1y4iA)R267 Warning: unaligning (T0339)A290 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1y4iA)R267 Warning: unaligning (T0339)P322 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y4iA)Q305 Warning: unaligning (T0339)G323 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y4iA)Q305 T0339 16 :PEVIQAMTKAMWE 1y4iA 36 :TFVFDSAEQGAAR T0339 30 :WGNPSSPYSAGRKAKDIINAARESLAKMIGGKPQ 1y4iA 49 :FALEESGYIYTRLGNPTTDALEKKLAVLERGEAG T0339 66 :IFTSGGTESNNLVIHSV 1y4iA 83 :LATASGISAITTTLLTL T0339 91 :TSKGH 1y4iA 100 :CQQGD T0339 109 :HFI 1y4iA 105 :HIV T0339 114 :SVEHDSIRLPLEHLVEEQVAAVTFVPVSK 1y4iA 110 :SAIYGCTHAFLSHSMPKFGINVRFVDAGK T0339 149 :VDDILAAVRPTTRLVTIMLA 1y4iA 139 :PEEIRAAMRPETKVVYIETP T0339 171 :ETGIVMPVPEISQ 1y4iA 161 :PTLSLVDIETVAG T0339 188 :LNQER 1y4iA 174 :IAHQQ T0339 199 :PILVHTDAAQALGKQRVDV 1y4iA 179 :GALLVVDNTFMSPYCQQPL T0339 219 :DLGVDFLT 1y4iA 198 :QLGADIVV T0339 229 :G 1y4iA 208 :V T0339 232 :FYGPR 1y4iA 212 :INGHG T0339 237 :IGALYIR 1y4iA 220 :GGIIVGK T0339 244 :GLGEFTP 1y4iA 228 :EFIDQAR T0339 251 :LYPMLFG 1y4iA 237 :GLKDITG T0339 267 :GTENTPMIAGLGKAAELVTQNC 1y4iA 244 :GCMSPFNAWLTLRGVKTLGIRM T0339 291 :YEAHMRDVRDYLEER 1y4iA 268 :HCENALKIARFLEGH T0339 306 :LEA 1y4iA 293 :LSS T0339 312 :QKRIHLNS 1y4iA 296 :HPQYELGQ T0339 324 :TQRLPNTCNFSIRGPRLQGHVVLAQCRV 1y4iA 306 :MSLPGGIISFEIAGGLEAGRRMINSVEL T0339 352 :LMASVGAACH 1y4iA 336 :LAVSLGDTET T0339 362 :SDHGDQPSPVLLSYGVPFDVARNALRLSVGR 1y4iA 349 :HPASMTHSPVAPEERLKAGITDGLIRLSVGL T0339 397 :AEVDLVVQDLKQAVAQ 1y4iA 380 :EDPEDIINDLEHAIRK Number of specific fragments extracted= 24 number of extra gaps= 5 total=3439 Will force an alignment to be made, even if fragment is small Number of alignments=156 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pffA/T0339-1pffA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pffA expands to /projects/compbio/data/pdb/1pff.pdb.gz 1pffA:# T0339 read from 1pffA/T0339-1pffA-t06-local-adpstyle5.a2m # 1pffA read from 1pffA/T0339-1pffA-t06-local-adpstyle5.a2m # adding 1pffA to template set # found chain 1pffA in template set Warning: unaligning (T0339)N169 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1pffA)N158 Warning: unaligning (T0339)N170 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1pffA)N158 Warning: unaligning (T0339)I227 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1pffA)S206 Warning: unaligning (T0339)V228 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1pffA)S206 Warning: unaligning (T0339)S334 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1pffA)V316 Warning: unaligning (T0339)I335 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1pffA)V316 Warning: unaligning (T0339)R336 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1pffA)D318 T0339 49 :AARESLAKMIGG 1pffA 66 :ALEGKIAKLEHA T0339 63 :QDIIFTSGGTESNNLVIHSV 1pffA 78 :EACAATASGMGAIAASVWTF T0339 91 :TSKGH 1pffA 98 :LKAGD T0339 109 :HFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVSK 1pffA 103 :HLISDDCLYGCTHALFEHQLRKFGVEVDFIDMAV T0339 149 :VDDILAAVRPTTRLVTIMLA 1pffA 137 :PGNIEKHLKPNTRIVYFETP T0339 171 :ETGIVMPVPEISQ 1pffA 159 :PTLKVIDIEDAVK T0339 188 :LNQER 1pffA 172 :QARKQ T0339 198 :PPILVHTDAAQALGKQRVDV 1pffA 177 :KDILVIVDNTFASPILTNPL T0339 219 :DLGVDFLT 1pffA 197 :DLGVDIVV T0339 229 :GHK 1pffA 207 :ATK T0339 232 :FYGPR 1pffA 211 :INGHT T0339 237 :IGALYIR 1pffA 219 :AGLVCSR T0339 244 :GLGEFT 1pffA 227 :DIIAKV T0339 250 :PLYPMLFG 1pffA 235 :QGIKDITG T0339 267 :GTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEER 1pffA 243 :AIISPHDAWLITRGTLTLDMRVKRAAENAQKVAEFLHEH T0339 306 :LEA 1pffA 292 :LPD T0339 312 :QKRIHLNSQFP 1pffA 295 :HPGHEIAKKQM T0339 325 :QRLPNTCNF 1pffA 306 :KMFGSMIAF T0339 337 :GP 1pffA 319 :GL T0339 340 :LQGHVVLAQCRV 1pffA 321 :EKAKKVLDNCHV T0339 352 :LMASVGAACH 1pffA 335 :LAVSLGGPES T0339 362 :SDHGDQPSPVLLSYGVPFDVARNALRLSVGR 1pffA 348 :HPASMTHAGVPKEEREAAGLTDNLIRLSVGC T0339 397 :AEVDLVVQDLKQAVAQ 1pffA 379 :ENVQDIIDDLKQALDL Number of specific fragments extracted= 23 number of extra gaps= 3 total=3462 Will force an alignment to be made, even if fragment is small Number of alignments=157 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ctzA/T0339-2ctzA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ctzA expands to /projects/compbio/data/pdb/2ctz.pdb.gz 2ctzA:# T0339 read from 2ctzA/T0339-2ctzA-t06-local-adpstyle5.a2m # 2ctzA read from 2ctzA/T0339-2ctzA-t06-local-adpstyle5.a2m # adding 2ctzA to template set # found chain 2ctzA in template set Warning: unaligning (T0339)P33 because of BadResidue code BAD_PEPTIDE in next template residue (2ctzA)E47 Warning: unaligning (T0339)S34 because of BadResidue code BAD_PEPTIDE at template residue (2ctzA)E47 Warning: unaligning (T0339)S35 because of BadResidue code BAD_PEPTIDE at template residue (2ctzA)F48 Warning: unaligning (T0339)F137 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ctzA)T128 Warning: unaligning (T0339)V138 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ctzA)T128 Warning: unaligning (T0339)P177 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ctzA)L163 Warning: unaligning (T0339)V178 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ctzA)L163 Warning: unaligning (T0339)I227 because of BadResidue code BAD_PEPTIDE in next template residue (2ctzA)S203 Warning: unaligning (T0339)V228 because of BadResidue code BAD_PEPTIDE at template residue (2ctzA)S203 Warning: unaligning (T0339)F232 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2ctzA)G209 Warning: unaligning (T0339)Y233 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2ctzA)G209 Warning: unaligning (T0339)G234 because of BadResidue code BAD_PEPTIDE at template residue (2ctzA)G210 Warning: unaligning (T0339)L251 because of BadResidue code BAD_PEPTIDE at template residue (2ctzA)P238 Warning: unaligning (T0339)T268 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ctzA)L272 Warning: unaligning (T0339)E269 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ctzA)L272 Warning: unaligning (T0339)G365 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ctzA)T380 Warning: unaligning (T0339)D366 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ctzA)T380 Warning: unaligning (T0339)A385 because of BadResidue code BAD_PEPTIDE in next template residue (2ctzA)V400 Warning: unaligning (T0339)L386 because of BadResidue code BAD_PEPTIDE at template residue (2ctzA)V400 T0339 22 :MTKAMWEAWGN 2ctzA 35 :SPEHAANLFAL T0339 36 :PYSAGRKAKDIINAARESLAKMIGGKPQ 2ctzA 49 :GNIYSRIMNPTVDVLEKRLAALEGGKAA T0339 66 :IFTSGGTESNNLVIHSV 2ctzA 77 :LATASGHAAQFLALTTL T0339 91 :TSKGH 2ctzA 94 :AQAGD T0339 109 :HFITSSVEHDSIRLPLEHLVEEQVAAVT 2ctzA 99 :NIVSTPNLYGGTFNQFKVTLKRLGIEVR T0339 139 :PVSK 2ctzA 129 :SREE T0339 148 :EVDDILAAVRPTTRLVTIMLANNETGIVM 2ctzA 133 :RPEEFLALTDEKTRAWWVESIGNPALNIP T0339 179 :PEISQ 2ctzA 164 :EALAQ T0339 188 :LNQER 2ctzA 169 :AAREK T0339 199 :PILVHTDAAQALGKQR 2ctzA 174 :GVALIVDNTFGMGGYL T0339 215 :VDV 2ctzA 191 :RPL T0339 219 :DLGVDFLT 2ctzA 194 :AWGAALVT T0339 229 :GHK 2ctzA 204 :LTK T0339 235 :PR 2ctzA 211 :HG T0339 237 :IGALYIR 2ctzA 215 :IAGAIVD T0339 244 :GLGEFTP 2ctzA 223 :GNFPWEG T0339 252 :YPMLFGGG 2ctzA 239 :QPGYHGLR T0339 260 :QERNFRPG 2ctzA 263 :DGLRDQGQ T0339 270 :NTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEER 2ctzA 273 :GPFEAWVVLLGMETLSLRAERHVENTLHLAHWLLEQ T0339 306 :LEA 2ctzA 319 :LPH T0339 312 :QKRIHLNSQFPGTQR 2ctzA 322 :HPHHDRAQKYFKGKP T0339 328 :PNTCNFSIRGPRLQGHVVLAQCRV 2ctzA 337 :GAVLTFGLKGGYEAAKRFISRLKL T0339 352 :LMASVGAACH 2ctzA 363 :HLANVGDTRT T0339 362 :SDH 2ctzA 376 :HPA T0339 367 :QPSPVLLSYGVPFDVARN 2ctzA 381 :THSQLSPEEQAQAGVSPE T0339 387 :RLSVGR 2ctzA 401 :RLSVGL T0339 397 :AEVDLVVQDLKQAV 2ctzA 407 :EHVEDLKAELKEAL Number of specific fragments extracted= 27 number of extra gaps= 9 total=3489 Will force an alignment to be made, even if fragment is small Number of alignments=158 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n8pA/T0339-1n8pA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1n8pA expands to /projects/compbio/data/pdb/1n8p.pdb.gz 1n8pA:# T0339 read from 1n8pA/T0339-1n8pA-t06-local-adpstyle5.a2m # 1n8pA read from 1n8pA/T0339-1n8pA-t06-local-adpstyle5.a2m # adding 1n8pA to template set # found chain 1n8pA in template set Warning: unaligning (T0339)N32 because of BadResidue code BAD_PEPTIDE in next template residue (1n8pA)P43 Warning: unaligning (T0339)P33 because of BadResidue code BAD_PEPTIDE at template residue (1n8pA)P43 Warning: unaligning (T0339)L167 because of BadResidue code BAD_PEPTIDE in next template residue (1n8pA)P147 Warning: unaligning (T0339)A168 because of BadResidue code BAD_PEPTIDE at template residue (1n8pA)P147 T0339 28 :EAWG 1n8pA 38 :SSPA T0339 34 :SSPYSAGRKAKDIINAARESLAKMIGGKPQ 1n8pA 44 :IGTYEYSRSQNPNRENLERAVAALENAQYG T0339 66 :IFTSGGTESNNLVIHS 1n8pA 74 :LAFSSGSATTATILQS T0339 91 :TSKGH 1n8pA 90 :LPQGS T0339 109 :HFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVS 1n8pA 95 :HAVSIGDVYGGTHRYFTKVANAHGVETSFTNDL T0339 149 :VDDILAAVRPTTRLVTIM 1n8pA 128 :LNDLPQLIKENTKLVWIE T0339 169 :NNETGIVMPVPEISQ 1n8pA 148 :TNPTLKVTDIQKVAD T0339 188 :LNQERVAAG 1n8pA 163 :LIKKHAAGQ T0339 199 :PILVHTDAAQALGKQRVDV 1n8pA 172 :DVILVVDNTFLSPYISNPL T0339 219 :DLGVDFLTIVGHK 1n8pA 191 :NFGADIVVHSATK T0339 232 :FYGPR 1n8pA 205 :INGHS T0339 237 :IGALYIR 1n8pA 213 :LGVLATN T0339 244 :G 1n8pA 221 :K T0339 245 :LGEFTPLYPMLFG 1n8pA 223 :LYERLQFLQNAIG T0339 267 :GTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEER 1n8pA 236 :AIPSPFDAWLTHRGLKTLHLRVRQAALSANKIAEFLAAD T0339 306 :LEA 1n8pA 286 :LKT T0339 312 :QKRIHLNSQFPGTQRLPNTCNFSIRGPRLQGHVVLAQCRV 1n8pA 289 :HPNYDVVLKQHRDALGGGMISFRIKGGAEAASKFASSTRL T0339 352 :LMASVGAACH 1n8pA 331 :LAESLGGIES T0339 362 :SDHGDQPSPVLLSYGVPFDVARNALRLSVGR 1n8pA 344 :VPAVMTHGGIPKEAREASGVFDDLVRISVGI T0339 397 :AEVDLVVQDLKQAVAQL 1n8pA 375 :EDTDDLLEDIKQALKQA Number of specific fragments extracted= 20 number of extra gaps= 2 total=3509 Will force an alignment to be made, even if fragment is small Number of alignments=159 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qgnA/T0339-1qgnA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qgnA expands to /projects/compbio/data/pdb/1qgn.pdb.gz 1qgnA:# T0339 read from 1qgnA/T0339-1qgnA-t06-local-adpstyle5.a2m # 1qgnA read from 1qgnA/T0339-1qgnA-t06-local-adpstyle5.a2m # adding 1qgnA to template set # found chain 1qgnA in template set T0339 33 :PSSPYSAGRKAKDIINAARESLAKMIGGKPQ 1qgnA 102 :RRASFEYGRYGNPTTVVLEEKISALEGAEST T0339 66 :IFTSGGTESNNLVIHSV 1qgnA 133 :LLMASGMCASTVMLLAL T0339 91 :TSKGH 1qgnA 150 :VPAGG T0339 109 :HFITSSVEHDSIRLPLEHLVEEQVAAVTFVPVS 1qgnA 155 :HIVTTTDCYRKTRIFIETILPKMGITATVIDPA T0339 148 :EVDDILAAVR 1qgnA 188 :DVGALELALN T0339 158 :PTTRLVTIMLANNETGIVMPVPEISQ 1qgnA 199 :KKVNLFFTESPTNPFLRCVDIELVSK T0339 188 :LNQER 1qgnA 225 :LCHEK T0339 199 :PILVHTDAAQALGKQRVDV 1qgnA 230 :GALVCIDGTFATPLNQKAL T0339 219 :DLGVDFLTIVGHK 1qgnA 249 :ALGADLVLHSATK T0339 232 :FYGPR 1qgnA 263 :LGGHN T0339 237 :IGALYIR 1qgnA 271 :AGCISGP T0339 244 :GLGEFTPLYPMLFG 1qgnA 279 :KLVSEIRNLHHILG T0339 267 :GTENTPMIAGLGKAAELVTQNCEAYEAHMRDVRDYLEER 1qgnA 293 :GALNPNAAYLIIRGMKTLHLRVQQQNSTALRMAEILEAH T0339 306 :LEA 1qgnA 342 :LQS T0339 312 :QKRIHLNSQFP 1qgnA 345 :HPEHHIAKKQM T0339 325 :QRLPNTCNFSIRGPRLQGHVVLAQCRV 1qgnA 356 :TGFGGAVSFEVDGDLLTTAKFVDALKI T0339 352 :LMASVGAACH 1qgnA 385 :IAPSFGGCES T0339 362 :SDHGDQPSPVLLSYGVPFDVARNALRLSVGR 1qgnA 398 :QPAIMSYWDLSQSDRAKYGIMDNLVRFSFGV T0339 397 :AEVDLVVQDLKQAVAQ 1qgnA 429 :EDFDDLKADILQALDS Number of specific fragments extracted= 19 number of extra gaps= 0 total=3528 Will force an alignment to be made, even if fragment is small Number of alignments=160 # command:CPU_time= 73.581 sec, elapsed time= 78.649 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 160 Adding 86320 constraints to all_contacts Done adding distance constraints # command:CPU_time= 74.046 sec, elapsed time= 79.162 sec. # command:Reading probabilities from T0339.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 79.950 Optimizing... Probability sum: -702.690, CN propb: -702.690 weights: 0.385 constraints: 1246 # command:CPU_time= 1025.170 sec, elapsed time= 1031.051 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 1246 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 1246 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 5002 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 5002 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 76780 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 76780 # command:CPU_time= 1026.694 sec, elapsed time= 1033.570 sec. # command: