parameters: 0.6 1.3 0.5 200 50 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.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 /projects/compbio/experiments/protein-predict/casp7/T0294/ # command:# Making conformation for sequence T0294 numbered 1 through 328 Created new target T0294 from T0294.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0294/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0294//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0294/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0294//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0294/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0294/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0294/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f1kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f1kA expands to /projects/compbio/data/pdb/2f1k.pdb.gz 2f1kA:Skipped atom 152, because occupancy 0.4 <= existing 0.600 in 2f1kA Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 452, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 809, because occupancy 0.500 <= existing 0.500 in 2f1kA Bad short name: OD3 for alphabet: pdb_atoms Skipped atom 1215, because occupancy 0.400 <= existing 0.600 in 2f1kA Skipped atom 1217, because occupancy 0.400 <= existing 0.600 in 2f1kA Skipped atom 1219, because occupancy 0.400 <= existing 0.600 in 2f1kA Skipped atom 1221, because occupancy 0.400 <= existing 0.600 in 2f1kA Skipped atom 1223, because occupancy 0.400 <= existing 0.600 in 2f1kA Skipped atom 1576, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1578, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1717, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1719, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1721, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1723, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1725, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1727, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1729, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1731, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1858, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1860, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1862, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1864, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1866, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1868, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1870, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1872, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1874, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1876, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1878, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1967, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1969, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1988, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1990, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1992, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1994, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1996, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1998, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 2000, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 2002, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 2004, because occupancy 0.500 <= existing 0.500 in 2f1kA # T0294 read from 2f1kA/merged-good-all-a2m # 2f1kA read from 2f1kA/merged-good-all-a2m # adding 2f1kA to template set # found chain 2f1kA in template set Warning: unaligning (T0294)S154 because first residue in template chain is (2f1kA)M1 Warning: unaligning (T0294)G267 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f1kA)A115 Warning: unaligning (T0294)D269 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f1kA)A115 Warning: unaligning (T0294)V270 because of BadResidue code BAD_PEPTIDE in next template residue (2f1kA)T117 Warning: unaligning (T0294)T271 because of BadResidue code BAD_PEPTIDE at template residue (2f1kA)T117 Warning: unaligning (T0294)S272 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f1kA)A118 Warning: unaligning (T0294)P273 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f1kA)Q120 Warning: unaligning (T0294)E274 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f1kA)Q120 Warning: unaligning (T0294)N303 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f1kA)L151 Warning: unaligning (T0294)M305 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f1kA)L151 T0294 155 :TVGIIGLGRIGQAIARRLKPFGV 2f1kA 2 :KIGVVGLGLIGASLAGDLRRRGH # choosing archetypes in rotamer library T0294 179 :RFLYTGRQPR 2f1kA 25 :YLIGVSRQQS T0294 189 :PEEAAEFQA 2f1kA 36 :CEKAVERQL T0294 198 :EFVSTPELAAQSDFIVVACS 2f1kA 47 :EAGQDLSLLQTAKIIFLCTP T0294 224 :GLC 2f1kA 68 :QLI T0294 228 :KDFFQKM 2f1kA 71 :LPTLEKL T0294 235 :KETAVFINISR 2f1kA 82 :SPTAIVTDVAS T0294 249 :VNQDDLYQALA 2f1kA 93 :VKTAIAEPASQ T0294 260 :SGKIAAA 2f1kA 106 :SGFIGGH T0294 276 :LPTNHPLLTLK 2f1kA 124 :GAEENLFVNAP T0294 288 :CVILP 2f1kA 135 :YVLTP T0294 296 :SATHRTR 2f1kA 142 :YTDPEQL T0294 306 :SLL 2f1kA 152 :RSV Number of specific fragments extracted= 13 number of extra gaps= 0 total=13 Number of alignments=1 # 2f1kA read from 2f1kA/merged-good-all-a2m # found chain 2f1kA in template set Warning: unaligning (T0294)S154 because first residue in template chain is (2f1kA)M1 Warning: unaligning (T0294)G267 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f1kA)A115 Warning: unaligning (T0294)D269 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f1kA)A115 Warning: unaligning (T0294)L276 because of BadResidue code BAD_PEPTIDE in next template residue (2f1kA)T117 Warning: unaligning (T0294)P277 because of BadResidue code BAD_PEPTIDE at template residue (2f1kA)T117 Warning: unaligning (T0294)T278 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f1kA)A118 Warning: unaligning (T0294)N279 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f1kA)Q120 Warning: unaligning (T0294)H280 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f1kA)Q120 T0294 155 :TVGIIGLGRIGQAIARRLKPFGV 2f1kA 2 :KIGVVGLGLIGASLAGDLRRRGH T0294 179 :RFLYTGRQPR 2f1kA 25 :YLIGVSRQQS T0294 189 :PEEAAEFQA 2f1kA 36 :CEKAVERQL T0294 198 :EFVSTPELAAQSDFIVVACS 2f1kA 47 :EAGQDLSLLQTAKIIFLCTP T0294 224 :GLC 2f1kA 68 :QLI T0294 228 :KDFFQKM 2f1kA 71 :LPTLEKL T0294 235 :KETAVFINISR 2f1kA 82 :SPTAIVTDVAS T0294 249 :VNQDDLYQALA 2f1kA 93 :VKTAIAEPASQ T0294 260 :SGKIAAA 2f1kA 106 :SGFIGGH T0294 281 :PLLTLKN 2f1kA 121 :GIDGAEE Number of specific fragments extracted= 10 number of extra gaps= 0 total=23 Number of alignments=2 # 2f1kA read from 2f1kA/merged-good-all-a2m # found chain 2f1kA in template set Warning: unaligning (T0294)S154 because first residue in template chain is (2f1kA)M1 Warning: unaligning (T0294)G267 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f1kA)A115 Warning: unaligning (T0294)P275 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f1kA)A115 Warning: unaligning (T0294)L276 because of BadResidue code BAD_PEPTIDE in next template residue (2f1kA)T117 Warning: unaligning (T0294)P277 because of BadResidue code BAD_PEPTIDE at template residue (2f1kA)T117 Warning: unaligning (T0294)T278 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f1kA)A118 Warning: unaligning (T0294)N279 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f1kA)Q120 Warning: unaligning (T0294)H280 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f1kA)Q120 T0294 155 :TVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQ 2f1kA 2 :KIGVVGLGLIGASLAGDLRRRGHYLIGVSRQQ T0294 191 :E 2f1kA 34 :S T0294 192 :AAEFQAEFVSTPELAAQSDFIVVACS 2f1kA 41 :ERQLVDEAGQDLSLLQTAKIIFLCTP T0294 224 :GLC 2f1kA 68 :QLI T0294 228 :KDFFQKM 2f1kA 71 :LPTLEKL T0294 235 :KETAVFINIS 2f1kA 82 :SPTAIVTDVA T0294 248 :VVNQDDLYQALA 2f1kA 92 :SVKTAIAEPASQ T0294 260 :SGKIAAA 2f1kA 106 :SGFIGGH T0294 281 :PLLTLK 2f1kA 121 :GIDGAE Number of specific fragments extracted= 9 number of extra gaps= 0 total=32 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qp8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qp8A expands to /projects/compbio/data/pdb/1qp8.pdb.gz 1qp8A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0294 read from 1qp8A/merged-good-all-a2m # 1qp8A read from 1qp8A/merged-good-all-a2m # adding 1qp8A to template set # found chain 1qp8A in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1qp8A)M1 Warning: unaligning (T0294)H53 because of BadResidue code BAD_PEPTIDE in next template residue (1qp8A)A34 Warning: unaligning (T0294)G54 because of BadResidue code BAD_PEPTIDE at template residue (1qp8A)A34 T0294 8 :KVFVTRRIPAEGRVALARA 1qp8A 2 :ELYVNFELPPEAEEELRKY T0294 29 :CEVE 1qp8A 21 :FKIV T0294 35 :D 1qp8A 25 :R T0294 39 :PIP 1qp8A 26 :GGD T0294 49 :VAGA 1qp8A 29 :LGNV T0294 58 :LLSDHVDKRILDAA 1qp8A 35 :ALVSRITAEELAKM T0294 73 :ANLKVISTMSVGIDHLAL 1qp8A 49 :PRLKFIQVVTAGLDHLPW T0294 95 :KR 1qp8A 67 :ES T0294 97 :GIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWKPL 1qp8A 72 :HVTVAGNAGSNADAVAEFALALLLAPYKRIIQYGEKMKRGDYGRDVEI T0294 149 :YGLTQSTVGIIGLGRIGQAIARRLKPFGV 1qp8A 120 :PLIQGEKVAVLGLGEIGTRVGKILAALGA T0294 179 :RFLYTGRQPR 1qp8A 149 :QVRGFSRTPK T0294 196 :QAEFV 1qp8A 161 :PWRFT T0294 201 :STPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNH 1qp8A 167 :SLEEALREARAAVCALPLNKHTRGLVKYQHLALMAEDAVFVNVGRAEVLDRDGVLRILKERPQFIFASDVWWGRNDFAKD T0294 281 :PLLTLKNCVILPHIGS 1qp8A 248 :EFFSLPNVVATPWVAG T0294 297 :ATHRTRNTMSLLAANNLLAGLRGEPMPSELK 1qp8A 266 :GNERVWRQMVMEAVRNLITYATGGRPRNIAK Number of specific fragments extracted= 15 number of extra gaps= 1 total=47 Number of alignments=4 # 1qp8A read from 1qp8A/merged-good-all-a2m # found chain 1qp8A in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1qp8A)M1 Warning: unaligning (T0294)H53 because of BadResidue code BAD_PEPTIDE in next template residue (1qp8A)A34 T0294 8 :KVFVTRRIPAEGRVALARAA 1qp8A 2 :ELYVNFELPPEAEEELRKYF T0294 30 :EVEQWD 1qp8A 22 :KIVRGG T0294 41 :P 1qp8A 28 :D T0294 49 :VAGA 1qp8A 29 :LGNV T0294 58 :LLSDHVDKRILDAA 1qp8A 35 :ALVSRITAEELAKM T0294 73 :ANLKVISTMSVGIDHLA 1qp8A 49 :PRLKFIQVVTAGLDHLP T0294 96 :RGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWK 1qp8A 71 :PHVTVAGNAGSNADAVAEFALALLLAPYKRIIQYGEKMKRGDYGRDV T0294 147 :CGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1qp8A 118 :EIPLIQGEKVAVLGLGEIGTRVGKILAALGA T0294 179 :RFLYTGRQPR 1qp8A 149 :QVRGFSRTPK T0294 195 :FQAEFV 1qp8A 160 :GPWRFT T0294 201 :STPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNH 1qp8A 167 :SLEEALREARAAVCALPLNKHTRGLVKYQHLALMAEDAVFVNVGRAEVLDRDGVLRILKERPQFIFASDVWWGRNDFAKD T0294 281 :PLLTLKNCVILPHIGS 1qp8A 248 :EFFSLPNVVATPWVAG T0294 297 :ATHRTRNTMSLLAANNLLAGLRGEPMPSELKL 1qp8A 266 :GNERVWRQMVMEAVRNLITYATGGRPRNIAKR Number of specific fragments extracted= 13 number of extra gaps= 1 total=60 Number of alignments=5 # 1qp8A read from 1qp8A/merged-good-all-a2m # found chain 1qp8A in template set Warning: unaligning (T0294)L58 because of BadResidue code BAD_PEPTIDE at template residue (1qp8A)A34 T0294 35 :DSDEPIPAKELERGVAGAHGL 1qp8A 4 :YVNFELPPEAEEELRKYFKIV T0294 59 :LSDHVDKRILDAAGANLKVISTMSVGIDHLALD 1qp8A 35 :ALVSRITAEELAKMPRLKFIQVVTAGLDHLPWE T0294 96 :RGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWK 1qp8A 71 :PHVTVAGNAGSNADAVAEFALALLLAPYKRIIQYGEKMKRGDYGRDV T0294 147 :CGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRP 1qp8A 118 :EIPLIQGEKVAVLGLGEIGTRVGKILAALGAQVRGFSRTPKEG T0294 195 :FQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNH 1qp8A 161 :PWRFTNSLEEALREARAAVCALPLNKHTRGLVKYQHLALMAEDAVFVNVGRAEVLDRDGVLRILKERPQFIFASDVWWGRNDFAKD T0294 281 :PLLTLKNCVILPHIGS 1qp8A 248 :EFFSLPNVVATPWVAG T0294 297 :ATHRTRNTMSLLAANNLLAGLRGEPMPSELK 1qp8A 266 :GNERVWRQMVMEAVRNLITYATGGRPRNIAK Number of specific fragments extracted= 7 number of extra gaps= 1 total=67 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x13A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1x13A expands to /projects/compbio/data/pdb/1x13.pdb.gz 1x13A:# T0294 read from 1x13A/merged-good-all-a2m # 1x13A read from 1x13A/merged-good-all-a2m # adding 1x13A to template set # found chain 1x13A in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1x13A)G1001 Warning: unaligning (T0294)T202 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1x13A)G1223 Warning: unaligning (T0294)E320 because of BadResidue code BAD_PEPTIDE in next template residue (1x13A)D1343 Warning: unaligning (T0294)P321 because of BadResidue code BAD_PEPTIDE at template residue (1x13A)D1343 T0294 8 :KVFVTRR 1x13A 1002 :RIGIPRE T0294 15 :IPAEGRVALAR 1x13A 1018 :ATPKTVEQLLK T0294 27 :ADCEVEQWDS 1x13A 1029 :LGFTVAVESG T0294 39 :PIPAKELERG 1x13A 1044 :SFDDKAFVQA T0294 51 :GAHGL 1x13A 1054 :GAEIV T0294 56 :LCLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLT 1x13A 1068 :IILKVNAPLDDEIALLNPGTTLVSFIWPAQNPELMQKLAERNVTVMAMDSVPR T0294 109 :DTTAELAVSLLLTTCRRLP 1x13A 1131 :SSMANIAGYRAIVEAAHEF T0294 139 :TSW 1x13A 1150 :GRF T0294 146 :LCGY 1x13A 1153 :FTGQ T0294 150 :GLTQSTVGIIGLGRIGQAIARRLKPFGV 1x13A 1162 :KVPPAKVMVIGAGVAGLAAIGAANSLGA T0294 179 :RFLYTGRQP 1x13A 1190 :IVRAFDTRP T0294 188 :RPEEAAEFQAEFVS 1x13A 1200 :VKEQVQSMGAEFLE T0294 204 :ELAAQSDFIVV 1x13A 1244 :AQAKEVDIIVT T0294 216 :CSLTPA 1x13A 1255 :TALIPG T0294 222 :TEGLCNKDFFQKMKETAVFINISR 1x13A 1263 :APKLITREMVDSMKAGSVIVDLAA T0294 246 :GDV 1x13A 1290 :GNC T0294 260 :SGKIAA 1x13A 1297 :PGEIFT T0294 277 :PTNH 1x13A 1303 :TENG T0294 288 :CVILPH 1x13A 1307 :VKVIGY T0294 294 :IGSATHRTRNTMSLLAANNLLAGLRG 1x13A 1316 :PGRLPTQSSQLYGTNLVNLLKLLCKE T0294 322 :M 1x13A 1344 :G Number of specific fragments extracted= 21 number of extra gaps= 1 total=88 Number of alignments=7 # 1x13A read from 1x13A/merged-good-all-a2m # found chain 1x13A in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1x13A)G1001 Warning: unaligning (T0294)T202 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1x13A)G1223 Warning: unaligning (T0294)E320 because of BadResidue code BAD_PEPTIDE in next template residue (1x13A)D1343 Warning: unaligning (T0294)P321 because of BadResidue code BAD_PEPTIDE at template residue (1x13A)D1343 T0294 8 :KVFVTRR 1x13A 1002 :RIGIPRE T0294 15 :IPAEGRVALARA 1x13A 1018 :ATPKTVEQLLKL T0294 28 :DCEVEQWDS 1x13A 1030 :GFTVAVESG T0294 39 :PIPAKELERG 1x13A 1044 :SFDDKAFVQA T0294 51 :GAHGL 1x13A 1054 :GAEIV T0294 56 :LCLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLT 1x13A 1068 :IILKVNAPLDDEIALLNPGTTLVSFIWPAQNPELMQKLAERNVTVMAMDSVPR T0294 109 :DTTAELAVSLLLTTCRRL 1x13A 1131 :SSMANIAGYRAIVEAAHE T0294 138 :WTSWKP 1x13A 1149 :FGRFFT T0294 144 :LWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1x13A 1156 :QITAAGKVPPAKVMVIGAGVAGLAAIGAANSLGA T0294 179 :RFLYTGRQPR 1x13A 1190 :IVRAFDTRPE T0294 189 :PEEAAEFQAEFVS 1x13A 1201 :KEQVQSMGAEFLE T0294 203 :PELAAQSDFIVVAC 1x13A 1243 :AAQAKEVDIIVTTA T0294 218 :LTPA 1x13A 1257 :LIPG T0294 222 :TEGLCNKDFFQKMKETAVFINIS 1x13A 1263 :APKLITREMVDSMKAGSVIVDLA T0294 245 :RGDV 1x13A 1289 :GGNC T0294 277 :PTNHPLLTLKN 1x13A 1295 :TVPGEIFTTEN T0294 288 :CVILP 1x13A 1307 :VKVIG T0294 293 :HIGSATHRTRNTMSLLAANNLLAGLRG 1x13A 1315 :LPGRLPTQSSQLYGTNLVNLLKLLCKE T0294 322 :M 1x13A 1344 :G Number of specific fragments extracted= 19 number of extra gaps= 1 total=107 Number of alignments=8 # 1x13A read from 1x13A/merged-good-all-a2m # found chain 1x13A in template set Warning: unaligning (T0294)E320 because of BadResidue code BAD_PEPTIDE in next template residue (1x13A)D1343 Warning: unaligning (T0294)P321 because of BadResidue code BAD_PEPTIDE at template residue (1x13A)D1343 T0294 22 :ALARAADCEVEQWDS 1x13A 1024 :EQLLKLGFTVAVESG T0294 39 :PIPAKELERGV 1x13A 1044 :SFDDKAFVQAG T0294 50 :AGAHGLLCLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTP 1x13A 1062 :SVWQSEIILKVNAPLDDEIALLNPGTTLVSFIWPAQNPELMQKLAERNVTVMAMD T0294 105 :DVLTDTTAELAVSLLLTTCRRL 1x13A 1127 :LDALSSMANIAGYRAIVEAAHE T0294 138 :WTS 1x13A 1149 :FGR T0294 141 :WKPLWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEEAAEFQAEFVS 1x13A 1153 :FTGQITAAGKVPPAKVMVIGAGVAGLAAIGAANSLGAIVRAFDTRPEVKEQVQSMGAEFLE T0294 202 :TPELAAQSDFIVV 1x13A 1242 :FAAQAKEVDIIVT T0294 216 :CSLTPA 1x13A 1255 :TALIPG T0294 222 :TEGLCNKDFFQKMKETAVFINISR 1x13A 1263 :APKLITREMVDSMKAGSVIVDLAA T0294 247 :D 1x13A 1291 :N T0294 260 :SGKIAA 1x13A 1297 :PGEIFT T0294 277 :PTNH 1x13A 1303 :TENG T0294 281 :PL 1x13A 1314 :DL T0294 294 :IGSATHRTRNTMSLLAANNLLAGLRG 1x13A 1316 :PGRLPTQSSQLYGTNLVNLLKLLCKE T0294 322 :MPSELKL 1x13A 1344 :GNITVDF Number of specific fragments extracted= 15 number of extra gaps= 1 total=122 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1psdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1psdA expands to /projects/compbio/data/pdb/1psd.pdb.gz 1psdA:# T0294 read from 1psdA/merged-good-all-a2m # 1psdA read from 1psdA/merged-good-all-a2m # adding 1psdA to template set # found chain 1psdA in template set Warning: unaligning (T0294)P3 because first residue in template chain is (1psdA)E7 T0294 4 :VRLMKVFVTRRIPAEGRVALARA 1psdA 8 :KDKIKFLLVEGVHQKALESLRAA T0294 28 :DC 1psdA 31 :GY T0294 30 :EVEQW 1psdA 34 :NIEFH T0294 37 :DEPIPAKELERGVAGAHGLLCLLSDHVDKRILDAA 1psdA 39 :KGALDDEQLKESIRDAHFIGLRSRTHLTEDVINAA T0294 73 :ANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWK 1psdA 74 :EKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLLLLRGVPEANAKAHRGVWNKLA T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1psdA 144 :AGSFEARGKKLGIIGYGHIGTQLGILAESLGM T0294 179 :RFLYTGRQPRP 1psdA 176 :YVYFYDIENKL T0294 195 :FQAEFV 1psdA 189 :GNATQV T0294 201 :STPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNH 1psdA 196 :HLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVVDIPALCDALASKHLAGAAIDVFPTEPATNSD T0294 281 :PLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPSE 1psdA 280 :PLCEFDNVLLTPHIGGSTQEAQENIGLEVAGKLIKYSDNGSTLSA Number of specific fragments extracted= 10 number of extra gaps= 0 total=132 Number of alignments=10 # 1psdA read from 1psdA/merged-good-all-a2m # found chain 1psdA in template set Warning: unaligning (T0294)P3 because first residue in template chain is (1psdA)E7 T0294 4 :VRLMKVFVTRRIPAEGRVALARA 1psdA 8 :KDKIKFLLVEGVHQKALESLRAA T0294 28 :DCEVEQWD 1psdA 31 :GYTNIEFH T0294 37 :DEPIPAKELERGVAGAHGLLCLLSDHVDKRILDAA 1psdA 39 :KGALDDEQLKESIRDAHFIGLRSRTHLTEDVINAA T0294 73 :ANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWK 1psdA 74 :EKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLLLLRGVPEANAKAHRGVWNKLA T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1psdA 144 :AGSFEARGKKLGIIGYGHIGTQLGILAESLGM T0294 179 :RFLYTGRQPR 1psdA 176 :YVYFYDIENK T0294 189 :P 1psdA 187 :P T0294 194 :EFQAEFV 1psdA 188 :LGNATQV T0294 201 :STPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNH 1psdA 196 :HLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVVDIPALCDALASKHLAGAAIDVFPTEPATNSD T0294 281 :PLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPSE 1psdA 280 :PLCEFDNVLLTPHIGGSTQEAQENIGLEVAGKLIKYSDNGSTLSA Number of specific fragments extracted= 10 number of extra gaps= 0 total=142 Number of alignments=11 # 1psdA read from 1psdA/merged-good-all-a2m # found chain 1psdA in template set T0294 19 :GRVALARAADCEVEQWDSDEPIPAKELERGVAGAHGLLCLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWK 1psdA 20 :HQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLRSRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLLLLRGVPEANAKAHRGVWNKLA T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEE 1psdA 144 :AGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFYDIENKLPLG T0294 195 :FQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNH 1psdA 190 :NATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVVDIPALCDALASKHLAGAAIDVFPTEPATNSD T0294 281 :PLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPSELKL 1psdA 280 :PLCEFDNVLLTPHIGGSTQEAQENIGLEVAGKLIKYSDNGSTLSAVNF Number of specific fragments extracted= 4 number of extra gaps= 0 total=146 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gdhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gdhA expands to /projects/compbio/data/pdb/1gdh.pdb.gz 1gdhA:# T0294 read from 1gdhA/merged-good-all-a2m # 1gdhA read from 1gdhA/merged-good-all-a2m # adding 1gdhA to template set # found chain 1gdhA in template set Warning: unaligning (T0294)L6 because first residue in template chain is (1gdhA)K2 Warning: unaligning (T0294)E190 because of BadResidue code BAD_PEPTIDE in next template residue (1gdhA)D185 Warning: unaligning (T0294)E191 because of BadResidue code BAD_PEPTIDE at template residue (1gdhA)D185 Warning: unaligning (T0294)S244 because of BadResidue code BAD_PEPTIDE in next template residue (1gdhA)R240 Warning: unaligning (T0294)R245 because of BadResidue code BAD_PEPTIDE at template residue (1gdhA)R240 T0294 7 :MKVFVTRRIPAEGRVALAR 1gdhA 3 :KKILITWPLPEAAMARARE T0294 28 :DCEVEQWDSDEPIPAKELERGVAGAHGLLCLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWKPLWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1gdhA 22 :SYDVIAHGDDPKITIDEMIETAKSVDALLITLNEKCRKEVIDRIPENIKCISTYSIGFDHIDLDACKARGIKVGNAPHGVTVATAEIAMLLLLGSARRAGEGEKMIRTRSWPGWEPLELVGEKLDNKTLGIYGFGSIGQALAKRAQGFDM T0294 179 :RFLYTGRQP 1gdhA 172 :DIDYFDTHR T0294 188 :RP 1gdhA 182 :SS T0294 192 :AAEFQAEFV 1gdhA 186 :EASYQATFH T0294 201 :STPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINI 1gdhA 196 :SLDSLLSVSQFFSLNAPSTPETRYFFNKATIKSLPQGAIVVNT T0294 246 :GDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNH 1gdhA 241 :GDLVDNELVVAALEAGRLAYAGFDVFAGEPNINEG T0294 282 :LLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPSE 1gdhA 276 :YYDLPNTFLFPHIGSAATQAREDMAHQANDLIDALFGGADMSYA Number of specific fragments extracted= 8 number of extra gaps= 2 total=154 Number of alignments=13 # 1gdhA read from 1gdhA/merged-good-all-a2m # found chain 1gdhA in template set Warning: unaligning (T0294)L6 because first residue in template chain is (1gdhA)K2 Warning: unaligning (T0294)E190 because of BadResidue code BAD_PEPTIDE in next template residue (1gdhA)D185 Warning: unaligning (T0294)E191 because of BadResidue code BAD_PEPTIDE at template residue (1gdhA)D185 Warning: unaligning (T0294)S244 because of BadResidue code BAD_PEPTIDE in next template residue (1gdhA)R240 Warning: unaligning (T0294)R245 because of BadResidue code BAD_PEPTIDE at template residue (1gdhA)R240 T0294 7 :MKVFVTRRIPAEGRVALARA 1gdhA 3 :KKILITWPLPEAAMARARES T0294 29 :CEVEQWDSDEPIPAKELERGVAGAHGLLCLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWKPLWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1gdhA 23 :YDVIAHGDDPKITIDEMIETAKSVDALLITLNEKCRKEVIDRIPENIKCISTYSIGFDHIDLDACKARGIKVGNAPHGVTVATAEIAMLLLLGSARRAGEGEKMIRTRSWPGWEPLELVGEKLDNKTLGIYGFGSIGQALAKRAQGFDM T0294 179 :RFLYTGRQPR 1gdhA 172 :DIDYFDTHRA T0294 189 :P 1gdhA 183 :S T0294 192 :AAEFQAEFV 1gdhA 186 :EASYQATFH T0294 201 :STPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINI 1gdhA 196 :SLDSLLSVSQFFSLNAPSTPETRYFFNKATIKSLPQGAIVVNT T0294 246 :GDVVNQDDLYQALASGKIAAAGLDVTSPEP 1gdhA 241 :GDLVDNELVVAALEAGRLAYAGFDVFAGEP T0294 277 :PTNHPLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPSE 1gdhA 271 :NINEGYYDLPNTFLFPHIGSAATQAREDMAHQANDLIDALFGGADMSYA Number of specific fragments extracted= 8 number of extra gaps= 2 total=162 Number of alignments=14 # 1gdhA read from 1gdhA/merged-good-all-a2m # found chain 1gdhA in template set Warning: unaligning (T0294)E190 because of BadResidue code BAD_PEPTIDE in next template residue (1gdhA)D185 Warning: unaligning (T0294)E191 because of BadResidue code BAD_PEPTIDE at template residue (1gdhA)D185 Warning: unaligning (T0294)S244 because of BadResidue code BAD_PEPTIDE in next template residue (1gdhA)R240 Warning: unaligning (T0294)R245 because of BadResidue code BAD_PEPTIDE at template residue (1gdhA)R240 T0294 19 :GRVALARAADCEVEQWDSDEPIPAKELERGVAGAHGLLCLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWKPLWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRP 1gdhA 13 :EAAMARARESYDVIAHGDDPKITIDEMIETAKSVDALLITLNEKCRKEVIDRIPENIKCISTYSIGFDHIDLDACKARGIKVGNAPHGVTVATAEIAMLLLLGSARRAGEGEKMIRTRSWPGWEPLELVGEKLDNKTLGIYGFGSIGQALAKRAQGFDMDIDYFDTHRASS T0294 192 :AAEF 1gdhA 186 :EASY T0294 196 :QAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINI 1gdhA 191 :ATFHDSLDSLLSVSQFFSLNAPSTPETRYFFNKATIKSLPQGAIVVNT T0294 246 :GDVVNQDDLYQALASGKIAAAGLDVTSPEPLP 1gdhA 241 :GDLVDNELVVAALEAGRLAYAGFDVFAGEPNI T0294 279 :NHPLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPSEL 1gdhA 273 :NEGYYDLPNTFLFPHIGSAATQAREDMAHQANDLIDALFGGADMSYAL Number of specific fragments extracted= 5 number of extra gaps= 2 total=167 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a9fA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a9fA expands to /projects/compbio/data/pdb/2a9f.pdb.gz 2a9fA:# T0294 read from 2a9fA/merged-good-all-a2m # 2a9fA read from 2a9fA/merged-good-all-a2m # adding 2a9fA to template set # found chain 2a9fA in template set Warning: unaligning (T0294)R185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2a9fA)D238 Warning: unaligning (T0294)P189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2a9fA)D238 Warning: unaligning (T0294)E320 because of BadResidue code BAD_PEPTIDE in next template residue (2a9fA)A360 Warning: unaligning (T0294)P321 because of BadResidue code BAD_PEPTIDE at template residue (2a9fA)A360 T0294 5 :RL 2a9fA 65 :KN T0294 8 :KVFVTR 2a9fA 67 :TVAVIS T0294 14 :RIPAEG 2a9fA 82 :DIGPEA T0294 20 :RVALARAADCEVEQWDSD 2a9fA 96 :AALFKAFAGVDAIPIVLD T0294 39 :PIPAK 2a9fA 114 :TKDTE T0294 44 :ELERGVAGAHGLLCLL 2a9fA 123 :IVKALAPTFGGINLED T0294 63 :VD 2a9fA 139 :IS T0294 65 :KRILDAA 2a9fA 145 :FEIEQRL T0294 94 :KKR 2a9fA 152 :IKE T0294 97 :GIRVGY 2a9fA 156 :HIPVFH T0294 108 :TDTTAELAVSLLLTTCR 2a9fA 164 :QHGTAIVVLAAIFNSLK T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTG 2a9fA 181 :LLKKSLDEVSIVVNGGGSAGLSITRKLLAAGATKVTVVD T0294 190 :EEAAEF 2a9fA 239 :IAKVTN T0294 196 :QAEFVSTPELAAQSDFIVVA 2a9fA 247 :FKSGTLEDALEGADIFIGVS T0294 222 :TEGLCNKDFFQKMKETAVFINISRGDV 2a9fA 267 :APGVLKAEWISKMAARPVIFAMANPIP T0294 249 :VNQDDLY 2a9fA 295 :IYPDEAL T0294 260 :SGKIAAAGLDVTSPEPLPTN 2a9fA 302 :EAGAYIVGTGRSDFPNQINN T0294 281 :PLL 2a9fA 322 :VLA T0294 284 :TLKN 2a9fA 336 :RAKT T0294 297 :AT 2a9fA 340 :IT T0294 303 :NTMSLLAANNLLAGLRG 2a9fA 342 :VEMQIAAAKGIASLVPD T0294 322 :M 2a9fA 361 :L Number of specific fragments extracted= 22 number of extra gaps= 1 total=189 Number of alignments=16 # 2a9fA read from 2a9fA/merged-good-all-a2m # found chain 2a9fA in template set Warning: unaligning (T0294)P187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2a9fA)D238 Warning: unaligning (T0294)P189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2a9fA)D238 Warning: unaligning (T0294)E320 because of BadResidue code BAD_PEPTIDE in next template residue (2a9fA)A360 Warning: unaligning (T0294)P321 because of BadResidue code BAD_PEPTIDE at template residue (2a9fA)A360 T0294 5 :RLMKVFVTR 2a9fA 66 :NTVAVISDG T0294 17 :AEGRVA 2a9fA 86 :EAAMPV T0294 23 :LARAADCEVEQWDSD 2a9fA 99 :FKAFAGVDAIPIVLD T0294 39 :PIPAKEL 2a9fA 114 :TKDTEEI T0294 46 :ERGVAGAHGLLCLL 2a9fA 125 :KALAPTFGGINLED T0294 63 :VDKRILDAA 2a9fA 139 :ISAPRCFEI T0294 90 :LDEIKKR 2a9fA 148 :EQRLIKE T0294 97 :GIRVGY 2a9fA 156 :HIPVFH T0294 108 :TDTTAELAVSLLLTTCR 2a9fA 164 :QHGTAIVVLAAIFNSLK T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTG 2a9fA 181 :LLKKSLDEVSIVVNGGGSAGLSITRKLLAAGATKVTVVD T0294 186 :Q 2a9fA 233 :A T0294 190 :EEAAE 2a9fA 239 :IAKVT T0294 195 :FQAEFVSTPELAAQSDFIVVA 2a9fA 246 :EFKSGTLEDALEGADIFIGVS T0294 222 :TEGLCNKDFFQKMKETAVFINISRGDV 2a9fA 267 :APGVLKAEWISKMAARPVIFAMANPIP T0294 249 :VNQDDLY 2a9fA 295 :IYPDEAL T0294 260 :SGKIAAAGL 2a9fA 302 :EAGAYIVGT T0294 270 :VTSPEPLPTNHPLL 2a9fA 311 :GRSDFPNQINNVLA T0294 284 :TLKN 2a9fA 336 :RAKT T0294 297 :AT 2a9fA 340 :IT T0294 303 :NTMSLLAANNLLAGLRG 2a9fA 342 :VEMQIAAAKGIASLVPD T0294 322 :M 2a9fA 361 :L Number of specific fragments extracted= 21 number of extra gaps= 1 total=210 Number of alignments=17 # 2a9fA read from 2a9fA/merged-good-all-a2m # found chain 2a9fA in template set Warning: unaligning (T0294)E320 because of BadResidue code BAD_PEPTIDE in next template residue (2a9fA)A360 Warning: unaligning (T0294)P321 because of BadResidue code BAD_PEPTIDE at template residue (2a9fA)A360 T0294 44 :ELERGVAGAHGLLCLLSDHVDKRILD 2a9fA 96 :AALFKAFAGVDAIPIVLDTKDTEEII T0294 70 :AAGANLKVISTMSVGIDHL 2a9fA 126 :ALAPTFGGINLEDISAPRC T0294 90 :LDEIKK 2a9fA 148 :EQRLIK T0294 96 :RGIRVGY 2a9fA 155 :CHIPVFH T0294 108 :TDTTAELAVSLLLTTCR 2a9fA 164 :QHGTAIVVLAAIFNSLK T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 2a9fA 181 :LLKKSLDEVSIVVNGGGSAGLSITRKLLAAGA T0294 178 :QRFLYTG 2a9fA 214 :KVTVVDK T0294 185 :RQPR 2a9fA 227 :QEAA T0294 195 :FQAEFVSTPELAAQSDFIVVACS 2a9fA 246 :EFKSGTLEDALEGADIFIGVSAP T0294 224 :GLCNKDFFQKMKETAVFINISRG 2a9fA 269 :GVLKAEWISKMAARPVIFAMANP T0294 247 :DVVNQDD 2a9fA 293 :PEIYPDE T0294 257 :AL 2a9fA 300 :AL T0294 260 :SGKIAAAGLD 2a9fA 302 :EAGAYIVGTG T0294 277 :PTNH 2a9fA 312 :RSDF T0294 283 :LTL 2a9fA 338 :KTI T0294 298 :T 2a9fA 341 :T T0294 303 :NTMSLLAANNLLAGLRG 2a9fA 342 :VEMQIAAAKGIASLVPD T0294 322 :M 2a9fA 361 :L Number of specific fragments extracted= 18 number of extra gaps= 1 total=228 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f8gA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f8gA expands to /projects/compbio/data/pdb/1f8g.pdb.gz 1f8gA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0294 read from 1f8gA/merged-good-all-a2m # 1f8gA read from 1f8gA/merged-good-all-a2m # adding 1f8gA to template set # found chain 1f8gA in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1f8gA)M1 T0294 8 :KVFVTRR 1f8gA 2 :KIAIPKE T0294 15 :IPAEGRVALAR 1f8gA 18 :ISPEVVKKLVG T0294 27 :ADCEVEQWDS 1f8gA 29 :LGFEVIVEQG T0294 39 :PIPAKELERG 1f8gA 44 :SITDDALTAA T0294 49 :VAGAHGLLCLLSDHVDKR 1f8gA 65 :LSQADVVWKVQRPMTAEE T0294 68 :LDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTP 1f8gA 87 :VALIKEGAVLMCHLGALTNRPVVEALTKRKITAYAME T0294 106 :VLTDTTAELAVSLLL 1f8gA 135 :DILSSQSNLAGYRAV T0294 121 :TTCRRL 1f8gA 151 :DGAYEF T0294 138 :WTSWKPLWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1f8gA 157 :ARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKRLGA T0294 179 :RFLYTGRQP 1f8gA 197 :VVMATDVRA T0294 188 :RPEEAAEFQAEFVS 1f8gA 207 :TKEQVESLGGKFIT T0294 204 :ELAAQSDFIVVACSLTPA 1f8gA 253 :KELVKTDIAITTALIPGK T0294 224 :GLCNKDFFQKMKETAVFINISRGDVV 1f8gA 274 :VLITEEMVTKMKPGSVIIDLAVEAGG T0294 273 :PEPLPTNHPLLTLKNCVILPH 1f8gA 300 :NCPLSEPGKIVVKHGVKIVGH T0294 294 :IGSATHR 1f8gA 324 :PSRVAAD T0294 305 :MSLLAANNLLAGL 1f8gA 331 :ASPLFAKNLLNFL Number of specific fragments extracted= 16 number of extra gaps= 0 total=244 Number of alignments=19 # 1f8gA read from 1f8gA/merged-good-all-a2m # found chain 1f8gA in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1f8gA)M1 T0294 8 :KVFVTRR 1f8gA 2 :KIAIPKE T0294 15 :IPAEGRVALARA 1f8gA 18 :ISPEVVKKLVGL T0294 28 :DCEVEQWDS 1f8gA 30 :GFEVIVEQG T0294 39 :PIPAKELERG 1f8gA 44 :SITDDALTAA T0294 49 :VAGAHGLLCLLSDHVD 1f8gA 65 :LSQADVVWKVQRPMTA T0294 66 :RI 1f8gA 81 :EE T0294 68 :LDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLT 1f8gA 87 :VALIKEGAVLMCHLGALTNRPVVEALTKRKITAYAMELMPR T0294 109 :DTTAELAVSLLLTTC 1f8gA 138 :SSQSNLAGYRAVIDG T0294 134 :KNGGWTSWKPLWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1f8gA 153 :AYEFARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKRLGA T0294 179 :RFLYTGRQPR 1f8gA 197 :VVMATDVRAA T0294 189 :PEEAAEFQAEFVST 1f8gA 208 :KEQVESLGGKFITV T0294 203 :PELAAQSDFIVVACSLTPA 1f8gA 252 :LKELVKTDIAITTALIPGK T0294 222 :TE 1f8gA 273 :PV T0294 225 :LCNKDFFQKMKETAVFINIS 1f8gA 275 :LITEEMVTKMKPGSVIIDLA T0294 246 :GDV 1f8gA 299 :GNC T0294 275 :PLPTNHPLLTLKNCVILPH 1f8gA 302 :PLSEPGKIVVKHGVKIVGH T0294 294 :IGSAT 1f8gA 324 :PSRVA T0294 303 :NTMSLLAANNLLAGL 1f8gA 329 :ADASPLFAKNLLNFL Number of specific fragments extracted= 18 number of extra gaps= 0 total=262 Number of alignments=20 # 1f8gA read from 1f8gA/merged-good-all-a2m # found chain 1f8gA in template set T0294 23 :LARAADCEVEQWDS 1f8gA 25 :KLVGLGFEVIVEQG T0294 39 :PIPAKELERG 1f8gA 44 :SITDDALTAA T0294 49 :VAGAHGLLCLLSDHVDKRI 1f8gA 64 :ALSQADVVWKVQRPMTAEE T0294 68 :LDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTP 1f8gA 87 :VALIKEGAVLMCHLGALTNRPVVEALTKRKITAYAME T0294 105 :DVLTDTTAELAVSLLLTTCRR 1f8gA 134 :MDILSSQSNLAGYRAVIDGAY T0294 136 :GGWTSWKPLWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEEAAEFQAEFVS 1f8gA 155 :EFARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKRLGAVVMATDVRAATKEQVESLGGKFIT T0294 202 :TPELAAQSDFIVVACSLTPA 1f8gA 251 :VLKELVKTDIAITTALIPGK T0294 225 :LCNKDFFQKMKETAVFINISRGDVV 1f8gA 275 :LITEEMVTKMKPGSVIIDLAVEAGG T0294 273 :PEPLPTNHPLLTLKNCVILPHIGSATHR 1f8gA 300 :NCPLSEPGKIVVKHGVKIVGHTNVPSRV T0294 302 :RNTMSLLAANNLLAGL 1f8gA 328 :AADASPLFAKNLLNFL Number of specific fragments extracted= 10 number of extra gaps= 0 total=272 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2go1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0294/2go1A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0294/2go1A/merged-good-all-a2m.gz for input Trying 2go1A/merged-good-all-a2m Error: Couldn't open file 2go1A/merged-good-all-a2m or 2go1A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2nacA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0294 read from 2nacA/merged-good-all-a2m # 2nacA read from 2nacA/merged-good-all-a2m # found chain 2nacA in training set Warning: unaligning (T0294)I159 because of BadResidue code BAD_PEPTIDE in next template residue (2nacA)A198 Warning: unaligning (T0294)G160 because of BadResidue code BAD_PEPTIDE at template residue (2nacA)A198 T0294 21 :VALARAADCEVEQW 2nacA 60 :RKYLESNGHTLVVT T0294 36 :SDEPI 2nacA 77 :DGPDS T0294 44 :ELERGVAGAHGLLC 2nacA 82 :VFERELVDADVVIS T0294 58 :LLSDHVDKRILDAA 2nacA 98 :FWPAYLTPERIAKA T0294 73 :ANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWKPL 2nacA 112 :KNLKLALTAGIGSDHVDLQSAIDRNVTVAEVTYCNSISVAEHVVMMILSLVRNYLPSHEWARKGGWNIADCV T0294 146 :LCGYGLTQSTVGI 2nacA 184 :SHAYDLEAMHVGT T0294 161 :LGRIGQAIARRLKPFGV 2nacA 199 :AGRIGLAVLRRLAPFDV T0294 179 :RFLYTGRQP 2nacA 216 :HLHYTDRHR T0294 188 :RPEEAAEFQAEFV 2nacA 226 :PESVEKELNLTWH T0294 201 :STPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNHPLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPSE 2nacA 240 :TREDMYPVCDVVTLNCPLHPETEHMINDETLKLFKRGAYIVNTARGKLCDRDAVARALESGRLAGYAGDVWFPQPAPKDHPWRTMPYNGMTPHISGTTLTAQARYAAGTREILECFFEGRPIRDE Number of specific fragments extracted= 10 number of extra gaps= 1 total=282 Number of alignments=22 # 2nacA read from 2nacA/merged-good-all-a2m # found chain 2nacA in training set Warning: unaligning (T0294)I159 because of BadResidue code BAD_PEPTIDE in next template residue (2nacA)A198 Warning: unaligning (T0294)G160 because of BadResidue code BAD_PEPTIDE at template residue (2nacA)A198 T0294 21 :VALARA 2nacA 61 :KYLESN T0294 28 :DCEVEQWD 2nacA 67 :GHTLVVTS T0294 36 :SDEPI 2nacA 77 :DGPDS T0294 44 :ELERGVAGAHGLLCLLSD 2nacA 82 :VFERELVDADVVISQPFW T0294 62 :HVDKRILDAA 2nacA 102 :YLTPERIAKA T0294 73 :ANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWKPL 2nacA 112 :KNLKLALTAGIGSDHVDLQSAIDRNVTVAEVTYCNSISVAEHVVMMILSLVRNYLPSHEWARKGGWNIADCV T0294 146 :LCGYGLTQSTVGI 2nacA 184 :SHAYDLEAMHVGT T0294 161 :LGRIGQAIARRLKPFGV 2nacA 199 :AGRIGLAVLRRLAPFDV T0294 179 :RFLYTGRQPR 2nacA 216 :HLHYTDRHRL T0294 189 :PEEAAEFQAEFV 2nacA 227 :ESVEKELNLTWH T0294 201 :STPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNHPLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPSE 2nacA 240 :TREDMYPVCDVVTLNCPLHPETEHMINDETLKLFKRGAYIVNTARGKLCDRDAVARALESGRLAGYAGDVWFPQPAPKDHPWRTMPYNGMTPHISGTTLTAQARYAAGTREILECFFEGRPIRDE Number of specific fragments extracted= 11 number of extra gaps= 1 total=293 Number of alignments=23 # 2nacA read from 2nacA/merged-good-all-a2m # found chain 2nacA in training set Warning: unaligning (T0294)I159 because of BadResidue code BAD_PEPTIDE in next template residue (2nacA)A198 Warning: unaligning (T0294)G160 because of BadResidue code BAD_PEPTIDE at template residue (2nacA)A198 T0294 24 :ARAADCEVEQWDSDEPIPAKELERGVAGAHGLLCLLSDH 2nacA 61 :KYLESNGHTLVVTSDKDGPDSVFERELVDADVVISQPFW T0294 63 :VDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWK 2nacA 102 :YLTPERIAKAKNLKLALTAGIGSDHVDLQSAIDRNVTVAEVTYCNSISVAEHVVMMILSLVRNYLPSHEWARKGGWNIAD T0294 144 :LWLCGYGLTQSTVGI 2nacA 182 :CVSHAYDLEAMHVGT T0294 161 :LGRIGQAIARRLKPFGVQRFLYTGRQPRPEEAAEF 2nacA 199 :AGRIGLAVLRRLAPFDVHLHYTDRHRLPESVEKEL T0294 196 :QAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNHPLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPSE 2nacA 235 :LTWHATREDMYPVCDVVTLNCPLHPETEHMINDETLKLFKRGAYIVNTARGKLCDRDAVARALESGRLAGYAGDVWFPQPAPKDHPWRTMPYNGMTPHISGTTLTAQARYAAGTREILECFFEGRPIRDE Number of specific fragments extracted= 5 number of extra gaps= 1 total=298 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2d0iA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2d0iA expands to /projects/compbio/data/pdb/2d0i.pdb.gz 2d0iA:# T0294 read from 2d0iA/merged-good-all-a2m # 2d0iA read from 2d0iA/merged-good-all-a2m # adding 2d0iA to template set # found chain 2d0iA in template set Warning: unaligning (T0294)R5 because first residue in template chain is (2d0iA)M1 T0294 6 :LMKVFVTRRIPAEGRVALAR 2d0iA 2 :RPKVGVLLKMKREALEELKK T0294 28 :DCEVEQWD 2d0iA 22 :YADVEIIL T0294 39 :PIPAKELERGVAGAHGLLCLLSDHVDKRILDAA 2d0iA 30 :YPSGEELKGVIGRFDGIIVSPTTKITREVLENA T0294 73 :ANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWKPL 2d0iA 63 :ERLKVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAVAEFTVGLIINLMRKIHYADKFIRRGEWESHAKI T0294 146 :LCGY 2d0iA 135 :WTGF T0294 150 :GLTQSTVGIIGLGRIGQAIARRLKPFGV 2d0iA 143 :SLYGKKVGILGMGAIGKAIARRLIPFGV T0294 179 :RFLYTGRQPRPEEAAEFQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMK 2d0iA 171 :KLYYWSRHRKVNVEKELKARYMDIDELLEKSDIVILALPLTRDTYHIINEERVKKLE T0294 237 :TAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEP 2d0iA 228 :GKYLVNIGRGALVDEKAVTEAIKQGKLKGYATDVFEKEP T0294 277 :PTNHPLLTL 2d0iA 267 :VREHELFKY T0294 286 :KNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPS 2d0iA 277 :WETVLTPHYAGLALEAQEDVGFRAVENLLKVLRGEVPED Number of specific fragments extracted= 10 number of extra gaps= 0 total=308 Number of alignments=25 # 2d0iA read from 2d0iA/merged-good-all-a2m # found chain 2d0iA in template set Warning: unaligning (T0294)R5 because first residue in template chain is (2d0iA)M1 T0294 6 :LMKVFVTRRIPAEGRVALARAA 2d0iA 2 :RPKVGVLLKMKREALEELKKYA T0294 30 :EVEQWD 2d0iA 24 :DVEIIL T0294 39 :PIPAKELERGVAGAHGLLCLLSDHVDKRILDAA 2d0iA 30 :YPSGEELKGVIGRFDGIIVSPTTKITREVLENA T0294 73 :ANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWKPLW 2d0iA 63 :ERLKVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAVAEFTVGLIINLMRKIHYADKFIRRGEWESHAKIW T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 2d0iA 139 :KRIESLYGKKVGILGMGAIGKAIARRLIPFGV T0294 179 :RFLYTGRQPRPEEAAEFQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMK 2d0iA 171 :KLYYWSRHRKVNVEKELKARYMDIDELLEKSDIVILALPLTRDTYHIINEERVKKLE T0294 237 :TAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEP 2d0iA 228 :GKYLVNIGRGALVDEKAVTEAIKQGKLKGYATDVFEKEP T0294 277 :PTNHPLLTL 2d0iA 267 :VREHELFKY T0294 286 :KNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPS 2d0iA 277 :WETVLTPHYAGLALEAQEDVGFRAVENLLKVLRGEVPED Number of specific fragments extracted= 9 number of extra gaps= 0 total=317 Number of alignments=26 # 2d0iA read from 2d0iA/merged-good-all-a2m # found chain 2d0iA in template set T0294 18 :EGRVALARAADCEVEQWDS 2d0iA 12 :KREALEELKKYADVEIILY T0294 41 :PAKELERGVAGAHGLLCLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWKPLWLC 2d0iA 31 :PSGEELKGVIGRFDGIIVSPTTKITREVLENAERLKVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAVAEFTVGLIINLMRKIHYADKFIRRGEWESHAKIWTG T0294 148 :GYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEE 2d0iA 141 :IESLYGKKVGILGMGAIGKAIARRLIPFGVKLYYWSRHRKVNVE T0294 193 :AEFQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKM 2d0iA 185 :KELKARYMDIDELLEKSDIVILALPLTRDTYHIINEERVKKL T0294 236 :ETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLP 2d0iA 227 :EGKYLVNIGRGALVDEKAVTEAIKQGKLKGYATDVFEKEPVR T0294 279 :NHPLLTL 2d0iA 269 :EHELFKY T0294 286 :KNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPSELK 2d0iA 277 :WETVLTPHYAGLALEAQEDVGFRAVENLLKVLRGEVPEDLVN Number of specific fragments extracted= 7 number of extra gaps= 0 total=324 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xwfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xwfA expands to /projects/compbio/data/pdb/1xwf.pdb.gz 1xwfA:# T0294 read from 1xwfA/merged-good-all-a2m # 1xwfA read from 1xwfA/merged-good-all-a2m # adding 1xwfA to template set # found chain 1xwfA in template set T0294 1 :SRPVRLMKVFVTRRIPAE 1xwfA 41 :SKPLKGARIAGCLHMTVE T0294 19 :GRVALARAADCEVEQWDSDEPIPAKELERGV 1xwfA 61 :VLIETLVALGAEVRWSSCNIFSTQDHAAAAI T0294 50 :AGAH 1xwfA 94 :AGIP T0294 56 :LCLLSDHVDKRILDAAG 1xwfA 98 :VFAWKGETDEEYLWCIE T0294 73 :A 1xwfA 121 :D T0294 74 :NLKVIST 1xwfA 123 :PLNMILD T0294 83 :VGIDHLAL 1xwfA 130 :DGGDLTNL T0294 92 :EIKKR 1xwfA 138 :IHTKH T0294 97 :GIRVGYTPDVLTDTTAE 1xwfA 173 :KVPAINVNDSVTNSKFD T0294 114 :LAVSLLLTTCRR 1xwfA 193 :GCRESLIDGIKR T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1xwfA 205 :ATDVMIAGKVAVVAGYGDVGKGCAQALRGFGA T0294 179 :RFLYTGRQPRPEEAAEF 1xwfA 237 :RVIITEIDPINALQAAM T0294 196 :QAEFVSTPELAAQSDFIVVAC 1xwfA 255 :GYEVTTMDEACKEGNIFVTTT T0294 221 :ATEGLCNKDFFQKMKETAVFINISRGDV 1xwfA 276 :GCVDIILGRHFEQMKDDAIVCNIGHFDV T0294 249 :VNQDDLYQ 1xwfA 305 :IDVKWLNE T0294 264 :A 1xwfA 320 :I T0294 267 :GLDVTS 1xwfA 323 :QVDRYL T0294 276 :LPTNH 1xwfA 329 :LKNGH T0294 282 :LLTLK 1xwfA 338 :LAEGR T0294 292 :PHIGSATHRTRNTMSLLAANNLL 1xwfA 351 :GHPSFVMSNSFTNQVMAQIELWT Number of specific fragments extracted= 20 number of extra gaps= 0 total=344 Number of alignments=28 # 1xwfA read from 1xwfA/merged-good-all-a2m # found chain 1xwfA in template set T0294 7 :MKVFVTR 1xwfA 71 :AEVRWSS T0294 14 :RIPAEGRVALARA 1xwfA 82 :STQDHAAAAIAKA T0294 28 :DCEVEQWD 1xwfA 95 :GIPVFAWK T0294 39 :PIPAKELERGV 1xwfA 103 :GETDEEYLWCI T0294 50 :AG 1xwfA 120 :KD T0294 52 :AHGLLCLLSD 1xwfA 124 :LNMILDDGGD T0294 64 :DKRIL 1xwfA 142 :HPQLL T0294 73 :ANLKVISTMS 1xwfA 147 :SGIRGISEET T0294 90 :LDEIKKR 1xwfA 160 :VHNLYKM T0294 97 :GIRVGYTPDVLTDTTAEL 1xwfA 173 :KVPAINVNDSVTNSKFDN T0294 115 :AVSLLLTTCRR 1xwfA 194 :CRESLIDGIKR T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1xwfA 205 :ATDVMIAGKVAVVAGYGDVGKGCAQALRGFGA T0294 179 :RFLYTGRQPR 1xwfA 237 :RVIITEIDPI T0294 189 :PEEAAEFQAEFVSTPELAAQSDFIVVAC 1xwfA 248 :ALQAAMEGYEVTTMDEACKEGNIFVTTT T0294 221 :ATEGLCNKDFFQKMKETAVFINISRGDV 1xwfA 276 :GCVDIILGRHFEQMKDDAIVCNIGHFDV T0294 249 :VNQDDLYQ 1xwfA 305 :IDVKWLNE Number of specific fragments extracted= 16 number of extra gaps= 0 total=360 Number of alignments=29 # 1xwfA read from 1xwfA/merged-good-all-a2m # found chain 1xwfA in template set T0294 34 :WDSDEPIPAKELERGV 1xwfA 98 :VFAWKGETDEEYLWCI T0294 50 :AGAHGLLCLLSDHVDKRIL 1xwfA 120 :KDGPLNMILDDGGDLTNLI T0294 69 :DAAGANLKVISTMS 1xwfA 143 :PQLLSGIRGISEET T0294 90 :LDEIKK 1xwfA 160 :VHNLYK T0294 96 :RGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAI 1xwfA 172 :LKVPAINVNDSVTNSKFDNLYGCRESLIDGIKRAT T0294 148 :GYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEEAAEFQAEFVSTPELAAQSDFIVVACSLTP 1xwfA 207 :DVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQAAMEGYEVTTMDEACKEGNIFVTTTGCVD T0294 225 :LCNKDFFQKMKETAVFINISRGDV 1xwfA 280 :IILGRHFEQMKDDAIVCNIGHFDV T0294 249 :VNQDDLYQ 1xwfA 305 :IDVKWLNE Number of specific fragments extracted= 8 number of extra gaps= 0 total=368 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gtmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gtmA expands to /projects/compbio/data/pdb/1gtm.pdb.gz 1gtmA:# T0294 read from 1gtmA/merged-good-all-a2m # 1gtmA read from 1gtmA/merged-good-all-a2m # adding 1gtmA to template set # found chain 1gtmA in template set Warning: unaligning (T0294)K173 because of BadResidue code BAD_PEPTIDE in next template residue (1gtmA)D234 Warning: unaligning (T0294)P174 because of BadResidue code BAD_PEPTIDE at template residue (1gtmA)D234 Warning: unaligning (T0294)L258 because of BadResidue code BAD_PEPTIDE in next template residue (1gtmA)E332 Warning: unaligning (T0294)A259 because of BadResidue code BAD_PEPTIDE at template residue (1gtmA)E332 T0294 14 :RIPAEGRVALARA 1gtmA 113 :KLSDREKERLARG T0294 45 :LERGVAG 1gtmA 126 :YIRAIYD T0294 56 :LCLLSDHVDKRILDAA 1gtmA 140 :IPAPDVYTNPQIMAWM T0294 90 :LDEIKKR 1gtmA 156 :MDEYETI T0294 104 :PDVLTDTTAELAVSLLLTTCR 1gtmA 183 :SLGRIEATARGASYTIREAAK T0294 146 :LCGY 1gtmA 204 :VLGW T0294 150 :GLTQSTVGIIGLGRIGQAIARRL 1gtmA 209 :TLKGKTIAIQGYGNAGYYLAKIM T0294 175 :FGV 1gtmA 235 :FGM T0294 179 :RFLYTGRQP 1gtmA 238 :KVVAVSDSK T0294 188 :RPEEAAE 1gtmA 256 :NADEVLK T0294 195 :FQAEFVSTPELAA 1gtmA 274 :PGATNITNEELLE T0294 209 :SDFIVVAC 1gtmA 289 :VDVLAPAA T0294 217 :SLTPATEGLCN 1gtmA 300 :VITKKNADNIK T0294 238 :AVFINISRGDVVNQDDLYQA 1gtmA 311 :AKIVAEVANGPVTPEADEIL T0294 260 :SGKIA 1gtmA 333 :KGILQ T0294 275 :PLPT 1gtmA 362 :YYWT T0294 298 :THRTRNTMSLL 1gtmA 366 :IEEVRERLDKK T0294 309 :AANNLLAGL 1gtmA 380 :AFYDVYNIA Number of specific fragments extracted= 18 number of extra gaps= 2 total=386 Number of alignments=31 # 1gtmA read from 1gtmA/merged-good-all-a2m # found chain 1gtmA in template set Warning: unaligning (T0294)K173 because of BadResidue code BAD_PEPTIDE in next template residue (1gtmA)D234 Warning: unaligning (T0294)P174 because of BadResidue code BAD_PEPTIDE at template residue (1gtmA)D234 Warning: unaligning (T0294)L258 because of BadResidue code BAD_PEPTIDE in next template residue (1gtmA)E332 Warning: unaligning (T0294)A259 because of BadResidue code BAD_PEPTIDE at template residue (1gtmA)E332 T0294 98 :IRVGYTPDVLTDTTAELAVSLLLTTCR 1gtmA 69 :GGIRWHPEETLSTVKALAAWMTWKTAV T0294 125 :RLP 1gtmA 97 :DLP T0294 146 :L 1gtmA 100 :Y T0294 151 :LTQSTVGIIGLGRIGQAIARRL 1gtmA 210 :LKGKTIAIQGYGNAGYYLAKIM T0294 175 :FGV 1gtmA 235 :FGM T0294 179 :RFLYTGRQP 1gtmA 238 :KVVAVSDSK T0294 188 :RPEEA 1gtmA 256 :NADEV T0294 195 :FQAEFVSTPELAA 1gtmA 274 :PGATNITNEELLE T0294 209 :SDFIVVAC 1gtmA 289 :VDVLAPAA T0294 217 :SLTPATEGLCN 1gtmA 300 :VITKKNADNIK T0294 238 :AVFINISRGDVVNQDDLYQA 1gtmA 311 :AKIVAEVANGPVTPEADEIL T0294 260 :SGK 1gtmA 333 :KGI T0294 289 :VILP 1gtmA 336 :LQIP T0294 293 :HIGSAT 1gtmA 344 :NAGGVT T0294 299 :HRTRNTMSLL 1gtmA 367 :EEVRERLDKK T0294 309 :AANNLLAGL 1gtmA 380 :AFYDVYNIA Number of specific fragments extracted= 16 number of extra gaps= 2 total=402 Number of alignments=32 # 1gtmA read from 1gtmA/merged-good-all-a2m # found chain 1gtmA in template set Warning: unaligning (T0294)P174 because of BadResidue code BAD_PEPTIDE at template residue (1gtmA)D234 Warning: unaligning (T0294)L258 because of BadResidue code BAD_PEPTIDE in next template residue (1gtmA)E332 Warning: unaligning (T0294)A259 because of BadResidue code BAD_PEPTIDE at template residue (1gtmA)E332 T0294 107 :LTDTTAELAVSLLLTTCRR 1gtmA 186 :RIEATARGASYTIREAAKV T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLK 1gtmA 205 :LGWDTLKGKTIAIQGYGNAGYYLAKIMS T0294 175 :FGVQRFLYTGRQP 1gtmA 235 :FGMKVVAVSDSKG T0294 188 :RPEE 1gtmA 256 :NADE T0294 193 :AEFQAEFVSTPELAA 1gtmA 272 :DFPGATNITNEELLE T0294 209 :SDFIVVAC 1gtmA 289 :VDVLAPAA T0294 217 :SLTPATEGLCN 1gtmA 300 :VITKKNADNIK T0294 238 :AVFINISRGDVVNQDDLYQA 1gtmA 311 :AKIVAEVANGPVTPEADEIL T0294 260 :SGKIA 1gtmA 333 :KGILQ T0294 281 :PLLT 1gtmA 362 :YYWT T0294 298 :THRTRNTMSLL 1gtmA 366 :IEEVRERLDKK T0294 309 :AANNLLAGL 1gtmA 380 :AFYDVYNIA Number of specific fragments extracted= 12 number of extra gaps= 2 total=414 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gpjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gpjA expands to /projects/compbio/data/pdb/1gpj.pdb.gz 1gpjA:Skipped atom 116, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 118, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 120, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 122, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 124, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 126, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 128, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 622, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 624, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 626, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 628, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 634, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 845, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 847, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 849, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 851, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 853, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 855, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 857, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 859, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 861, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 986, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 988, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 990, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 992, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 994, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 996, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 998, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1000, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1002, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1065, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 1067, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 1069, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 1071, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 1073, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 1075, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 1077, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 1079, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 1485, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1487, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1489, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1491, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1493, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1495, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1497, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1499, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1501, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1503, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1505, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1763, because occupancy 0.200 <= existing 0.800 in 1gpjA Skipped atom 1765, because occupancy 0.200 <= existing 0.800 in 1gpjA Skipped atom 1767, because occupancy 0.200 <= existing 0.800 in 1gpjA Skipped atom 1769, because occupancy 0.200 <= existing 0.800 in 1gpjA Skipped atom 1771, because occupancy 0.200 <= existing 0.800 in 1gpjA Skipped atom 1773, because occupancy 0.200 <= existing 0.800 in 1gpjA Skipped atom 1775, because occupancy 0.200 <= existing 0.800 in 1gpjA Skipped atom 1777, because occupancy 0.200 <= existing 0.800 in 1gpjA Skipped atom 1999, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2001, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2003, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2005, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2007, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2009, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2011, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2013, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2015, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2036, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2038, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2040, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2042, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2044, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2046, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2048, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2050, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2052, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2054, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2056, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2230, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2232, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2234, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2236, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2238, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2240, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2242, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2244, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2246, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2585, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 2587, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 2589, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 2591, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 2593, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 2595, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 2597, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 2599, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 2601, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 2675, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2677, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2679, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2681, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2683, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2685, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2687, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2689, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2691, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2693, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2695, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2770, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2772, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2774, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2776, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2778, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2780, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2782, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2784, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2786, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2824, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2826, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2828, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2830, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2832, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2834, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2836, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2838, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2840, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3007, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3009, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3011, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3013, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3015, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3017, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3019, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3021, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3023, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3118, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3120, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3122, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3124, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3126, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3128, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3130, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3132, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3202, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3204, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3206, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3208, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3210, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3212, because occupancy 0.500 <= existing 0.500 in 1gpjA # T0294 read from 1gpjA/merged-good-all-a2m # 1gpjA read from 1gpjA/merged-good-all-a2m # adding 1gpjA to template set # found chain 1gpjA in template set Warning: unaligning (T0294)D35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1gpjA)R59 Warning: unaligning (T0294)S36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gpjA)R59 T0294 14 :RIPAEGRVALARAADCEVEQW 1gpjA 24 :FESDEAVRDIVESFGLSGSVL T0294 37 :D 1gpjA 60 :D T0294 41 :PAKELERGV 1gpjA 61 :RAEELGDLI T0294 50 :AGA 1gpjA 71 :DDA T0294 59 :LSDHVDKRILDAAGA 1gpjA 94 :SMMVGEQEILRQVKK T0294 90 :LDEIKKRGIR 1gpjA 110 :YDRAARLGTL T0294 109 :DTTAELAVSLLLTTCRR 1gpjA 120 :DEALKIVFRRAINLGKR T0294 133 :VKN 1gpjA 137 :ARE T0294 136 :GGWTSWKPLW 1gpjA 141 :TRISEGAVSI T0294 146 :LC 1gpjA 161 :EL T0294 149 :YGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQ 1gpjA 163 :GSLHDKTVLVVGAGEMGKTVAKSLVDRGVRAVLVANRT T0294 189 :PEEAAEF 1gpjA 201 :YERAVEL T0294 196 :QAEFVSTPEL 1gpjA 212 :GGEAVRFDEL T0294 206 :AAQSDFIVVA 1gpjA 225 :LARSDVVVSA T0294 219 :TPATEGLCNKDFFQKM 1gpjA 235 :TAAPHPVIHVDDVREA T0294 235 :KETAVFINISRGDVVN 1gpjA 257 :RSPILIIDIANPRDVE T0294 251 :QDDLYQALAS 1gpjA 286 :IDDLRVIARE T0294 298 :THRTRNTMSLLAANNLLAGL 1gpjA 307 :VEKLIEEELSTVEEELEKLK Number of specific fragments extracted= 18 number of extra gaps= 1 total=432 Number of alignments=34 # 1gpjA read from 1gpjA/merged-good-all-a2m # found chain 1gpjA in template set Warning: unaligning (T0294)P39 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gpjA)R59 T0294 16 :PAEGRVALARAADC 1gpjA 26 :SDEAVRDIVESFGL T0294 30 :EVEQWDSDE 1gpjA 41 :GSVLLQTSN T0294 40 :IPAKELERGV 1gpjA 60 :DRAEELGDLI T0294 50 :AGAH 1gpjA 71 :DDAW T0294 59 :LSDHVDKRILDAAGA 1gpjA 94 :SMMVGEQEILRQVKK T0294 90 :LDEIKKRGI 1gpjA 110 :YDRAARLGT T0294 108 :TDTTAELAVSLLLTTCR 1gpjA 119 :LDEALKIVFRRAINLGK T0294 132 :EVKNG 1gpjA 136 :RAREE T0294 142 :KPLWLCGYG 1gpjA 141 :TRISEGAVS T0294 151 :LTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPR 1gpjA 165 :LHDKTVLVVGAGEMGKTVAKSLVDRGVRAVLVANRTYE T0294 189 :PEEAAEFQAEFVSTPEL 1gpjA 205 :VELARDLGGEAVRFDEL T0294 206 :AAQSDFIVVAC 1gpjA 225 :LARSDVVVSAT T0294 220 :PATEGLCNKDFFQKM 1gpjA 236 :AAPHPVIHVDDVREA T0294 235 :KETAVFINISRGDVVN 1gpjA 257 :RSPILIIDIANPRDVE T0294 251 :QDDLYQALASG 1gpjA 286 :IDDLRVIAREN T0294 298 :THRTRNTMSLLAANNLLAGL 1gpjA 307 :VEKLIEEELSTVEEELEKLK Number of specific fragments extracted= 16 number of extra gaps= 1 total=448 Number of alignments=35 # 1gpjA read from 1gpjA/merged-good-all-a2m # found chain 1gpjA in template set T0294 90 :LDEIKKRGIR 1gpjA 110 :YDRAARLGTL T0294 108 :TD 1gpjA 120 :DE T0294 118 :LLLTTCRRLPEAIEEVKN 1gpjA 122 :ALKIVFRRAINLGKRARE T0294 148 :GYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1gpjA 162 :LGSLHDKTVLVVGAGEMGKTVAKSLVDRGV T0294 178 :QRFLYTGRQPR 1gpjA 193 :AVLVANRTYER T0294 192 :AAEFQAEFVSTPEL 1gpjA 208 :ARDLGGEAVRFDEL T0294 206 :AAQSDFIVVA 1gpjA 225 :LARSDVVVSA T0294 219 :TPATEGLCNKDFFQKM 1gpjA 235 :TAAPHPVIHVDDVREA T0294 235 :KETAVFINISRGDVV 1gpjA 257 :RSPILIIDIANPRDV T0294 279 :NHPLLTLKNCVILP 1gpjA 272 :EEGVENIEDVEVRT T0294 298 :THRTRNTMSLLAANNLLAGL 1gpjA 307 :VEKLIEEELSTVEEELEKLK Number of specific fragments extracted= 11 number of extra gaps= 0 total=459 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dxy/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dxy expands to /projects/compbio/data/pdb/1dxy.pdb.gz 1dxy:Warning: there is no chain 1dxy will retry with 1dxyA Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 1dxy Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 1dxy Skipped atom 1210, because occupancy 0.500 <= existing 0.500 in 1dxy Skipped atom 1212, because occupancy 0.500 <= existing 0.500 in 1dxy Skipped atom 1214, because occupancy 0.500 <= existing 0.500 in 1dxy Skipped atom 1216, because occupancy 0.500 <= existing 0.500 in 1dxy Skipped atom 1218, because occupancy 0.500 <= existing 0.500 in 1dxy Skipped atom 1220, because occupancy 0.500 <= existing 0.500 in 1dxy # T0294 read from 1dxy/merged-good-all-a2m # 1dxy read from 1dxy/merged-good-all-a2m # adding 1dxy to template set # found chain 1dxy in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1dxy)M1 T0294 8 :KVFVTRRIP 1dxy 2 :KIIAYGARV T0294 17 :AEGRVALARAADCEVEQW 1dxy 13 :IQYFKQWAKDTGNTLEYH T0294 37 :DEPIPAKEL 1dxy 31 :TEFLDENTV T0294 47 :RGVAGAHGLLCLLSDHVDKRILDAAGA 1dxy 40 :EWAKGFDGINSLQTTPYAAGVFEKMHA T0294 74 :NLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWKP 1dxy 68 :GIKFLTIRNVGTDNIDMTAMKQYGIRLSNVPAYSPAAIAEFALTDTLYLLRNMGKVQAQLQAGDYEKAGT T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1dxy 138 :FIGKELGQQTVGVMGTGHIGQVAIKLFKGFGA T0294 179 :RFLYTGRQPRP 1dxy 170 :KVIAYDPYPMK T0294 196 :QAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPE 1dxy 185 :DFDYVSLEDLFKQSDVIDLHVPGIEQNTHIINEAAFNLMKPGAIVINTARPNLIDTQAMLSNLKSGKLAGVGIDTYEYE T0294 282 :LLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPSELKL 1dxy 284 :LLGMPNVVLSPHIAYYTETAVHNMVYFSLQHLVDFLTKGETSTEVTG Number of specific fragments extracted= 9 number of extra gaps= 0 total=468 Number of alignments=37 # 1dxy read from 1dxy/merged-good-all-a2m # found chain 1dxy in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1dxy)M1 T0294 8 :KVFVTRRIP 1dxy 2 :KIIAYGARV T0294 17 :AEGRVALARAADCEVEQWD 1dxy 13 :IQYFKQWAKDTGNTLEYHT T0294 38 :EPIPAKEL 1dxy 32 :EFLDENTV T0294 47 :RGVAGAHGLLCLLSDHVDKRILDAAGA 1dxy 40 :EWAKGFDGINSLQTTPYAAGVFEKMHA T0294 74 :NLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWKP 1dxy 68 :GIKFLTIRNVGTDNIDMTAMKQYGIRLSNVPAYSPAAIAEFALTDTLYLLRNMGKVQAQLQAGDYEKAGT T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1dxy 138 :FIGKELGQQTVGVMGTGHIGQVAIKLFKGFGA T0294 179 :RFLYTGRQPRPEEA 1dxy 170 :KVIAYDPYPMKGDH T0294 195 :FQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPE 1dxy 184 :PDFDYVSLEDLFKQSDVIDLHVPGIEQNTHIINEAAFNLMKPGAIVINTARPNLIDTQAMLSNLKSGKLAGVGIDTYEYE T0294 281 :PLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPSELKL 1dxy 283 :ELLGMPNVVLSPHIAYYTETAVHNMVYFSLQHLVDFLTKGETSTEVTG Number of specific fragments extracted= 9 number of extra gaps= 0 total=477 Number of alignments=38 # 1dxy read from 1dxy/merged-good-all-a2m # found chain 1dxy in template set T0294 19 :GRVALARAADCEVEQWDSDEPIPAKEL 1dxy 13 :IQYFKQWAKDTGNTLEYHTEFLDENTV T0294 48 :GVAGAHGLLCLLSDHVDKRILDAAG 1dxy 40 :EWAKGFDGINSLQTTPYAAGVFEKM T0294 73 :ANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWK 1dxy 67 :YGIKFLTIRNVGTDNIDMTAMKQYGIRLSNVPAYSPAAIAEFALTDTLYLLRNMGKVQAQLQAGDYEKAG T0294 145 :WLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEE 1dxy 137 :TFIGKELGQQTVGVMGTGHIGQVAIKLFKGFGAKVIAYDPYPMKGDH T0294 195 :FQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPE 1dxy 184 :PDFDYVSLEDLFKQSDVIDLHVPGIEQNTHIINEAAFNLMKPGAIVINTARPNLIDTQAMLSNLKSGKLAGVGIDTYEYE T0294 281 :PLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPSELK 1dxy 283 :ELLGMPNVVLSPHIAYYTETAVHNMVYFSLQHLVDFLTKGETSTEVT Number of specific fragments extracted= 6 number of extra gaps= 0 total=483 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j49A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0294/1j49A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0294/1j49A/merged-good-all-a2m.gz for input Trying 1j49A/merged-good-all-a2m Error: Couldn't open file 1j49A/merged-good-all-a2m or 1j49A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wxdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wxdA expands to /projects/compbio/data/pdb/1wxd.pdb.gz 1wxdA:# T0294 read from 1wxdA/merged-good-all-a2m # 1wxdA read from 1wxdA/merged-good-all-a2m # adding 1wxdA to template set # found chain 1wxdA in template set Warning: unaligning (T0294)L6 because first residue in template chain is (1wxdA)M1 T0294 7 :MKV 1wxdA 2 :LRF T0294 10 :FVTRRIP 1wxdA 6 :VLGHPVA T0294 17 :AEGRVALARAADC 1wxdA 17 :PAMHAFALESLGL T0294 30 :EVEQWDS 1wxdA 32 :SYEAWDT T0294 41 :PAKEL 1wxdA 39 :PLEAL T0294 65 :KRILDAAGANLKVISTMS 1wxdA 44 :PGRLKEVRRAFRGVNLTL T0294 83 :VGIDHL 1wxdA 69 :AHLDWV T0294 90 :LDEIKKR 1wxdA 75 :SPEAQRI T0294 100 :VGYT 1wxdA 96 :GFNT T0294 115 :AVSLLLTTCR 1wxdA 100 :DAPGFLEALK T0294 146 :LCGYGLTQ 1wxdA 110 :AGGIPLKG T0294 155 :TVGIIGLGRIGQAIARRLKPFGV 1wxdA 118 :PALVLGAGGAGRAVAFALREAGL T0294 179 :RFLYTGRQPRP 1wxdA 141 :EVWVWNRTPQR T0294 190 :EEAAEFQAEFVSTPE 1wxdA 154 :ALAEEFGLRAVPLEK T0294 206 :AAQSDFIVVACSLTPA 1wxdA 169 :AREARLLVNATRVGLE T0294 222 :TEGLCNKDF 1wxdA 187 :SASPLPAEL T0294 234 :MKETAVFINISRGDVVN 1wxdA 196 :FPEEGAAVDLVYRPLWT T0294 253 :DLYQALASGKIAA 1wxdA 213 :RFLREAKAKGLKV T0294 271 :TSP 1wxdA 226 :QTG T0294 303 :NTMSLLAANNLLAGLRGEPMP 1wxdA 229 :LPMLAWQGALAFRLWTGLLPD Number of specific fragments extracted= 20 number of extra gaps= 0 total=503 Number of alignments=40 # 1wxdA read from 1wxdA/merged-good-all-a2m # found chain 1wxdA in template set Warning: unaligning (T0294)L6 because first residue in template chain is (1wxdA)M1 T0294 7 :MKVFVTRRIP 1wxdA 2 :LRFAVLGHPV T0294 17 :AEGRVALARAADC 1wxdA 17 :PAMHAFALESLGL T0294 30 :EVEQWD 1wxdA 32 :SYEAWD T0294 40 :IPAKEL 1wxdA 38 :TPLEAL T0294 65 :KRILDAAGANLKVISTMS 1wxdA 44 :PGRLKEVRRAFRGVNLTL T0294 83 :VGIDHLA 1wxdA 66 :AALAHLD T0294 90 :LDEIKKRGI 1wxdA 75 :SPEAQRIGA T0294 106 :VLTDTTAELA 1wxdA 98 :NTDAPGFLEA T0294 133 :VKNGGWTSWK 1wxdA 108 :LKAGGIPLKG T0294 155 :TVGIIGLGRIGQAIARRLKPFGV 1wxdA 118 :PALVLGAGGAGRAVAFALREAGL T0294 179 :RFLYTGRQPR 1wxdA 141 :EVWVWNRTPQ T0294 189 :PEEAAEFQAEFVSTPE 1wxdA 153 :LALAEEFGLRAVPLEK T0294 206 :AAQSDFIVVACSLTPA 1wxdA 169 :AREARLLVNATRVGLE T0294 222 :TEGLCNKDF 1wxdA 187 :SASPLPAEL T0294 234 :MKETAVFINISRGDVVN 1wxdA 196 :FPEEGAAVDLVYRPLWT T0294 253 :DLYQALASGKIAA 1wxdA 213 :RFLREAKAKGLKV T0294 271 :TSP 1wxdA 226 :QTG T0294 303 :NTMSLLAANNLLAGLRGEPMP 1wxdA 229 :LPMLAWQGALAFRLWTGLLPD Number of specific fragments extracted= 18 number of extra gaps= 0 total=521 Number of alignments=41 # 1wxdA read from 1wxdA/merged-good-all-a2m # found chain 1wxdA in template set T0294 24 :ARAADCEVEQWDSDEPIPAKELERGVA 1wxdA 26 :SLGLEGSYEAWDTPLEALPGRLKEVRR T0294 52 :AHGLLCLLSDHVD 1wxdA 53 :AFRGVNLTLPLKE T0294 70 :AAGAN 1wxdA 66 :AALAH T0294 85 :IDHL 1wxdA 71 :LDWV T0294 90 :LDEIKKRGIR 1wxdA 75 :SPEAQRIGAV T0294 105 :DVLTDTTAEL 1wxdA 98 :NTDAPGFLEA T0294 133 :VKNGGWTSWK 1wxdA 108 :LKAGGIPLKG T0294 155 :TVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEE 1wxdA 118 :PALVLGAGGAGRAVAFALREAGLEVWVWNRTPQRALA T0294 192 :AAEFQAEFVSTPE 1wxdA 156 :AEEFGLRAVPLEK T0294 206 :AAQSDFIVVACSLTPA 1wxdA 169 :AREARLLVNATRVGLE T0294 222 :TEGLCNKD 1wxdA 187 :SASPLPAE T0294 233 :KMKETAVFINISRGDVVNQ 1wxdA 195 :LFPEEGAAVDLVYRPLWTR T0294 254 :LYQALASGKIAA 1wxdA 214 :FLREAKAKGLKV T0294 289 :V 1wxdA 226 :Q T0294 303 :NTMSLLAANNLLAGLRGEPMP 1wxdA 229 :LPMLAWQGALAFRLWTGLLPD Number of specific fragments extracted= 15 number of extra gaps= 0 total=536 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vpdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0294 read from 1vpdA/merged-good-all-a2m # 1vpdA read from 1vpdA/merged-good-all-a2m # found chain 1vpdA in training set Warning: unaligning (T0294)S154 because first residue in template chain is (1vpdA)M3 Warning: unaligning (T0294)T155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vpdA)K4 Warning: unaligning (T0294)A197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vpdA)E47 Warning: unaligning (T0294)E198 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vpdA)E47 T0294 156 :VGIIGLGRIGQAIARRLKPFGV 1vpdA 5 :VGFIGLGIMGKPMSKNLLKAGY T0294 179 :RFLYTGR 1vpdA 27 :SLVVSDR T0294 188 :RPEEAAEF 1vpdA 34 :NPEAIADV T0294 196 :Q 1vpdA 45 :G T0294 199 :FV 1vpdA 48 :TA T0294 201 :STPELAAQSDFIVVACSLTPATEGLCNKD 1vpdA 51 :TAKAIAEQCDVIITMLPNSPHVKEVALGE T0294 230 :FFQKMKETAVFINISR 1vpdA 82 :IIEGAKPGTVLIDMSS T0294 249 :VNQDDLYQA 1vpdA 98 :IAPLASREI T0294 258 :LASGKIA 1vpdA 110 :LKAKGVE T0294 267 :GLDVTSPE 1vpdA 117 :MLDAPVSG T0294 286 :KNCVILPHIGSATHRTRNTMSLLAA 1vpdA 157 :GSVVHTGDIGAGNVTKLANQVIVAL T0294 312 :NLLAGL 1vpdA 182 :NIAAMS Number of specific fragments extracted= 12 number of extra gaps= 1 total=548 Number of alignments=43 # 1vpdA read from 1vpdA/merged-good-all-a2m # found chain 1vpdA in training set Warning: unaligning (T0294)S154 because first residue in template chain is (1vpdA)M3 Warning: unaligning (T0294)T155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vpdA)K4 Warning: unaligning (T0294)A197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vpdA)E47 Warning: unaligning (T0294)E198 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vpdA)E47 T0294 156 :VGIIGLGRIGQAIARRLKPFGV 1vpdA 5 :VGFIGLGIMGKPMSKNLLKAGY T0294 179 :RFLYTGRQPR 1vpdA 27 :SLVVSDRNPE T0294 189 :PEEAAEFQ 1vpdA 38 :IADVIAAG T0294 199 :FV 1vpdA 48 :TA T0294 201 :STPELAAQSDFIVVACSLTPATEGLCNKD 1vpdA 51 :TAKAIAEQCDVIITMLPNSPHVKEVALGE T0294 230 :FFQKMKETAVFINISR 1vpdA 82 :IIEGAKPGTVLIDMSS T0294 249 :VNQDDLYQA 1vpdA 98 :IAPLASREI T0294 258 :LASGKIAAAGLDVTSPE 1vpdA 110 :LKAKGVEMLDAPVSGGE T0294 286 :KNCVILPHIGSATHRTRNTMSLLAA 1vpdA 157 :GSVVHTGDIGAGNVTKLANQVIVAL T0294 312 :NLLAGL 1vpdA 182 :NIAAMS Number of specific fragments extracted= 10 number of extra gaps= 1 total=558 Number of alignments=44 # 1vpdA read from 1vpdA/merged-good-all-a2m # found chain 1vpdA in training set Warning: unaligning (T0294)S154 because first residue in template chain is (1vpdA)M3 Warning: unaligning (T0294)T155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vpdA)K4 Warning: unaligning (T0294)Q196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vpdA)E47 Warning: unaligning (T0294)A197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vpdA)E47 T0294 156 :VGIIGLGRIGQAIARRLKPFGVQRFLYTGRQ 1vpdA 5 :VGFIGLGIMGKPMSKNLLKAGYSLVVSDRNP T0294 190 :EE 1vpdA 36 :EA T0294 192 :AAEF 1vpdA 42 :IAAG T0294 198 :EFVSTPELAAQSDFIVVACSLTPATEGLCNKD 1vpdA 48 :TASTAKAIAEQCDVIITMLPNSPHVKEVALGE T0294 230 :FFQKMKETAVFINISR 1vpdA 82 :IIEGAKPGTVLIDMSS T0294 249 :VNQDD 1vpdA 98 :IAPLA T0294 254 :LYQALASGKIAAAGLDVTS 1vpdA 106 :ISDALKAKGVEMLDAPVSG T0294 286 :KNCVILPHIGSATHRTRNTMSLLAA 1vpdA 157 :GSVVHTGDIGAGNVTKLANQVIVAL T0294 312 :NLLAGL 1vpdA 182 :NIAAMS Number of specific fragments extracted= 9 number of extra gaps= 1 total=567 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b3rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b3rA expands to /projects/compbio/data/pdb/1b3r.pdb.gz 1b3rA:# T0294 read from 1b3rA/merged-good-all-a2m # 1b3rA read from 1b3rA/merged-good-all-a2m # adding 1b3rA to template set # found chain 1b3rA in template set T0294 1 :SRPVRLMKVFVTRRIPAE 1b3rA 41 :SKPLKGARIAGCLHMTVE T0294 19 :GRVALARAADCEVEQWDSDEPIPAKELERGV 1b3rA 61 :VLIETLVALGAEVRWSSCNIFSTQDHAAAAI T0294 50 :AGAHG 1b3rA 94 :AGIPV T0294 57 :CLLSDHVDKRILDAAG 1b3rA 99 :FAWKGETDEEYLWCIE T0294 74 :NLKVIS 1b3rA 123 :PLNMIL T0294 82 :SVGIDHLAL 1b3rA 129 :DDGGDLTNL T0294 92 :EIKKR 1b3rA 138 :IHTKH T0294 97 :GIRVGYTPDVLTDTTAE 1b3rA 173 :KVPAINVNDSVTKSKFD T0294 114 :LAVSLLLTTCRR 1b3rA 193 :GCRESLIDGIKR T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1b3rA 205 :ATDVMIAGKVAVVAGYGDVGKGCAQALRGFGA T0294 179 :RFLYTGRQPRPEEAAEF 1b3rA 237 :RVIITEIDPINALQAAM T0294 196 :QAEFVSTPELAAQSDFIVVAC 1b3rA 255 :GYEVTTMDEACKEGNIFVTTT T0294 221 :ATEGLCNKDFFQKMKETAVFINISRGDV 1b3rA 276 :GCVDIILGRHFEQMKDDAIVCNIGHFDV T0294 249 :VNQDDLYQ 1b3rA 305 :IDVKWLNE T0294 264 :AAAGLDVTSP 1b3rA 320 :IKPQVDRYLL T0294 277 :PTNH 1b3rA 330 :KNGH T0294 282 :LLTLK 1b3rA 338 :LAEGR T0294 292 :PHIGSATH 1b3rA 351 :GHPSFVMS T0294 303 :NTMSLLAANNLLAGLRGEPMPSELK 1b3rA 359 :NSFTNQVMAQIELWTHPDKYPVGVH Number of specific fragments extracted= 19 number of extra gaps= 0 total=586 Number of alignments=46 # 1b3rA read from 1b3rA/merged-good-all-a2m # found chain 1b3rA in template set T0294 7 :MKVFVTR 1b3rA 71 :AEVRWSS T0294 14 :RIPAEGRVALARA 1b3rA 82 :STQDHAAAAIAKA T0294 28 :DCEVEQWD 1b3rA 95 :GIPVFAWK T0294 39 :PIPAKELERGV 1b3rA 103 :GETDEEYLWCI T0294 50 :AG 1b3rA 120 :KD T0294 52 :AHGLLCLLS 1b3rA 124 :LNMILDDGG T0294 64 :DKRIL 1b3rA 142 :HPQLL T0294 73 :ANLKVISTMS 1b3rA 147 :SGIRGISEET T0294 90 :LDEIKKR 1b3rA 160 :VHNLYKM T0294 98 :IRVGYTPDVLTDTTAE 1b3rA 174 :VPAINVNDSVTKSKFD T0294 114 :LAVSLLLTTCRR 1b3rA 193 :GCRESLIDGIKR T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1b3rA 205 :ATDVMIAGKVAVVAGYGDVGKGCAQALRGFGA T0294 179 :RFLYTGRQPR 1b3rA 237 :RVIITEIDPI T0294 189 :PEEAAEFQAEFVSTPELAAQSDFIVVAC 1b3rA 248 :ALQAAMEGYEVTTMDEACKEGNIFVTTT T0294 221 :ATEGLCNKDFFQKMKETAVFINISRGDV 1b3rA 276 :GCVDIILGRHFEQMKDDAIVCNIGHFDV T0294 249 :VNQDDLYQ 1b3rA 305 :IDVKWLNE Number of specific fragments extracted= 16 number of extra gaps= 0 total=602 Number of alignments=47 # 1b3rA read from 1b3rA/merged-good-all-a2m # found chain 1b3rA in template set T0294 34 :WDSDEPIPAKELERGV 1b3rA 98 :VFAWKGETDEEYLWCI T0294 50 :AGAHGLLCLLSDHVDKRIL 1b3rA 120 :KDGPLNMILDDGGDLTNLI T0294 69 :DAAGANLKVISTMS 1b3rA 143 :PQLLSGIRGISEET T0294 90 :LDEIKK 1b3rA 160 :VHNLYK T0294 96 :RG 1b3rA 169 :NG T0294 98 :IRVGYTPDVLT 1b3rA 174 :VPAINVNDSVT T0294 109 :DTTAELAVSLLLTTC 1b3rA 192 :YGCRESLIDGIKRAT T0294 148 :GYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEEAAEFQAEFVSTPELAAQSDFIVVACSL 1b3rA 207 :DVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQAAMEGYEVTTMDEACKEGNIFVTTTGC T0294 223 :EGLCNKDFFQKMKETAVFINISRGD 1b3rA 278 :VDIILGRHFEQMKDDAIVCNIGHFD T0294 248 :VVNQDDLYQ 1b3rA 304 :EIDVKWLNE Number of specific fragments extracted= 10 number of extra gaps= 0 total=612 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mx3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mx3A expands to /projects/compbio/data/pdb/1mx3.pdb.gz 1mx3A:# T0294 read from 1mx3A/merged-good-all-a2m # 1mx3A read from 1mx3A/merged-good-all-a2m # adding 1mx3A to template set # found chain 1mx3A in template set Warning: unaligning (T0294)L6 because first residue in template chain is (1mx3A)M27 Warning: unaligning (T0294)R179 because of BadResidue code BAD_PEPTIDE in next template residue (1mx3A)V200 Warning: unaligning (T0294)F180 because of BadResidue code BAD_PEPTIDE at template residue (1mx3A)V200 T0294 7 :MKVFVTRRIPAEGRVALARAA 1mx3A 28 :PLVALLDGRDCTVEMPILKDV T0294 29 :CEVEQWDSDE 1mx3A 49 :ATVAFCDAQS T0294 39 :PIP 1mx3A 61 :EIH T0294 43 :KELER 1mx3A 64 :EKVLN T0294 51 :GAHGLLCLLSDHVDKRILDAA 1mx3A 69 :EAVGALMYHTITLTREDLEKF T0294 73 :ANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNG 1mx3A 90 :KALRIIVRIGSGFDNIDIKSAGDLGIAVCNVPAASVEETADSTLCHILNLYRRATWLHQALREG T0294 137 :GWTSWKPLW 1mx3A 155 :RVQSVEQIR T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1mx3A 167 :SGAARIRGETLGIIGLGRVGQAVALRAKAFGF T0294 181 :LYTGRQPRPEEAAEFQAEFV 1mx3A 201 :LFYDPYLSDGVERALGLQRV T0294 201 :STPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNH 1mx3A 222 :TLQDLLFHSDCVTLHCGLNEHNHHLINDFTVKQMRQGAFLVNTARGGLVDEKALAQALKEGRIRGAALDVHESEPFSFSQ T0294 281 :PLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPS 1mx3A 303 :PLKDAPNLICTPHAAWYSEQASIEMREEAAREIRRAITGRIPDS Number of specific fragments extracted= 11 number of extra gaps= 1 total=623 Number of alignments=49 # 1mx3A read from 1mx3A/merged-good-all-a2m # found chain 1mx3A in template set Warning: unaligning (T0294)L6 because first residue in template chain is (1mx3A)M27 Warning: unaligning (T0294)R179 because of BadResidue code BAD_PEPTIDE in next template residue (1mx3A)V200 Warning: unaligning (T0294)F180 because of BadResidue code BAD_PEPTIDE at template residue (1mx3A)V200 T0294 7 :MKVFVTRRIP 1mx3A 28 :PLVALLDGRD T0294 17 :AEGRVALARA 1mx3A 39 :TVEMPILKDV T0294 29 :CEVEQWDSDE 1mx3A 49 :ATVAFCDAQS T0294 39 :PIPAKELER 1mx3A 61 :EIHEKVLNE T0294 52 :AHGLLCLLSDHVDKRILDAA 1mx3A 70 :AVGALMYHTITLTREDLEKF T0294 73 :ANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNG 1mx3A 90 :KALRIIVRIGSGFDNIDIKSAGDLGIAVCNVPAASVEETADSTLCHILNLYRRATWLHQALREG T0294 138 :WTSWKP 1mx3A 154 :TRVQSV T0294 144 :LWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1mx3A 165 :VASGAARIRGETLGIIGLGRVGQAVALRAKAFGF T0294 181 :LYTGRQPRPEEAAEFQAEFV 1mx3A 201 :LFYDPYLSDGVERALGLQRV T0294 201 :STPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNH 1mx3A 222 :TLQDLLFHSDCVTLHCGLNEHNHHLINDFTVKQMRQGAFLVNTARGGLVDEKALAQALKEGRIRGAALDVHESEPFSFSQ T0294 281 :PLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPS 1mx3A 303 :PLKDAPNLICTPHAAWYSEQASIEMREEAAREIRRAITGRIPDS Number of specific fragments extracted= 11 number of extra gaps= 1 total=634 Number of alignments=50 # 1mx3A read from 1mx3A/merged-good-all-a2m # found chain 1mx3A in template set Warning: unaligning (T0294)Q178 because of BadResidue code BAD_PEPTIDE in next template residue (1mx3A)V200 Warning: unaligning (T0294)R179 because of BadResidue code BAD_PEPTIDE at template residue (1mx3A)V200 T0294 25 :RAADCEVEQWDSDE 1mx3A 45 :LKDVATVAFCDAQS T0294 39 :PIPAKELER 1mx3A 61 :EIHEKVLNE T0294 53 :HGLLCLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLP 1mx3A 70 :AVGALMYHTITLTREDLEKFKALRIIVRIGSGFDNIDIKSAGDLGIAVCNVPAASVEETADSTLCHILNLYRRAT T0294 129 :AIEEVKNGGWTSWKP 1mx3A 145 :WLHQALREGTRVQSV T0294 144 :LWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1mx3A 165 :VASGAARIRGETLGIIGLGRVGQAVALRAKAFGF T0294 180 :FLYTGRQPRPEEAAEFQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNH 1mx3A 201 :LFYDPYLSDGVERALGLQRVSTLQDLLFHSDCVTLHCGLNEHNHHLINDFTVKQMRQGAFLVNTARGGLVDEKALAQALKEGRIRGAALDVHESEPFSFSQ T0294 281 :PLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGE 1mx3A 303 :PLKDAPNLICTPHAAWYSEQASIEMREEAAREIRRAITGR Number of specific fragments extracted= 7 number of extra gaps= 1 total=641 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dldA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2dldA expands to /projects/compbio/data/pdb/2dld.pdb.gz 2dldA:# T0294 read from 2dldA/merged-good-all-a2m # 2dldA read from 2dldA/merged-good-all-a2m # adding 2dldA to template set # found chain 2dldA in template set Warning: unaligning (T0294)L6 because first residue in template chain is (2dldA)M1 Warning: unaligning (T0294)A27 because of BadResidue code BAD_PEPTIDE at template residue (2dldA)K25 Warning: unaligning (T0294)S82 because of BadResidue code BAD_PEPTIDE in next template residue (2dldA)V79 Warning: unaligning (T0294)V83 because of BadResidue code BAD_PEPTIDE at template residue (2dldA)V79 Warning: unaligning (T0294)A115 because of BadResidue code BAD_PEPTIDE in next template residue (2dldA)A112 Warning: unaligning (T0294)V116 because of BadResidue code BAD_PEPTIDE at template residue (2dldA)A112 Warning: unaligning (T0294)L282 because of BadResidue code BAD_PEPTIDE in next template residue (2dldA)P279 Warning: unaligning (T0294)L283 because of BadResidue code BAD_PEPTIDE at template residue (2dldA)P279 Warning: unaligning (T0294)S296 because of BadResidue code BAD_PEPTIDE in next template residue (2dldA)Y301 Warning: unaligning (T0294)A297 because of BadResidue code BAD_PEPTIDE at template residue (2dldA)Y301 Warning: unaligning (T0294)L317 because of BadResidue code BAD_PEPTIDE in next template residue (2dldA)N322 Warning: unaligning (T0294)R318 because of BadResidue code BAD_PEPTIDE at template residue (2dldA)N322 T0294 7 :MKVFVTRRIP 2dldA 2 :TKVFAYAIRK T0294 17 :AEGRVALARA 2dldA 14 :EPFLNEWKEA T0294 28 :DCEVEQW 2dldA 26 :DIDVDYT T0294 37 :DEPIPAKE 2dldA 33 :DKLLTPET T0294 46 :ERGVAGAHGLLCLLSDHVDKRILDAAGA 2dldA 41 :AKLAKGADGVVVYQQLDYTADTLQALAD T0294 74 :NLKVISTM 2dldA 70 :GVTKMSLR T0294 84 :GIDHLALDEIKKRGIRVGYTPDVLTDTTAEL 2dldA 80 :GVDNIDMDKAKELGFQITNVPVYSPNAIAEH T0294 117 :SLLLTTCRRLPEAIEEVKNGGWTSWK 2dldA 113 :IQAARVLRQDKRMDEKMAKRDLRWAP T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 2dldA 139 :TIGREVRDQVVGVVGTGHIGQVFMRIMEGFGA T0294 179 :RFLYTGRQPRPEEAAE 2dldA 171 :KVIAYDIFKNPELEKK T0294 196 :QAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPE 2dldA 187 :GYYVDSLDDLYKQADVISLHVPDVPANVHMINDKSIAEMKDGVVIVNCSRGRLVDTDAVIRGLDSGKIFGFVMDTYEDE T0294 275 :PLPTNHP 2dldA 271 :KDWEGKE T0294 284 :T 2dldA 280 :D T0294 285 :LKNCVILPHIG 2dldA 289 :RPNVLVTPHTA T0294 298 :THRTRNTMSLLAANNLLAG 2dldA 302 :TTHAVRNMVVKAFNNNLKL T0294 319 :GEPMPSE 2dldA 323 :GEKPDSP Number of specific fragments extracted= 16 number of extra gaps= 6 total=657 Number of alignments=52 # 2dldA read from 2dldA/merged-good-all-a2m # found chain 2dldA in template set Warning: unaligning (T0294)L6 because first residue in template chain is (2dldA)M1 Warning: unaligning (T0294)A27 because of BadResidue code BAD_PEPTIDE in next template residue (2dldA)K25 Warning: unaligning (T0294)S82 because of BadResidue code BAD_PEPTIDE in next template residue (2dldA)V79 Warning: unaligning (T0294)V83 because of BadResidue code BAD_PEPTIDE at template residue (2dldA)V79 Warning: unaligning (T0294)A115 because of BadResidue code BAD_PEPTIDE in next template residue (2dldA)A112 Warning: unaligning (T0294)V116 because of BadResidue code BAD_PEPTIDE at template residue (2dldA)A112 Warning: unaligning (T0294)L282 because of BadResidue code BAD_PEPTIDE in next template residue (2dldA)P279 Warning: unaligning (T0294)L283 because of BadResidue code BAD_PEPTIDE at template residue (2dldA)P279 Warning: unaligning (T0294)S296 because of BadResidue code BAD_PEPTIDE in next template residue (2dldA)Y301 Warning: unaligning (T0294)A297 because of BadResidue code BAD_PEPTIDE at template residue (2dldA)Y301 Warning: unaligning (T0294)L317 because of BadResidue code BAD_PEPTIDE in next template residue (2dldA)N322 Warning: unaligning (T0294)R318 because of BadResidue code BAD_PEPTIDE at template residue (2dldA)N322 T0294 7 :MKVFVTR 2dldA 2 :TKVFAYA T0294 15 :IP 2dldA 9 :IR T0294 17 :AEGRVALARA 2dldA 14 :EPFLNEWKEA T0294 28 :DCEVEQWD 2dldA 26 :DIDVDYTD T0294 38 :EPIPAKE 2dldA 34 :KLLTPET T0294 46 :ERGVAGAHGLLCLLSDHVDKRILDAAGA 2dldA 41 :AKLAKGADGVVVYQQLDYTADTLQALAD T0294 74 :NLKVISTM 2dldA 70 :GVTKMSLR T0294 84 :GIDHLALDEIKKRGIRVGYTPDVLTDTTAEL 2dldA 80 :GVDNIDMDKAKELGFQITNVPVYSPNAIAEH T0294 117 :SLLLTTCRRLPEAIEEVKNGGWTSWK 2dldA 113 :IQAARVLRQDKRMDEKMAKRDLRWAP T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 2dldA 139 :TIGREVRDQVVGVVGTGHIGQVFMRIMEGFGA T0294 179 :RFLYTGRQPRPEEAAE 2dldA 171 :KVIAYDIFKNPELEKK T0294 196 :QAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPE 2dldA 187 :GYYVDSLDDLYKQADVISLHVPDVPANVHMINDKSIAEMKDGVVIVNCSRGRLVDTDAVIRGLDSGKIFGFVMDTYEDE T0294 275 :PLPTNHP 2dldA 271 :KDWEGKE T0294 284 :T 2dldA 280 :D T0294 285 :LKNCVILPHIG 2dldA 289 :RPNVLVTPHTA T0294 298 :THRTRNTMSLLAANNLLAG 2dldA 302 :TTHAVRNMVVKAFNNNLKL T0294 319 :GEPMPSELKL 2dldA 323 :GEKPDSPVAL Number of specific fragments extracted= 17 number of extra gaps= 6 total=674 Number of alignments=53 # 2dldA read from 2dldA/merged-good-all-a2m # found chain 2dldA in template set Warning: unaligning (T0294)C29 because of BadResidue code BAD_PEPTIDE in next template residue (2dldA)K25 Warning: unaligning (T0294)S82 because of BadResidue code BAD_PEPTIDE in next template residue (2dldA)V79 Warning: unaligning (T0294)V83 because of BadResidue code BAD_PEPTIDE at template residue (2dldA)V79 Warning: unaligning (T0294)A115 because of BadResidue code BAD_PEPTIDE in next template residue (2dldA)A112 Warning: unaligning (T0294)V116 because of BadResidue code BAD_PEPTIDE at template residue (2dldA)A112 Warning: unaligning (T0294)S296 because of BadResidue code BAD_PEPTIDE in next template residue (2dldA)Y301 Warning: unaligning (T0294)A297 because of BadResidue code BAD_PEPTIDE at template residue (2dldA)Y301 Warning: unaligning (T0294)L317 because of BadResidue code BAD_PEPTIDE in next template residue (2dldA)N322 Warning: unaligning (T0294)R318 because of BadResidue code BAD_PEPTIDE at template residue (2dldA)N322 T0294 15 :IPAEGRVALARAAD 2dldA 10 :RKDEEPFLNEWKEA T0294 30 :EVEQWDSDEPIPAKEL 2dldA 26 :DIDVDYTDKLLTPETA T0294 48 :GVAGAHGLLCLLSDHVDKRILDAAG 2dldA 42 :KLAKGADGVVVYQQLDYTADTLQAL T0294 74 :NLKVISTM 2dldA 70 :GVTKMSLR T0294 84 :GIDHLALDEIKKRGIRVGYTPDVLTDTTAEL 2dldA 80 :GVDNIDMDKAKELGFQITNVPVYSPNAIAEH T0294 117 :SLLLTTCRRLPEAIEEVKNGGWTSWK 2dldA 113 :IQAARVLRQDKRMDEKMAKRDLRWAP T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQP 2dldA 139 :TIGREVRDQVVGVVGTGHIGQVFMRIMEGFGAKVIAYDIFKN T0294 190 :EEAAEFQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPE 2dldA 181 :PELEKKGYYVDSLDDLYKQADVISLHVPDVPANVHMINDKSIAEMKDGVVIVNCSRGRLVDTDAVIRGLDSGKIFGFVMDTYEDE T0294 275 :PLPTNH 2dldA 271 :KDWEGK T0294 281 :PLLTLKNCVILPHIG 2dldA 285 :DLIDRPNVLVTPHTA T0294 298 :THRTRNTMSLLAANNLLAG 2dldA 302 :TTHAVRNMVVKAFNNNLKL T0294 319 :GEPMPSEL 2dldA 323 :GEKPDSPV Number of specific fragments extracted= 12 number of extra gaps= 5 total=686 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g76A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2g76A expands to /projects/compbio/data/pdb/2g76.pdb.gz 2g76A:Skipped atom 746, because occupancy 0.500 <= existing 0.500 in 2g76A Skipped atom 750, because occupancy 0.500 <= existing 0.500 in 2g76A Skipped atom 752, because occupancy 0.500 <= existing 0.500 in 2g76A Skipped atom 754, because occupancy 0.500 <= existing 0.500 in 2g76A Skipped atom 756, because occupancy 0.500 <= existing 0.500 in 2g76A Skipped atom 767, because occupancy 0.300 <= existing 0.700 in 2g76A Skipped atom 771, because occupancy 0.300 <= existing 0.700 in 2g76A Skipped atom 773, because occupancy 0.300 <= existing 0.700 in 2g76A Skipped atom 775, because occupancy 0.300 <= existing 0.700 in 2g76A Skipped atom 777, because occupancy 0.300 <= existing 0.700 in 2g76A Skipped atom 1371, because occupancy 0.200 <= existing 0.800 in 2g76A Skipped atom 1375, because occupancy 0.200 <= existing 0.800 in 2g76A Skipped atom 1377, because occupancy 0.200 <= existing 0.800 in 2g76A Skipped atom 1379, because occupancy 0.200 <= existing 0.800 in 2g76A Skipped atom 1381, because occupancy 0.200 <= existing 0.800 in 2g76A Skipped atom 1383, because occupancy 0.200 <= existing 0.800 in 2g76A Skipped atom 2030, because occupancy 0.500 <= existing 0.500 in 2g76A Skipped atom 2034, because occupancy 0.500 <= existing 0.500 in 2g76A Skipped atom 2036, because occupancy 0.500 <= existing 0.500 in 2g76A # T0294 read from 2g76A/merged-good-all-a2m # 2g76A read from 2g76A/merged-good-all-a2m # adding 2g76A to template set # found chain 2g76A in template set Warning: unaligning (T0294)L6 because first residue in template chain is (2g76A)L5 Warning: unaligning (T0294)L317 because last residue in template chain is (2g76A)V306 T0294 7 :MKVFVTRRIPAEGRVALARA 2g76A 6 :RKVLISDSLDPCCRKILQDG T0294 28 :DCEVEQ 2g76A 26 :GLQVVE T0294 37 :DEPIPAKELERGVAGAHGLLCLLSDHVDKRILDAA 2g76A 32 :KQNLSKEELIAELQDCEGLIVRSATKVTADVINAA T0294 73 :ANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWK 2g76A 67 :EKLQVVGRAGTGVDNVDLEAATRKGILVMNTPNGNSLSAAELTCGMIMCLARQIPQATASMKDGKWERKK T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 2g76A 137 :FMGTELNGKTLGILGLGRIGREVATRMQSFGM T0294 179 :RFLYTGRQPRPEEAAEFQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEP 2g76A 169 :KTIGYDPIISPEVSASFGVQQLPLEEIWPLCDFITVHTPLLPSTTGLLNDNTFAQCKKGVRVVNCARGGIVDEGALLRALQSGQCAGAALDVFTEEP T0294 277 :PTNHPLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAG 2g76A 266 :PRDRALVDHENVISCPHLGASTKEAQSRCGEEIAVQFVDM Number of specific fragments extracted= 7 number of extra gaps= 0 total=693 Number of alignments=55 # 2g76A read from 2g76A/merged-good-all-a2m # found chain 2g76A in template set Warning: unaligning (T0294)L6 because first residue in template chain is (2g76A)L5 Warning: unaligning (T0294)L317 because last residue in template chain is (2g76A)V306 T0294 7 :MKVFVTRRIPAEGRVALARA 2g76A 6 :RKVLISDSLDPCCRKILQDG T0294 28 :DCEVEQWD 2g76A 26 :GLQVVEKQ T0294 39 :PIPAKELERGVAGAHGLLCLLSDHVDKRILDAA 2g76A 34 :NLSKEELIAELQDCEGLIVRSATKVTADVINAA T0294 73 :ANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWK 2g76A 67 :EKLQVVGRAGTGVDNVDLEAATRKGILVMNTPNGNSLSAAELTCGMIMCLARQIPQATASMKDGKWERKK T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 2g76A 137 :FMGTELNGKTLGILGLGRIGREVATRMQSFGM T0294 179 :RFLYTGRQPRPEEAAEFQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEP 2g76A 169 :KTIGYDPIISPEVSASFGVQQLPLEEIWPLCDFITVHTPLLPSTTGLLNDNTFAQCKKGVRVVNCARGGIVDEGALLRALQSGQCAGAALDVFTEEP T0294 277 :PTNHPLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAG 2g76A 266 :PRDRALVDHENVISCPHLGASTKEAQSRCGEEIAVQFVDM Number of specific fragments extracted= 7 number of extra gaps= 0 total=700 Number of alignments=56 # 2g76A read from 2g76A/merged-good-all-a2m # found chain 2g76A in template set Warning: unaligning (T0294)L317 because last residue in template chain is (2g76A)V306 T0294 19 :GRVALARAADCEVEQWDSDE 2g76A 15 :DPCCRKILQDGGLQVVEKQN T0294 41 :PAKELERGVAGAHGLLCLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWK 2g76A 35 :LSKEELIAELQDCEGLIVRSATKVTADVINAAEKLQVVGRAGTGVDNVDLEAATRKGILVMNTPNGNSLSAAELTCGMIMCLARQIPQATASMKDGKWERKK T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEE 2g76A 137 :FMGTELNGKTLGILGLGRIGREVATRMQSFGMKTIGYDPIISPEVS T0294 193 :AEFQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLP 2g76A 183 :ASFGVQQLPLEEIWPLCDFITVHTPLLPSTTGLLNDNTFAQCKKGVRVVNCARGGIVDEGALLRALQSGQCAGAALDVFTEEPPR T0294 279 :NHPLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAG 2g76A 268 :DRALVDHENVISCPHLGASTKEAQSRCGEEIAVQFVDM Number of specific fragments extracted= 5 number of extra gaps= 0 total=705 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gsdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0294/2gsdA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0294/2gsdA/merged-good-all-a2m.gz for input Trying 2gsdA/merged-good-all-a2m Error: Couldn't open file 2gsdA/merged-good-all-a2m or 2gsdA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j4aA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1j4aA expands to /projects/compbio/data/pdb/1j4a.pdb.gz 1j4aA:Skipped atom 485, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 487, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 489, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 491, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 493, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 587, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 589, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 591, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 1333, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 1335, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 1337, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 1339, because occupancy 0.000 <= existing 0.000 in 1j4aA Skipped atom 1341, because occupancy 0.000 <= existing 0.000 in 1j4aA Skipped atom 1470, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 1472, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 1474, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 1476, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 1555, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 1557, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 1559, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 1561, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 2073, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 2075, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 2077, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 2079, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 2081, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 2182, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 2184, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 2186, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 2188, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 2190, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 2360, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 2362, because occupancy 0.500 <= existing 0.500 in 1j4aA Skipped atom 2364, because occupancy 0.500 <= existing 0.500 in 1j4aA # T0294 read from 1j4aA/merged-good-all-a2m # 1j4aA read from 1j4aA/merged-good-all-a2m # adding 1j4aA to template set # found chain 1j4aA in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1j4aA)T2 Warning: unaligning (T0294)S296 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1j4aA)Y301 Warning: unaligning (T0294)A297 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1j4aA)Y301 T0294 8 :KVFVTRRIP 1j4aA 3 :KIFAYAIRE T0294 17 :AEGRVALARA 1j4aA 14 :KPFLKEWEDA T0294 27 :ADCEVEQW 1j4aA 25 :KDVEVEYT T0294 37 :DEPIPAKE 1j4aA 33 :DKLLTPET T0294 46 :ERGVAGAHGLLCLLSDHVDKRILDAAGA 1j4aA 41 :VALAKGADGVVVYQQLDYIAETLQALAD T0294 74 :NLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWK 1j4aA 70 :GITKMSLRNVGVDNIDMAKAKELGFQITNVPVYSPNAIAEHAAIQAARILRQDKAMDEKVARHDLRWAP T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1j4aA 139 :TIGREVRDQVVGVVGTGHIGQVFMQIMEGFGA T0294 179 :RFLYTGRQPRPEEAAE 1j4aA 171 :KVITYDIFRNPELEKK T0294 196 :QAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPE 1j4aA 187 :GYYVDSLDDLYKQADVISLHVPDVPANVHMINDESIAKMKQDVVIVNVSRGPLVDTDAVIRGLDSGKIFGYAMDVYEGE T0294 275 :PLPTNHPLLT 1j4aA 271 :EDWEGKEFPD T0294 285 :LKNCVILPHIG 1j4aA 289 :RPNVLVTPKTA T0294 298 :THRTRNTMSLLAANNLLAGLRGEPMPSELKL 1j4aA 302 :TTHAVRNMVVKAFDNNLELVEGKEAETPVKV Number of specific fragments extracted= 12 number of extra gaps= 1 total=717 Number of alignments=58 # 1j4aA read from 1j4aA/merged-good-all-a2m # found chain 1j4aA in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1j4aA)T2 Warning: unaligning (T0294)S296 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1j4aA)Y301 Warning: unaligning (T0294)A297 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1j4aA)Y301 T0294 8 :KVFVTR 1j4aA 3 :KIFAYA T0294 15 :IP 1j4aA 9 :IR T0294 17 :AEGRVALARAA 1j4aA 14 :KPFLKEWEDAH T0294 28 :DCEVEQWD 1j4aA 26 :DVEVEYTD T0294 38 :EPIPAKE 1j4aA 34 :KLLTPET T0294 46 :ERGVAGAHGLLCLLSDHVDKRILDAAGA 1j4aA 41 :VALAKGADGVVVYQQLDYIAETLQALAD T0294 74 :NLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWK 1j4aA 70 :GITKMSLRNVGVDNIDMAKAKELGFQITNVPVYSPNAIAEHAAIQAARILRQDKAMDEKVARHDLRWAP T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1j4aA 139 :TIGREVRDQVVGVVGTGHIGQVFMQIMEGFGA T0294 179 :RFLYTGRQPRPEEA 1j4aA 171 :KVITYDIFRNPELE T0294 194 :EFQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPE 1j4aA 185 :KKGYYVDSLDDLYKQADVISLHVPDVPANVHMINDESIAKMKQDVVIVNVSRGPLVDTDAVIRGLDSGKIFGYAMDVYEGE T0294 275 :PLPTNHPLLT 1j4aA 271 :EDWEGKEFPD T0294 285 :LKNCVILPHIG 1j4aA 289 :RPNVLVTPKTA T0294 298 :THRTRNTMSLLAANNLLAGLRGEPMPSELKL 1j4aA 302 :TTHAVRNMVVKAFDNNLELVEGKEAETPVKV Number of specific fragments extracted= 13 number of extra gaps= 1 total=730 Number of alignments=59 # 1j4aA read from 1j4aA/merged-good-all-a2m # found chain 1j4aA in template set Warning: unaligning (T0294)S296 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1j4aA)Y301 Warning: unaligning (T0294)A297 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1j4aA)Y301 T0294 21 :VALARAADCEVEQWDSDEPIPAK 1j4aA 17 :LKEWEDAHKDVEVEYTDKLLTPE T0294 48 :GVAGAHGLLCLLSDHVDKRILDAAG 1j4aA 42 :ALAKGADGVVVYQQLDYIAETLQAL T0294 73 :ANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWK 1j4aA 69 :NGITKMSLRNVGVDNIDMAKAKELGFQITNVPVYSPNAIAEHAAIQAARILRQDKAMDEKVARHDLRWAP T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEE 1j4aA 139 :TIGREVRDQVVGVVGTGHIGQVFMQIMEGFGAKVITYDIFRNPELE T0294 194 :EFQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNH 1j4aA 185 :KKGYYVDSLDDLYKQADVISLHVPDVPANVHMINDESIAKMKQDVVIVNVSRGPLVDTDAVIRGLDSGKIFGYAMDVYEGEVGIFNE T0294 281 :PLLTLKNCVILPHIG 1j4aA 285 :DLIARPNVLVTPKTA T0294 298 :THRTRNTMSLLAANNLLAGLRGEPMPSELKL 1j4aA 302 :TTHAVRNMVVKAFDNNLELVEGKEAETPVKV Number of specific fragments extracted= 7 number of extra gaps= 1 total=737 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pjcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1pjcA expands to /projects/compbio/data/pdb/1pjc.pdb.gz 1pjcA:# T0294 read from 1pjcA/merged-good-all-a2m # 1pjcA read from 1pjcA/merged-good-all-a2m # adding 1pjcA to template set # found chain 1pjcA in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1pjcA)M1 T0294 8 :KVFVTRRI 1pjcA 2 :EIGVPKEI T0294 16 :PAEGRVALAR 1pjcA 19 :SPSSVRTLVE T0294 27 :ADCEVEQWDS 1pjcA 29 :AGHTVFIETQ T0294 39 :PIPAKELERG 1pjcA 44 :GFADQDYVQA T0294 51 :GAHGL 1pjcA 54 :GAQVV T0294 56 :LCLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDV 1pjcA 69 :MVVKVKEPLPAEYDLMQKDQLLFTYLHLAAARELTEQLMRVGLTAIAYETV T0294 107 :LTDTTAELAVSLLLTTCRRLP 1pjcA 128 :LLTPMSIIAGRLSVQFGARFL T0294 137 :GWTSWKPLWLCGY 1pjcA 149 :ERQQGGRGVLLGG T0294 150 :GLTQSTVGIIGLGRIGQAIARRLKPFGV 1pjcA 164 :GVKPGKVVILGGGVVGTEAAKMAVGLGA T0294 179 :RFLYTGR 1pjcA 192 :QVQIFDI T0294 188 :RPEEAAE 1pjcA 199 :NVERLSY T0294 196 :QAEFV 1pjcA 213 :RVELL T0294 201 :STPELAAQSDFIVVAC 1pjcA 223 :EIETAVAEADLLIGAV T0294 218 :LTPA 1pjcA 239 :LVPG T0294 225 :LCNKDFFQKMKETAVFINISRGDV 1pjcA 248 :LVPASLVEQMRTGSVIVDVAVDQG T0294 270 :VTSPEPLPTNHPLLTLKNCVILP 1pjcA 274 :VETLHPTSHTQPTYEVFGVVHYG T0294 293 :HIGSATHRTRNTMSLLAANNLLAGL 1pjcA 300 :MPGAVPWTATQALNNSTLPYVVKLA Number of specific fragments extracted= 17 number of extra gaps= 0 total=754 Number of alignments=61 # 1pjcA read from 1pjcA/merged-good-all-a2m # found chain 1pjcA in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1pjcA)M1 T0294 8 :KVFVTRR 1pjcA 2 :EIGVPKE T0294 15 :IPAEGRVALARA 1pjcA 18 :LSPSSVRTLVEA T0294 28 :DCEVEQWDS 1pjcA 30 :GHTVFIETQ T0294 39 :PIPAKELERG 1pjcA 44 :GFADQDYVQA T0294 51 :GAHG 1pjcA 54 :GAQV T0294 55 :LLCLLS 1pjcA 69 :MVVKVK T0294 62 :HVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDV 1pjcA 75 :EPLPAEYDLMQKDQLLFTYLHLAAARELTEQLMRVGLTAIAYETV T0294 107 :LTDTTAELAVSLLLTTCRRL 1pjcA 128 :LLTPMSIIAGRLSVQFGARF T0294 134 :KNGGWTSWKPLWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1pjcA 148 :LERQQGGRGVLLGGVPGVKPGKVVILGGGVVGTEAAKMAVGLGA T0294 179 :RFLYTGRQPR 1pjcA 192 :QVQIFDINVE T0294 191 :EA 1pjcA 202 :RL T0294 195 :FQAEFV 1pjcA 212 :SRVELL T0294 201 :STPELAAQSDFIVVAC 1pjcA 223 :EIETAVAEADLLIGAV T0294 218 :LTPA 1pjcA 239 :LVPG T0294 222 :TE 1pjcA 246 :PI T0294 225 :LCNKDFFQKMKETAVFINIS 1pjcA 248 :LVPASLVEQMRTGSVIVDVA T0294 245 :RGDVV 1pjcA 270 :QGGCV T0294 271 :TSPEPLPTNHPLLTLKNCVILP 1pjcA 275 :ETLHPTSHTQPTYEVFGVVHYG T0294 293 :HIGSATHRTRNTMSLLAANNLLAGL 1pjcA 300 :MPGAVPWTATQALNNSTLPYVVKLA Number of specific fragments extracted= 19 number of extra gaps= 0 total=773 Number of alignments=62 # 1pjcA read from 1pjcA/merged-good-all-a2m # found chain 1pjcA in template set T0294 24 :ARAADCEVEQWDS 1pjcA 26 :LVEAGHTVFIETQ T0294 39 :PIPAKELERGV 1pjcA 44 :GFADQDYVQAG T0294 53 :HGLL 1pjcA 55 :AQVV T0294 57 :CLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTP 1pjcA 70 :VVKVKEPLPAEYDLMQKDQLLFTYLHLAAARELTEQLMRVGLTAIAYE T0294 105 :DVLTDTTAELAVSLLLTTCRRLPE 1pjcA 126 :LPLLTPMSIIAGRLSVQFGARFLE T0294 136 :GGWTSWKPLWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGR 1pjcA 150 :RQQGGRGVLLGGVPGVKPGKVVILGGGVVGTEAAKMAVGLGAQVQIFDIN T0294 189 :PEE 1pjcA 200 :VER T0294 192 :AAEFQAEFVS 1pjcA 211 :GSRVELLYSN T0294 202 :TPELAAQSDFIVVACSLTPA 1pjcA 224 :IETAVAEADLLIGAVLVPGR T0294 225 :LCNKDFFQKMKETAVFINISRGD 1pjcA 248 :LVPASLVEQMRTGSVIVDVAVDQ T0294 262 :KIA 1pjcA 271 :GGC T0294 270 :VTSPEPLPTNH 1pjcA 274 :VETLHPTSHTQ T0294 293 :HIGSATHRTRNTMSLLAANNLLAGL 1pjcA 300 :MPGAVPWTATQALNNSTLPYVVKLA Number of specific fragments extracted= 13 number of extra gaps= 0 total=786 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1li4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1li4A expands to /projects/compbio/data/pdb/1li4.pdb.gz 1li4A:# T0294 read from 1li4A/merged-good-all-a2m # 1li4A read from 1li4A/merged-good-all-a2m # adding 1li4A to template set # found chain 1li4A in template set T0294 1 :SRPVRLMKVFVTRRIPAE 1li4A 42 :SKPLKGARIAGCLHMTVE T0294 19 :GRVALARAADCEVEQWDSDEPIPAKELERGV 1li4A 62 :VLIETLVTLGAEVQWSSCNIFSTQDHAAAAI T0294 50 :AGAHGL 1li4A 95 :AGIPVY T0294 58 :LLSDHVDKRILDAAG 1li4A 101 :AWKGETDEEYLWCIE T0294 73 :A 1li4A 122 :D T0294 74 :NLKVIST 1li4A 124 :PLNMILD T0294 83 :VGIDHLAL 1li4A 131 :DGGDLTNL T0294 92 :EIKKR 1li4A 139 :IHTKY T0294 97 :GIRVGYTPDVLTDT 1li4A 174 :KVPAINVNDSVTKS T0294 111 :TAELAVSLLLTTCRR 1li4A 191 :NLYGCRESLIDGIKR T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1li4A 206 :ATDVMIAGKVAVVAGYGDVGKGCAQALRGFGA T0294 179 :RFLYTGRQPRPE 1li4A 238 :RVIITEIDPINA T0294 191 :EAAEFQAEFVSTPELAAQSDFIVVAC 1li4A 251 :QAAMEGYEVTTMDEACQEGNIFVTTT T0294 221 :ATEGLCNKDFFQKMKETAVFINISRGDV 1li4A 277 :GCIDIILGRHFEQMKDDAIVCNIGHFDV T0294 249 :VNQDDLYQ 1li4A 306 :IDVKWLNE T0294 263 :IAAAGLDVTS 1li4A 320 :NIKPQVDRYR T0294 277 :PTNHP 1li4A 330 :LKNGR T0294 282 :LLTL 1li4A 339 :LAEG T0294 292 :PHIGSATHRTRNTMSLLAANNLL 1li4A 352 :GHPSFVMSNSFTNQVMAQIELWT Number of specific fragments extracted= 19 number of extra gaps= 0 total=805 Number of alignments=64 # 1li4A read from 1li4A/merged-good-all-a2m # found chain 1li4A in template set T0294 7 :MKVFVTR 1li4A 72 :AEVQWSS T0294 14 :RIPAEGRVALARA 1li4A 83 :STQDHAAAAIAKA T0294 28 :DCEVEQWD 1li4A 96 :GIPVYAWK T0294 39 :PIPAKELERGV 1li4A 104 :GETDEEYLWCI T0294 50 :AG 1li4A 121 :KD T0294 52 :AHGLLCLLS 1li4A 125 :LNMILDDGG T0294 66 :RILDAA 1li4A 134 :DLTNLI T0294 73 :ANLKVISTMS 1li4A 148 :PGIRGISEET T0294 90 :LDEIKKR 1li4A 161 :VHNLYKM T0294 98 :IRVGYTPDV 1li4A 175 :VPAINVNDS T0294 107 :LTDTTAELAVSLLLTT 1li4A 191 :NLYGCRESLIDGIKRA T0294 147 :CGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1li4A 207 :TDVMIAGKVAVVAGYGDVGKGCAQALRGFGA T0294 179 :RFLYTGRQPR 1li4A 238 :RVIITEIDPI T0294 189 :PEEAAEFQAEFVSTPELAAQSDFIVVACSL 1li4A 249 :ALQAAMEGYEVTTMDEACQEGNIFVTTTGC T0294 223 :EGLCNKDFFQKMKETAVFINISRGDV 1li4A 279 :IDIILGRHFEQMKDDAIVCNIGHFDV T0294 249 :VNQDDLYQ 1li4A 306 :IDVKWLNE Number of specific fragments extracted= 16 number of extra gaps= 0 total=821 Number of alignments=65 # 1li4A read from 1li4A/merged-good-all-a2m # found chain 1li4A in template set T0294 37 :DEPIPAKELERGVAG 1li4A 102 :WKGETDEEYLWCIEQ T0294 52 :AHGLLCLLSDHVDKRIL 1li4A 123 :GPLNMILDDGGDLTNLI T0294 69 :DAAGANLKVISTMS 1li4A 144 :PQLLPGIRGISEET T0294 90 :LDEIKK 1li4A 161 :VHNLYK T0294 96 :RG 1li4A 170 :NG T0294 98 :IRVGYTPDV 1li4A 175 :VPAINVNDS T0294 107 :LTDTTAELAVSLLLTTC 1li4A 191 :NLYGCRESLIDGIKRAT T0294 148 :GYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEEAAEFQAEFVSTPELAAQSDFIVVACSLTP 1li4A 208 :DVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQAAMEGYEVTTMDEACQEGNIFVTTTGCID T0294 225 :LCNKDFFQKMKETAVFINISRGD 1li4A 281 :IILGRHFEQMKDDAIVCNIGHFD T0294 248 :VVNQDDLYQ 1li4A 305 :EIDVKWLNE Number of specific fragments extracted= 10 number of extra gaps= 0 total=831 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l7dA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1l7dA expands to /projects/compbio/data/pdb/1l7d.pdb.gz 1l7dA:# T0294 read from 1l7dA/merged-good-all-a2m # 1l7dA read from 1l7dA/merged-good-all-a2m # adding 1l7dA to template set # found chain 1l7dA in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1l7dA)M1 Warning: unaligning (T0294)T202 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1l7dA)K245 T0294 8 :KVFVTR 1l7dA 2 :KIAIPK T0294 14 :RIPAEGRVALAR 1l7dA 17 :AISPEVVKKLVG T0294 27 :ADCEVEQW 1l7dA 29 :LGFEVIVE T0294 39 :PIPAKELERG 1l7dA 44 :SITDDALTAA T0294 49 :VAGAHGLLCLLSDHVDKR 1l7dA 65 :LSQADVVWKVQRPMTAEE T0294 67 :ILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGY 1l7dA 86 :EVALIKEGAVLMCHLGALTNRPVVEALTKRKITAYA T0294 103 :TPDVLT 1l7dA 125 :MPRISR T0294 109 :DTTAELAVSLLLTTCRRLP 1l7dA 138 :SSQSNLAGYRAVIDGAYEF T0294 138 :WTSWKPLWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1l7dA 157 :ARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKRLGA T0294 179 :RFLYTGRQP 1l7dA 197 :VVMATDVRA T0294 188 :RPEEAAEFQAEFVS 1l7dA 207 :TKEQVESLGGKFIT T0294 204 :ELAAQSDFIVV 1l7dA 253 :KELVKTDIAIT T0294 216 :CSLTPA 1l7dA 264 :TALIPG T0294 222 :TEGLCNKDFFQKMKETAVFINISRGDV 1l7dA 272 :APVLITEEMVTKMKPGSVIIDLAVEAG T0294 250 :N 1l7dA 300 :N T0294 274 :EPLPTNHPLLTLKNCVILPH 1l7dA 301 :CPLSEPGKIVVKHGVKIVGH T0294 294 :IGSATH 1l7dA 324 :PSRVAA T0294 304 :TMSLLAANNLLAGL 1l7dA 330 :DASPLFAKNLLNFL Number of specific fragments extracted= 18 number of extra gaps= 0 total=849 Number of alignments=67 # 1l7dA read from 1l7dA/merged-good-all-a2m # found chain 1l7dA in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1l7dA)M1 T0294 8 :KVFVTR 1l7dA 2 :KIAIPK T0294 15 :IPAEGRVALARA 1l7dA 18 :ISPEVVKKLVGL T0294 28 :DCEVEQWDS 1l7dA 30 :GFEVIVEQG T0294 39 :PIPAKELERG 1l7dA 44 :SITDDALTAA T0294 49 :VAGAHGLLCLLS 1l7dA 65 :LSQADVVWKVQR T0294 62 :HVDKR 1l7dA 77 :PMTAE T0294 67 :ILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLT 1l7dA 86 :EVALIKEGAVLMCHLGALTNRPVVEALTKRKITAYAMELMPR T0294 109 :DTTAELAVSLLLTTCRRL 1l7dA 138 :SSQSNLAGYRAVIDGAYE T0294 138 :WTSWKPLWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1l7dA 157 :ARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKRLGA T0294 179 :RFLYTGRQPR 1l7dA 197 :VVMATDVRAA T0294 189 :PEEAAEFQAEFVS 1l7dA 208 :KEQVESLGGKFIT T0294 204 :ELAAQSDFIVV 1l7dA 253 :KELVKTDIAIT T0294 216 :CSLTPA 1l7dA 264 :TALIPG T0294 222 :TE 1l7dA 273 :PV T0294 225 :LCNKDFFQKMKETAVFINIS 1l7dA 275 :LITEEMVTKMKPGSVIIDLA T0294 245 :RGDVVN 1l7dA 300 :NCPLSE T0294 260 :SGKIAA 1l7dA 306 :PGKIVV T0294 285 :LKNCVILPH 1l7dA 312 :KHGVKIVGH T0294 294 :IGSAT 1l7dA 324 :PSRVA T0294 303 :NTMSLLAANNLLAGL 1l7dA 329 :ADASPLFAKNLLNFL Number of specific fragments extracted= 20 number of extra gaps= 0 total=869 Number of alignments=68 # 1l7dA read from 1l7dA/merged-good-all-a2m # found chain 1l7dA in template set Warning: unaligning (T0294)T202 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1l7dA)K245 T0294 24 :ARAADCEVEQWDS 1l7dA 48 :DALTAAGATIAST T0294 46 :ERGVAGAHGLLCLLSDHVDKRI 1l7dA 61 :AAQALSQADVVWKVQRPMTAEE T0294 68 :LDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTP 1l7dA 87 :VALIKEGAVLMCHLGALTNRPVVEALTKRKITAYAME T0294 105 :DVLTDTTAELAVSLLLTTCRRLP 1l7dA 134 :MDILSSQSNLAGYRAVIDGAYEF T0294 138 :WTSWKPLWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEEAAEFQAEFVS 1l7dA 157 :ARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKRLGAVVMATDVRAATKEQVESLGGKFIT T0294 205 :LAAQSDF 1l7dA 254 :ELVKTDI T0294 213 :VVACSLTPA 1l7dA 261 :AITTALIPG T0294 224 :GLCNKDFFQKMKETAVFINISRGDVVN 1l7dA 274 :VLITEEMVTKMKPGSVIIDLAVEAGGN T0294 260 :SGKIA 1l7dA 306 :PGKIV T0294 286 :KNCVILPHIGSATH 1l7dA 313 :HGVKIVGHTNVPSR T0294 301 :TRNTMSLLAANNLLAGL 1l7dA 327 :VAADASPLFAKNLLNFL Number of specific fragments extracted= 11 number of extra gaps= 0 total=880 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c1dA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0294 read from 1c1dA/merged-good-all-a2m # 1c1dA read from 1c1dA/merged-good-all-a2m # found chain 1c1dA in training set T0294 4 :VRLMKVFVTRR 1c1dA 74 :MGGGKSVIALP T0294 15 :IPAEGRVALARA 1c1dA 90 :IDPSTWARILRI T0294 45 :LER 1c1dA 102 :HAE T0294 67 :ILDAAGANL 1c1dA 105 :NIDKLSGNY T0294 78 :ISTMSVGIDHLALDEIKKR 1c1dA 114 :WTGPDVNTNSADMDTLNDT T0294 97 :GI 1c1dA 144 :GG T0294 104 :PDVLTDTTAELAVSLLLTTCR 1c1dA 146 :AGSSAFTTAVGVFEAMKATVA T0294 146 :LCGY 1c1dA 167 :HRGL T0294 150 :GLTQSTVGIIGLGRIGQAIARRLKPFGV 1c1dA 172 :SLDGLTVLVQGLGAVGGSLASLAAEAGA T0294 179 :RFLYTGRQP 1c1dA 200 :QLLVADTDT T0294 188 :RPEEAAEFQAEFVSTPELAAQ 1c1dA 210 :RVAHAVALGHTAVALEDVLST T0294 209 :SDFIVVACSL 1c1dA 232 :CDVFAPCAMG T0294 224 :GLCNKDFFQKMK 1c1dA 242 :GVITTEVARTLD T0294 238 :AVFINISRGDVVNQDDLYQALASGKIAAA 1c1dA 254 :CSVVAGAANNVIADEAASDILHARGILYA Number of specific fragments extracted= 14 number of extra gaps= 0 total=894 Number of alignments=70 # 1c1dA read from 1c1dA/merged-good-all-a2m # found chain 1c1dA in training set T0294 9 :VFVTRR 1c1dA 80 :VIALPA T0294 15 :IPAEGRVALARAA 1c1dA 90 :IDPSTWARILRIH T0294 65 :KRILDAAGANLK 1c1dA 103 :AENIDKLSGNYW T0294 79 :STMSVGIDHLALDEIKK 1c1dA 115 :TGPDVNTNSADMDTLND T0294 96 :RG 1c1dA 143 :RG T0294 103 :TPDVLTDTTAELAVSLLLTTCRR 1c1dA 145 :GAGSSAFTTAVGVFEAMKATVAH T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1c1dA 168 :RGLGSLDGLTVLVQGLGAVGGSLASLAAEAGA T0294 179 :RFLYTGRQPR 1c1dA 200 :QLLVADTDTE T0294 189 :PEEAAEFQAEFVSTPELAAQ 1c1dA 211 :VAHAVALGHTAVALEDVLST T0294 209 :SDFIVVACSLT 1c1dA 232 :CDVFAPCAMGG T0294 225 :LCNKDFFQKMK 1c1dA 243 :VITTEVARTLD T0294 238 :AVFINISRGDVVNQDDLYQALASGKIAAA 1c1dA 254 :CSVVAGAANNVIADEAASDILHARGILYA T0294 296 :SATHRTRNTMSLLAANNLLAGL 1c1dA 302 :GWSESVVHERAVAIGDTLNQVF Number of specific fragments extracted= 13 number of extra gaps= 0 total=907 Number of alignments=71 # 1c1dA read from 1c1dA/merged-good-all-a2m # found chain 1c1dA in training set T0294 40 :IPAKELERGVAG 1c1dA 90 :IDPSTWARILRI T0294 65 :KRILDAAGAN 1c1dA 103 :AENIDKLSGN T0294 77 :VISTMSVGIDHLALDEIKK 1c1dA 113 :YWTGPDVNTNSADMDTLND T0294 96 :RG 1c1dA 143 :RG T0294 103 :TPDVLTDTTAELAVSLLLTTCRR 1c1dA 145 :GAGSSAFTTAVGVFEAMKATVAH T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEEAAEFQAEFVSTPELAAQ 1c1dA 168 :RGLGSLDGLTVLVQGLGAVGGSLASLAAEAGAQLLVADTDTERVAHAVALGHTAVALEDVLST T0294 209 :SDFIVVAC 1c1dA 232 :CDVFAPCA T0294 218 :LT 1c1dA 240 :MG T0294 224 :GLCNKDFFQKMK 1c1dA 242 :GVITTEVARTLD T0294 238 :AVFINISRGDVVNQDDLYQALASGKIAAA 1c1dA 254 :CSVVAGAANNVIADEAASDILHARGILYA Number of specific fragments extracted= 10 number of extra gaps= 0 total=917 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lehA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lehA expands to /projects/compbio/data/pdb/1leh.pdb.gz 1lehA:# T0294 read from 1lehA/merged-good-all-a2m # 1lehA read from 1lehA/merged-good-all-a2m # adding 1lehA to template set # found chain 1lehA in template set T0294 7 :MKV 1lehA 38 :PAL T0294 10 :FVTRRIP 1lehA 43 :ARMWTYN T0294 17 :AEGRVALARA 1lehA 52 :EEAIEDALRL T0294 27 :ADCE 1lehA 72 :AGLN T0294 31 :VEQWDSDEPIPAK 1lehA 82 :VIIGDPFADKNED T0294 44 :ELERGVAG 1lehA 98 :ALGRFIQG T0294 55 :LLCLLSDHVDKRILDAAGAN 1lehA 110 :YITAEDVGTTVDDMDLIHQE T0294 85 :IDHLA 1lehA 130 :TDYVT T0294 90 :LDEIKKR 1lehA 137 :SPAFGSS T0294 106 :VLTDTTAELAVSLLL 1lehA 144 :GNPSPVTAYGVYRGM T0294 121 :TTCRRL 1lehA 160 :AAAKEA T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1lehA 166 :FGSDSLEGLAVSVQGLGNVAKALCKKLNTEGA T0294 179 :RFLYTGR 1lehA 198 :KLVVTDV T0294 188 :RPEEAAEF 1lehA 205 :NKAAVSAA T0294 196 :QAEFVSTPELAA 1lehA 217 :GADAVAPNAIYG T0294 209 :SDFIVVACS 1lehA 231 :CDIFAPCAL T0294 223 :EGLCNKDFFQKMKETAV 1lehA 240 :GAVLNDFTIPQLKAKVI T0294 243 :ISRGDV 1lehA 257 :AGSADN T0294 249 :VNQDDLYQALASGKIAA 1lehA 265 :KDPRHGKYLHELGIVYA Number of specific fragments extracted= 19 number of extra gaps= 0 total=936 Number of alignments=73 # 1lehA read from 1lehA/merged-good-all-a2m # found chain 1lehA in template set T0294 7 :MKVFVTRR 1lehA 79 :GKTVIIGD T0294 15 :IPAEGRVALARA 1lehA 91 :KNEDMFRALGRF T0294 27 :ADCEVEQWD 1lehA 106 :LNGRYITAE T0294 60 :SDHVDKRILDAAGANL 1lehA 115 :DVGTTVDDMDLIHQET T0294 86 :DHLA 1lehA 131 :DYVT T0294 90 :LDEIKKR 1lehA 137 :SPAFGSS T0294 106 :VLTDTTAELAVSLLLTTCRRL 1lehA 144 :GNPSPVTAYGVYRGMKAAAKE T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1lehA 166 :FGSDSLEGLAVSVQGLGNVAKALCKKLNTEGA T0294 179 :RFLYTGRQPR 1lehA 198 :KLVVTDVNKA T0294 193 :AEFQAEFVSTPELAA 1lehA 214 :AEEGADAVAPNAIYG T0294 209 :SDFIVVACSL 1lehA 231 :CDIFAPCALG T0294 224 :GLCNKDFFQKMKET 1lehA 241 :AVLNDFTIPQLKAK T0294 239 :VFINISRGDVVNQDDLYQALASGKIA 1lehA 255 :VIAGSADNQLKDPRHGKYLHELGIVY T0294 275 :P 1lehA 330 :P T0294 301 :TRNTMSLLAANNLLAGL 1lehA 331 :SYVAADRMAEERIAKVA T0294 318 :RGEPMPS 1lehA 350 :RSQFLQD Number of specific fragments extracted= 16 number of extra gaps= 0 total=952 Number of alignments=74 # 1lehA read from 1lehA/merged-good-all-a2m # found chain 1lehA in template set T0294 32 :EQWDSDEPIPAKEL 1lehA 82 :VIIGDPFADKNEDM T0294 46 :ERGVAGAHGLLCLLSDHVDKRILDAAGANL 1lehA 101 :RFIQGLNGRYITAEDVGTTVDDMDLIHQET T0294 86 :DHL 1lehA 131 :DYV T0294 89 :ALDEIKK 1lehA 136 :ISPAFGS T0294 106 :VLTDTTAELAVSLLLTTCRRL 1lehA 144 :GNPSPVTAYGVYRGMKAAAKE T0294 145 :WLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGR 1lehA 165 :AFGSDSLEGLAVSVQGLGNVAKALCKKLNTEGAKLVVTDVN T0294 189 :PEE 1lehA 206 :KAA T0294 192 :AAEFQAEFVSTPELAAQ 1lehA 213 :VAEEGADAVAPNAIYGV T0294 209 :SDFI 1lehA 231 :CDIF T0294 214 :VACSLTP 1lehA 235 :APCALGA T0294 225 :LCNKDFFQKMKETAV 1lehA 242 :VLNDFTIPQLKAKVI T0294 241 :INISRGDVVNQDDLYQALASGKIA 1lehA 257 :AGSADNQLKDPRHGKYLHELGIVY T0294 281 :PLLTLK 1lehA 297 :ELYGYN T0294 299 :HRTRNTMSLLAANNLLAGL 1lehA 303 :RTRAMKRVDGIYDSIEKIF Number of specific fragments extracted= 14 number of extra gaps= 0 total=966 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ybaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0294/1ybaA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0294/1ybaA/merged-good-all-a2m.gz for input Trying 1ybaA/merged-good-all-a2m Error: Couldn't open file 1ybaA/merged-good-all-a2m or 1ybaA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a7aA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a7aA expands to /projects/compbio/data/pdb/1a7a.pdb.gz 1a7aA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0294 read from 1a7aA/merged-good-all-a2m # 1a7aA read from 1a7aA/merged-good-all-a2m # adding 1a7aA to template set # found chain 1a7aA in template set T0294 1 :SRPVRLMKVFVTRRIPAE 1a7aA 42 :SKPLKGARIAGCLHMTVE T0294 19 :GRVALARAADCEVEQWDSDEPIPAKELERGV 1a7aA 62 :VLIETLVTLGAEVQWSSCNIFSTQNHAAAAI T0294 50 :AGAHGL 1a7aA 95 :AGIPVY T0294 59 :LSDHVDKRILDAA 1a7aA 101 :AWKGETDEEYLWC T0294 72 :GANLKVIST 1a7aA 122 :DGPLNMILD T0294 83 :VGIDHLAL 1a7aA 131 :DGGDLTNL T0294 92 :EIKKR 1a7aA 139 :IHTKY T0294 97 :GIRVGYTPDVLTDT 1a7aA 174 :KVPAINVNDSVTKS T0294 111 :TAELAVSLLLTTCRR 1a7aA 191 :NLYGCRESLIDGIKR T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1a7aA 206 :ATDVMIAGKVAVVAGYGDVGKGCAQALRGFGA T0294 179 :RFLYTGRQPRPE 1a7aA 238 :RVIITEIDPINA T0294 191 :EAAEFQAEFVSTPELAAQSDFIVVAC 1a7aA 251 :QAAMEGYEVTTMDEACQEGNIFVTTT T0294 221 :ATEGLCNKDFFQKMKETAVFINISRGDV 1a7aA 277 :GCIDIILGRHFEQMKDDAIVCNIGHFDV T0294 249 :VNQDDLYQ 1a7aA 306 :IDVKWLNE T0294 262 :KIAAAGLDVTS 1a7aA 319 :VNIKPQVDRYR T0294 277 :PTNHP 1a7aA 330 :LKNGR T0294 282 :LLT 1a7aA 339 :LAE T0294 292 :PHIGSATHRTRNTMSLLAANNLL 1a7aA 352 :GHPSFVMSNSFTNQVMAQIELWT Number of specific fragments extracted= 18 number of extra gaps= 0 total=984 Number of alignments=76 # 1a7aA read from 1a7aA/merged-good-all-a2m # found chain 1a7aA in template set T0294 7 :MKVFVTR 1a7aA 72 :AEVQWSS T0294 14 :RIPAEGRVALARA 1a7aA 83 :STQNHAAAAIAKA T0294 28 :DCEVEQWD 1a7aA 96 :GIPVYAWK T0294 39 :PIPAKELERGV 1a7aA 104 :GETDEEYLWCI T0294 50 :AG 1a7aA 121 :KD T0294 52 :AHGLLCLLS 1a7aA 125 :LNMILDDGG T0294 66 :RILDAA 1a7aA 134 :DLTNLI T0294 72 :GANLKVISTMS 1a7aA 147 :LPGIRGISEET T0294 89 :ALDEIKKRG 1a7aA 163 :NLYKMMANG T0294 98 :IRVGYTPDV 1a7aA 175 :VPAINVNDS T0294 107 :LTDTTAELAVSLLLT 1a7aA 191 :NLYGCRESLIDGIKR T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1a7aA 206 :ATDVMIAGKVAVVAGYGDVGKGCAQALRGFGA T0294 179 :RFLYTGRQPR 1a7aA 238 :RVIITEIDPI T0294 189 :PEEAAEFQAEFVSTPELAAQSDFIVVAC 1a7aA 249 :ALQAAMEGYEVTTMDEACQEGNIFVTTT T0294 221 :ATEGLCNKDFFQKMKETAVFINISRGDV 1a7aA 277 :GCIDIILGRHFEQMKDDAIVCNIGHFDV T0294 249 :VNQDDLYQ 1a7aA 306 :IDVKWLNE Number of specific fragments extracted= 16 number of extra gaps= 0 total=1000 Number of alignments=77 # 1a7aA read from 1a7aA/merged-good-all-a2m # found chain 1a7aA in template set T0294 34 :WDSDEPIPAKELERGV 1a7aA 99 :VYAWKGETDEEYLWCI T0294 50 :AGAHGLLCLLSDHVDKRILDAAGA 1a7aA 121 :KDGPLNMILDDGGDLTNLIHTKYP T0294 74 :NLKVISTMS 1a7aA 149 :GIRGISEET T0294 89 :ALDEIKKRG 1a7aA 163 :NLYKMMANG T0294 98 :IRVGYTPDVLT 1a7aA 175 :VPAINVNDSVT T0294 109 :DTTAELAVSLLLTTC 1a7aA 193 :YGCRESLIDGIKRAT T0294 148 :GYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEEAAEFQAEFVSTPELAAQSDFIVVACSLTP 1a7aA 208 :DVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQAAMEGYEVTTMDEACQEGNIFVTTTGCID T0294 225 :LCNKDFFQKMKETAVFINISRGD 1a7aA 281 :IILGRHFEQMKDDAIVCNIGHFD T0294 248 :VVNQDDLYQ 1a7aA 305 :EIDVKWLNE Number of specific fragments extracted= 9 number of extra gaps= 0 total=1009 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sayA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sayA expands to /projects/compbio/data/pdb/1say.pdb.gz 1sayA:# T0294 read from 1sayA/merged-good-all-a2m # 1sayA read from 1sayA/merged-good-all-a2m # adding 1sayA to template set # found chain 1sayA in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1sayA)M1 Warning: unaligning (T0294)L218 because of BadResidue code BAD_PEPTIDE in next template residue (1sayA)P241 Warning: unaligning (T0294)T219 because of BadResidue code BAD_PEPTIDE at template residue (1sayA)P241 T0294 8 :KVFVTRR 1sayA 2 :EIGVPKE T0294 15 :IPAEGRVALAR 1sayA 18 :LSPSSVRTLVE T0294 27 :ADCEVEQWDS 1sayA 29 :AGHTVFIETQ T0294 39 :PIPAKELERG 1sayA 44 :GFADQDYVQA T0294 51 :GAHGL 1sayA 54 :GAQVV T0294 56 :LCLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDV 1sayA 69 :MVVKVKEPLPAEYDLMQKDQLLFTYLHLAAARELTEQLMRVGLTAIAYETV T0294 107 :LTDTTAELAVSLLLTTCRRLP 1sayA 128 :LLTPMSIIAGRLSVQFGARFL T0294 137 :GWTSWKPLWLCGY 1sayA 149 :ERQQGGRGVLLGG T0294 150 :GLTQSTVGIIGLGRIGQAIARRLKPFGV 1sayA 164 :GVKPGKVVILGGGVVGTEAAKMAVGLGA T0294 179 :RFLYTGR 1sayA 192 :QVQIFDI T0294 188 :RPEEAAE 1sayA 199 :NVERLSY T0294 196 :QAEFV 1sayA 213 :RVELL T0294 201 :STPELAAQSDFIVVACS 1sayA 223 :EIETAVAEADLLIGAVL T0294 220 :PA 1sayA 242 :GR T0294 222 :TEGLCNKDFFQKMKETAVFINISRGDV 1sayA 245 :APILVPASLVEQMRTGSVIVDVAVDQG T0294 270 :VTSPEPLPTNHPLLTLKNCVILP 1sayA 274 :VETLHPTSHTQPTYEVFGVVHYG T0294 293 :HIGSATHRTRNTMSLLAANNLLAGL 1sayA 300 :MPGAVPWTATQALNNSTLPYVVKLA Number of specific fragments extracted= 17 number of extra gaps= 1 total=1026 Number of alignments=79 # 1sayA read from 1sayA/merged-good-all-a2m # found chain 1sayA in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1sayA)M1 Warning: unaligning (T0294)L218 because of BadResidue code BAD_PEPTIDE in next template residue (1sayA)P241 Warning: unaligning (T0294)T219 because of BadResidue code BAD_PEPTIDE at template residue (1sayA)P241 T0294 8 :KVFVTRR 1sayA 2 :EIGVPKE T0294 15 :IPAEGRVALARA 1sayA 18 :LSPSSVRTLVEA T0294 28 :DCEVEQWDS 1sayA 30 :GHTVFIETQ T0294 39 :PIPAKELERG 1sayA 44 :GFADQDYVQA T0294 51 :GAHG 1sayA 54 :GAQV T0294 56 :LCLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDV 1sayA 69 :MVVKVKEPLPAEYDLMQKDQLLFTYLHLAAARELTEQLMRVGLTAIAYETV T0294 107 :LTDTTAELAVSLLLTTCRRL 1sayA 128 :LLTPMSIIAGRLSVQFGARF T0294 134 :KNGGWTSWKPLWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1sayA 148 :LERQQGGRGVLLGGVPGVKPGKVVILGGGVVGTEAAKMAVGLGA T0294 179 :RFLYTGRQPR 1sayA 192 :QVQIFDINVE T0294 191 :EA 1sayA 202 :RL T0294 193 :AEFQAEFV 1sayA 210 :FGSRVELL T0294 201 :STPELAAQSDFIVVACS 1sayA 223 :EIETAVAEADLLIGAVL T0294 220 :PA 1sayA 242 :GR T0294 222 :TE 1sayA 246 :PI T0294 225 :LCNKDFFQKMKETAVFINIS 1sayA 248 :LVPASLVEQMRTGSVIVDVA T0294 245 :RGDVVN 1sayA 270 :QGGCVE T0294 272 :SPEPLPTNHPLLTLKNCVILP 1sayA 276 :TLHPTSHTQPTYEVFGVVHYG T0294 293 :HIGSATHRTRNTMSLLAANNLLAGL 1sayA 300 :MPGAVPWTATQALNNSTLPYVVKLA Number of specific fragments extracted= 18 number of extra gaps= 1 total=1044 Number of alignments=80 # 1sayA read from 1sayA/merged-good-all-a2m # found chain 1sayA in template set Warning: unaligning (T0294)L218 because of BadResidue code BAD_PEPTIDE in next template residue (1sayA)P241 Warning: unaligning (T0294)T219 because of BadResidue code BAD_PEPTIDE at template residue (1sayA)P241 T0294 24 :ARAADCEVEQWDSDE 1sayA 24 :RTLVEAGHTVFIETQ T0294 39 :PIPAKELERGV 1sayA 44 :GFADQDYVQAG T0294 53 :HGL 1sayA 55 :AQV T0294 56 :LCLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTP 1sayA 69 :MVVKVKEPLPAEYDLMQKDQLLFTYLHLAAARELTEQLMRVGLTAIAYE T0294 105 :DVLTDTTAELAVSLLLTTCRRLPE 1sayA 126 :LPLLTPMSIIAGRLSVQFGARFLE T0294 136 :GGWTSWKPLWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGR 1sayA 150 :RQQGGRGVLLGGVPGVKPGKVVILGGGVVGTEAAKMAVGLGAQVQIFDIN T0294 189 :PEE 1sayA 200 :VER T0294 192 :AAEFQAEFVS 1sayA 211 :GSRVELLYSN T0294 202 :TPELAAQSDFIVVACS 1sayA 224 :IETAVAEADLLIGAVL T0294 220 :PA 1sayA 242 :GR T0294 225 :LCNKDFFQKMKETAVFINISRGD 1sayA 248 :LVPASLVEQMRTGSVIVDVAVDQ T0294 262 :KI 1sayA 271 :GG T0294 270 :VTSPEPLPTNH 1sayA 274 :VETLHPTSHTQ T0294 293 :HIGSATHRTRNTMSLLAANNLLAGL 1sayA 300 :MPGAVPWTATQALNNSTLPYVVKLA Number of specific fragments extracted= 14 number of extra gaps= 1 total=1058 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c2xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2c2xA expands to /projects/compbio/data/pdb/2c2x.pdb.gz 2c2xA:# T0294 read from 2c2xA/merged-good-all-a2m # 2c2xA read from 2c2xA/merged-good-all-a2m # adding 2c2xA to template set # found chain 2c2xA in template set Warning: unaligning (T0294)A315 because of BadResidue code BAD_PEPTIDE in next template residue (2c2xA)R281 T0294 5 :RLMKV 2c2xA 31 :RTPGL T0294 10 :FVTRRIPAEGRVALA 2c2xA 37 :TILVGDDPGSQAYVR T0294 25 :RAADCEVEQWDSDEPIPAKELERG 2c2xA 58 :AKVGITSIRRDLPADISTATLNET T0294 68 :LDAA 2c2xA 82 :IDEL T0294 72 :GANLKVISTMSVGIDHLALDEIKKR 2c2xA 88 :NPDCTGYIVQLPLPKHLDENAALER T0294 102 :YTPDVLTDTTAE 2c2xA 118 :DADGLHPTNLGR T0294 114 :LAVSLLLTTCR 2c2xA 140 :CTPRGIVHLLR T0294 146 :LCGYGLTQSTVGIIGLG 2c2xA 151 :RYDISIAGAHVVVIGRG T0294 163 :RIGQAIARRLK 2c2xA 169 :TVGRPLGLLLT T0294 174 :PFGV 2c2xA 182 :SENA T0294 179 :RFLYTGR 2c2xA 186 :TVTLCHT T0294 198 :EFVSTPELAAQSDFIVVAC 2c2xA 193 :GTRDLPALTRQADIVVAAV T0294 221 :ATEGLCNKDF 2c2xA 212 :GVAHLLTADM T0294 234 :MKETAVFINIS 2c2xA 222 :VRPGAAVIDVG T0294 260 :SG 2c2xA 237 :DD T0294 265 :AAGLDV 2c2xA 239 :GLVGDV T0294 277 :PT 2c2xA 245 :HP T0294 281 :PLLT 2c2xA 247 :DVWE T0294 285 :LK 2c2xA 252 :AG T0294 289 :VILPHIGSATHRTRNTMSLLAANNLL 2c2xA 254 :HVSPNPGGVGPLTRAFLLTNVVELAE Number of specific fragments extracted= 20 number of extra gaps= 1 total=1078 Number of alignments=82 # 2c2xA read from 2c2xA/merged-good-all-a2m # found chain 2c2xA in template set Warning: unaligning (T0294)A315 because of BadResidue code BAD_PEPTIDE in next template residue (2c2xA)R281 T0294 4 :VRLMKVFVTRRIPAEGRVALARA 2c2xA 31 :RTPGLGTILVGDDPGSQAYVRGK T0294 27 :ADCEVEQWDSDEPIPAKELER 2c2xA 60 :VGITSIRRDLPADISTATLNE T0294 67 :ILDAA 2c2xA 81 :TIDEL T0294 72 :GANLKVISTMSVGIDHLALDEIKKR 2c2xA 88 :NPDCTGYIVQLPLPKHLDENAALER T0294 102 :YTPDVLTDTTAEL 2c2xA 118 :DADGLHPTNLGRL T0294 115 :AVSLLLTTCR 2c2xA 141 :TPRGIVHLLR T0294 146 :LCGYGLTQSTVGIIGLG 2c2xA 151 :RYDISIAGAHVVVIGRG T0294 163 :RIGQAIARRLK 2c2xA 169 :TVGRPLGLLLT T0294 174 :PFGV 2c2xA 182 :SENA T0294 179 :RFLYTGR 2c2xA 186 :TVTLCHT T0294 198 :EFVSTPELAAQSDFIVVAC 2c2xA 193 :GTRDLPALTRQADIVVAAV T0294 221 :ATEGLCNKDF 2c2xA 212 :GVAHLLTADM T0294 234 :MKETAVFINIS 2c2xA 222 :VRPGAAVIDVG T0294 260 :SGKIAA 2c2xA 237 :DDGLVG T0294 277 :PTNHPLLT 2c2xA 243 :DVHPDVWE T0294 285 :LK 2c2xA 252 :AG T0294 289 :VILPHIGSATHRTRNTMSLLAANNLL 2c2xA 254 :HVSPNPGGVGPLTRAFLLTNVVELAE Number of specific fragments extracted= 17 number of extra gaps= 1 total=1095 Number of alignments=83 # 2c2xA read from 2c2xA/merged-good-all-a2m # found chain 2c2xA in template set Warning: unaligning (T0294)A315 because of BadResidue code BAD_PEPTIDE in next template residue (2c2xA)R281 T0294 21 :VALARAADCEVEQWDSDEPIPAKELERGVA 2c2xA 54 :HADCAKVGITSIRRDLPADISTATLNETID T0294 68 :LDAAGANLKVISTMSVGIDHLALDEIKKR 2c2xA 84 :ELNANPDCTGYIVQLPLPKHLDENAALER T0294 102 :YTPDVLTDTTAEL 2c2xA 118 :DADGLHPTNLGRL T0294 115 :AVSLLLTTCR 2c2xA 141 :TPRGIVHLLR T0294 146 :LCGYGLTQSTVGIIGLG 2c2xA 151 :RYDISIAGAHVVVIGRG T0294 163 :RIGQAIARRLK 2c2xA 169 :TVGRPLGLLLT T0294 174 :PFGVQRFLYTGR 2c2xA 182 :SENATVTLCHTG T0294 199 :FVSTPELAAQSDFIVVACSL 2c2xA 194 :TRDLPALTRQADIVVAAVGV T0294 223 :EGLCNKDF 2c2xA 214 :AHLLTADM T0294 234 :MKETAVFINIS 2c2xA 222 :VRPGAAVIDVG T0294 279 :NH 2c2xA 237 :DD T0294 281 :PLLTL 2c2xA 247 :DVWEL T0294 286 :K 2c2xA 253 :G T0294 289 :VILPHIGSATHRTRNTMSLLAANNLL 2c2xA 254 :HVSPNPGGVGPLTRAFLLTNVVELAE Number of specific fragments extracted= 14 number of extra gaps= 1 total=1109 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hkuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0294/1hkuA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0294/1hkuA/merged-good-all-a2m.gz for input Trying 1hkuA/merged-good-all-a2m Error: Couldn't open file 1hkuA/merged-good-all-a2m or 1hkuA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xdwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xdwA expands to /projects/compbio/data/pdb/1xdw.pdb.gz 1xdwA:# T0294 read from 1xdwA/merged-good-all-a2m # 1xdwA read from 1xdwA/merged-good-all-a2m # adding 1xdwA to template set # found chain 1xdwA in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1xdwA)M1 Warning: unaligning (T0294)S154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xdwA)T148 Warning: unaligning (T0294)T155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xdwA)T148 Warning: unaligning (T0294)K327 because last residue in template chain is (1xdwA)K331 T0294 8 :KVFVTRRIP 1xdwA 2 :KVLCYGVRD T0294 17 :AEGRVALARAADCEVEQW 1xdwA 13 :LPIFEACNKEFGYDIKCV T0294 37 :DEPIPAKELERGVAGAHGLLCLLSDHVDKRILDAAGA 1xdwA 31 :PDYLNTKETAEMAAGFDAVILRGNCFANKQNLDIYKK T0294 74 :NLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRR 1xdwA 69 :GVKYILTRTAGTDHIDKEYAKELGFPMAFVPRYSPNAIAELAVTQAMMLLRH T0294 128 :EAIEEVKNGGWTSWKPLWLCGYGLTQ 1xdwA 121 :TAYTTSRTAKKNFKVDAFMFSKEVRN T0294 156 :VGIIGLGRIGQAIARRLKPFGV 1xdwA 149 :VGVVGLGRIGRVAAQIFHGMGA T0294 179 :RFLYTGRQPRP 1xdwA 171 :TVIGEDVFEIK T0294 194 :EFQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPE 1xdwA 184 :EDYCTQVSLDEVLEKSDIITIHAPYIKENGAVVTRDFLKKMKDGAILVNCARGQLVDTEAVIEAVESGKLGGYGCDVLDGE T0294 275 :PLPTNHPLLT 1xdwA 270 :KDLEGQKLEN T0294 286 :KNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPSEL 1xdwA 290 :PRVLITPHLGSYTDEAVKNMVEVSYQNLKDLAETGDCPNKI Number of specific fragments extracted= 10 number of extra gaps= 1 total=1119 Number of alignments=85 # 1xdwA read from 1xdwA/merged-good-all-a2m # found chain 1xdwA in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1xdwA)M1 Warning: unaligning (T0294)S154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xdwA)T148 Warning: unaligning (T0294)T155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xdwA)T148 Warning: unaligning (T0294)K327 because last residue in template chain is (1xdwA)K331 T0294 8 :KVFVTR 1xdwA 2 :KVLCYG T0294 15 :IPAEGRVALARA 1xdwA 8 :VRDVELPIFEAC T0294 27 :ADCEVEQWD 1xdwA 23 :FGYDIKCVP T0294 38 :EPIPAKELERGVAGAHGLLCLLSDHVDKRILDAAGA 1xdwA 32 :DYLNTKETAEMAAGFDAVILRGNCFANKQNLDIYKK T0294 74 :NLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRR 1xdwA 69 :GVKYILTRTAGTDHIDKEYAKELGFPMAFVPRYSPNAIAELAVTQAMMLLRH T0294 128 :EAIEEVKNGGWTSWKPLWLCGYGLTQ 1xdwA 121 :TAYTTSRTAKKNFKVDAFMFSKEVRN T0294 156 :VGIIGLGRIGQAIARRLKPFGV 1xdwA 149 :VGVVGLGRIGRVAAQIFHGMGA T0294 179 :RFLYTGRQPRPE 1xdwA 171 :TVIGEDVFEIKG T0294 194 :EFQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPE 1xdwA 184 :EDYCTQVSLDEVLEKSDIITIHAPYIKENGAVVTRDFLKKMKDGAILVNCARGQLVDTEAVIEAVESGKLGGYGCDVLDGE T0294 275 :PLPTNHPLLT 1xdwA 270 :KDLEGQKLEN T0294 286 :KNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPSEL 1xdwA 290 :PRVLITPHLGSYTDEAVKNMVEVSYQNLKDLAETGDCPNKI Number of specific fragments extracted= 11 number of extra gaps= 1 total=1130 Number of alignments=86 # 1xdwA read from 1xdwA/merged-good-all-a2m # found chain 1xdwA in template set Warning: unaligning (T0294)S154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xdwA)T148 Warning: unaligning (T0294)T155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xdwA)T148 Warning: unaligning (T0294)K327 because last residue in template chain is (1xdwA)K331 T0294 15 :IPAEGRVALARAADCEVEQWDSDEPIPAKELERG 1xdwA 9 :RDVELPIFEACNKEFGYDIKCVPDYLNTKETAEM T0294 50 :AGAHGLLCLLSDHVDKRILDAAGA 1xdwA 43 :AAGFDAVILRGNCFANKQNLDIYK T0294 74 :NLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRR 1xdwA 69 :GVKYILTRTAGTDHIDKEYAKELGFPMAFVPRYSPNAIAELAVTQAMMLLRH T0294 128 :EAIEEVKNGGWTSWKPLWLCGYGLTQ 1xdwA 121 :TAYTTSRTAKKNFKVDAFMFSKEVRN T0294 156 :VGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEE 1xdwA 149 :VGVVGLGRIGRVAAQIFHGMGATVIGEDVFEIKGIE T0294 195 :FQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNH 1xdwA 185 :DYCTQVSLDEVLEKSDIITIHAPYIKENGAVVTRDFLKKMKDGAILVNCARGQLVDTEAVIEAVESGKLGGYGCDVLDGEASVFGK T0294 286 :KNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPSEL 1xdwA 290 :PRVLITPHLGSYTDEAVKNMVEVSYQNLKDLAETGDCPNKI Number of specific fragments extracted= 7 number of extra gaps= 1 total=1137 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2nadA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2nadA expands to /projects/compbio/data/pdb/2nad.pdb.gz 2nadA:# T0294 read from 2nadA/merged-good-all-a2m # 2nadA read from 2nadA/merged-good-all-a2m # adding 2nadA to template set # found chain 2nadA in template set Warning: unaligning (T0294)E30 because of BadResidue code BAD_PEPTIDE in next template residue (2nadA)L70 Warning: unaligning (T0294)V31 because of BadResidue code BAD_PEPTIDE at template residue (2nadA)L70 T0294 21 :VALARAADC 2nadA 60 :RKYLESNGH T0294 32 :EQW 2nadA 71 :VVT T0294 35 :DSDEPI 2nadA 76 :KDGPDS T0294 44 :ELERGVAGAHGLLC 2nadA 82 :VFERELVDADVVIS T0294 58 :LLSDHVDKRILDAA 2nadA 98 :FWPAYLTPERIAKA T0294 73 :ANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWKP 2nadA 112 :KNLKLALTAGIGSDHVDLQSAIDRNVTVAEVTYCNSISVAEHVVMMILSLVRNYLPSHEWARKGGWNIADC T0294 145 :WLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 2nadA 183 :VSHAYDLEAMHVGTVAAGRIGLAVLRRLAPFDV T0294 179 :RFLYTGRQP 2nadA 216 :HLHYTDRHR T0294 188 :RPEEAAEFQAEFV 2nadA 226 :PESVEKELNLTWH T0294 201 :STPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNHPLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPSE 2nadA 240 :TREDMYPVCDVVTLNCPLHPETEHMINDETLKLFKRGAYIVNTARGKLCDRDAVARALESGRLAGYAGDVWFPQPAPKDHPWRTMPYNGMTPHISGTTLTAQARYAAGTREILECFFEGRPIRDE Number of specific fragments extracted= 10 number of extra gaps= 1 total=1147 Number of alignments=88 # 2nadA read from 2nadA/merged-good-all-a2m # found chain 2nadA in template set Warning: unaligning (T0294)E30 because of BadResidue code BAD_PEPTIDE in next template residue (2nadA)L70 Warning: unaligning (T0294)V31 because of BadResidue code BAD_PEPTIDE at template residue (2nadA)L70 T0294 20 :RVALARA 2nadA 60 :RKYLESN T0294 28 :DC 2nadA 67 :GH T0294 32 :EQWD 2nadA 71 :VVTS T0294 36 :SDEPI 2nadA 77 :DGPDS T0294 44 :ELERGVAGAHGLLCLLSD 2nadA 82 :VFERELVDADVVISQPFW T0294 62 :HVDKRILDAA 2nadA 102 :YLTPERIAKA T0294 73 :ANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWKPL 2nadA 112 :KNLKLALTAGIGSDHVDLQSAIDRNVTVAEVTYCNSISVAEHVVMMILSLVRNYLPSHEWARKGGWNIADCV T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 2nadA 184 :SHAYDLEAMHVGTVAAGRIGLAVLRRLAPFDV T0294 179 :RFLYTGRQPR 2nadA 216 :HLHYTDRHRL T0294 189 :PEEAAEFQAEFV 2nadA 227 :ESVEKELNLTWH T0294 201 :STPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNHPLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPSE 2nadA 240 :TREDMYPVCDVVTLNCPLHPETEHMINDETLKLFKRGAYIVNTARGKLCDRDAVARALESGRLAGYAGDVWFPQPAPKDHPWRTMPYNGMTPHISGTTLTAQARYAAGTREILECFFEGRPIRDE Number of specific fragments extracted= 11 number of extra gaps= 1 total=1158 Number of alignments=89 # 2nadA read from 2nadA/merged-good-all-a2m # found chain 2nadA in template set Warning: unaligning (T0294)E32 because of BadResidue code BAD_PEPTIDE in next template residue (2nadA)L70 Warning: unaligning (T0294)Q33 because of BadResidue code BAD_PEPTIDE at template residue (2nadA)L70 T0294 25 :RAADCEV 2nadA 62 :YLESNGH T0294 34 :WDSDEPIPAKELERGVAGAHGLLCLLSDH 2nadA 71 :VVTSDKDGPDSVFERELVDADVVISQPFW T0294 63 :VDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWK 2nadA 102 :YLTPERIAKAKNLKLALTAGIGSDHVDLQSAIDRNVTVAEVTYCNSISVAEHVVMMILSLVRNYLPSHEWARKGGWNIAD T0294 144 :LWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEEAAEFQ 2nadA 182 :CVSHAYDLEAMHVGTVAAGRIGLAVLRRLAPFDVHLHYTDRHRLPESVEKELN T0294 197 :AEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNHPLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLRGEPMPSE 2nadA 236 :TWHATREDMYPVCDVVTLNCPLHPETEHMINDETLKLFKRGAYIVNTARGKLCDRDAVARALESGRLAGYAGDVWFPQPAPKDHPWRTMPYNGMTPHISGTTLTAQARYAAGTREILECFFEGRPIRDE Number of specific fragments extracted= 5 number of extra gaps= 1 total=1163 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wwkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wwkA expands to /projects/compbio/data/pdb/1wwk.pdb.gz 1wwkA:# T0294 read from 1wwkA/merged-good-all-a2m # 1wwkA read from 1wwkA/merged-good-all-a2m # adding 1wwkA to template set # found chain 1wwkA in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1wwkA)M1 Warning: unaligning (T0294)G319 because last residue in template chain is (1wwkA)G304 T0294 8 :KVFVTRRIPAEGRVALAR 1wwkA 2 :KVLVAAPLHEKAIQVLKD T0294 27 :ADCEVEQ 1wwkA 20 :AGLEVIY T0294 37 :DEPIPAKELERGVAGAHGLLCLLSDHVDKRILDAA 1wwkA 27 :EEYPDEDRLVELVKDVEAIIVRSKPKVTRRVIESA T0294 73 :ANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWK 1wwkA 62 :PKLKVIARAGVGLDNIDVEAAKEKGIEVVNAPAASSRSVAELAVGLMFSVARKIAFADRKMREGVWAKKE T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1wwkA 132 :AMGIELEGKTIGIIGFGRIGYQVAKIANALGM T0294 179 :RFLYTGRQPRPEEAAEFQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNHPLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLR 1wwkA 164 :NILLYDPYPNEERAKEVNGKFVDLETLLKESDVVTIHVPLVESTYHLINEERLKLMKKTAILINTSRGPVVDTNALVKALKEGWIAGAGLDVFEEEPLPKDHPLTKFDNVVLTPHIGASTVEAQERAGVEVAEKVVKILK Number of specific fragments extracted= 6 number of extra gaps= 0 total=1169 Number of alignments=91 # 1wwkA read from 1wwkA/merged-good-all-a2m # found chain 1wwkA in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1wwkA)M1 Warning: unaligning (T0294)G319 because last residue in template chain is (1wwkA)G304 T0294 8 :KVFVTRRIPAEGRVALARA 1wwkA 2 :KVLVAAPLHEKAIQVLKDA T0294 28 :DCEVEQWD 1wwkA 21 :GLEVIYEE T0294 39 :PIPAKELERGVAGAHGLLCLLSDHVDKRILDAA 1wwkA 29 :YPDEDRLVELVKDVEAIIVRSKPKVTRRVIESA T0294 73 :ANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWK 1wwkA 62 :PKLKVIARAGVGLDNIDVEAAKEKGIEVVNAPAASSRSVAELAVGLMFSVARKIAFADRKMREGVWAKKE T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1wwkA 132 :AMGIELEGKTIGIIGFGRIGYQVAKIANALGM T0294 179 :RFLYTGRQPRPEEAAEFQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNHPLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLR 1wwkA 164 :NILLYDPYPNEERAKEVNGKFVDLETLLKESDVVTIHVPLVESTYHLINEERLKLMKKTAILINTSRGPVVDTNALVKALKEGWIAGAGLDVFEEEPLPKDHPLTKFDNVVLTPHIGASTVEAQERAGVEVAEKVVKILK Number of specific fragments extracted= 6 number of extra gaps= 0 total=1175 Number of alignments=92 # 1wwkA read from 1wwkA/merged-good-all-a2m # found chain 1wwkA in template set Warning: unaligning (T0294)G319 because last residue in template chain is (1wwkA)G304 T0294 20 :RVALARAADCEVEQWDSDE 1wwkA 11 :EKAIQVLKDAGLEVIYEEY T0294 41 :PAKELERGVAGAHGLLCLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWK 1wwkA 30 :PDEDRLVELVKDVEAIIVRSKPKVTRRVIESAPKLKVIARAGVGLDNIDVEAAKEKGIEVVNAPAASSRSVAELAVGLMFSVARKIAFADRKMREGVWAKKE T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEE 1wwkA 132 :AMGIELEGKTIGIIGFGRIGYQVAKIANALGMNILLYDPYPNEERA T0294 193 :AEFQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLDVTSPEPLPTNHPLLTLKNCVILPHIGSATHRTRNTMSLLAANNLLAGLR 1wwkA 178 :KEVNGKFVDLETLLKESDVVTIHVPLVESTYHLINEERLKLMKKTAILINTSRGPVVDTNALVKALKEGWIAGAGLDVFEEEPLPKDHPLTKFDNVVLTPHIGASTVEAQERAGVEVAEKVVKILK Number of specific fragments extracted= 4 number of extra gaps= 0 total=1179 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vl6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vl6A expands to /projects/compbio/data/pdb/1vl6.pdb.gz 1vl6A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 737, because occupancy 0.400 <= existing 0.600 in 1vl6A Skipped atom 739, because occupancy 0.400 <= existing 0.600 in 1vl6A Skipped atom 741, because occupancy 0.400 <= existing 0.600 in 1vl6A Skipped atom 743, because occupancy 0.400 <= existing 0.600 in 1vl6A Skipped atom 745, because occupancy 0.400 <= existing 0.600 in 1vl6A Skipped atom 747, because occupancy 0.400 <= existing 0.600 in 1vl6A Skipped atom 749, because occupancy 0.400 <= existing 0.600 in 1vl6A Skipped atom 751, because occupancy 0.400 <= existing 0.600 in 1vl6A Skipped atom 753, because occupancy 0.400 <= existing 0.600 in 1vl6A Skipped atom 755, because occupancy 0.400 <= existing 0.600 in 1vl6A Skipped atom 757, because occupancy 0.400 <= existing 0.600 in 1vl6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2670, because occupancy 0.500 <= existing 0.500 in 1vl6A Skipped atom 2672, because occupancy 0.500 <= existing 0.500 in 1vl6A Skipped atom 2674, because occupancy 0.500 <= existing 0.500 in 1vl6A Skipped atom 2676, because occupancy 0.500 <= existing 0.500 in 1vl6A Skipped atom 2678, because occupancy 0.500 <= existing 0.500 in 1vl6A Skipped atom 2680, because occupancy 0.500 <= existing 0.500 in 1vl6A Skipped atom 2682, because occupancy 0.500 <= existing 0.500 in 1vl6A Skipped atom 2684, because occupancy 0.500 <= existing 0.500 in 1vl6A Skipped atom 2686, because occupancy 0.500 <= existing 0.500 in 1vl6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0294 read from 1vl6A/merged-good-all-a2m # 1vl6A read from 1vl6A/merged-good-all-a2m # adding 1vl6A to template set # found chain 1vl6A in template set T0294 6 :L 1vl6A 58 :N T0294 8 :KVFVTR 1vl6A 59 :TVAVVS T0294 14 :RIPAEG 1vl6A 74 :NIGPYG T0294 20 :RVALARAADCEVEQWDSD 1vl6A 88 :AFLFKAFADIDAFPICLS T0294 39 :PIPAKELERG 1vl6A 106 :ESEEEKIISI T0294 68 :LDAAGANLKVISTMSVGIDHLA 1vl6A 116 :VKSLEPSFGGINLEDIGAPKCF T0294 90 :LDEIKK 1vl6A 140 :LQRLSE T0294 96 :RGIRVGY 1vl6A 147 :MNIPVFH T0294 108 :TDTTAELAVSLLLTTCR 1vl6A 156 :QQGTAVVVSAAFLNALK T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQ 1vl6A 173 :LTEKKIEEVKVVVNGIGAAGYNIVKFLLDLGVKNVVAVDRK T0294 187 :PRPEEAAE 1vl6A 224 :CLNEYHLE T0294 195 :F 1vl6A 236 :T T0294 196 :QAEFV 1vl6A 238 :PERLS T0294 201 :STPELAAQSDFIVVACSL 1vl6A 244 :DLETALEGADFFIGVSRG T0294 224 :GLCNKDFFQKMKETAVFINISRGDV 1vl6A 262 :NILKPEWIKKMSRKPVIFALANPVP T0294 249 :VNQDDLYQ 1vl6A 288 :IDPELARE T0294 261 :GKIAAAGLDVTSPEPLPTN 1vl6A 296 :AGAFIVATGRSDHPNQVNN T0294 281 :PLL 1vl6A 315 :LLA T0294 295 :GSATHRTR 1vl6A 319 :PGIMKGAV T0294 303 :NTMSLLAANNLLAGL 1vl6A 334 :KNMLLSAVEAIARSC T0294 320 :E 1vl6A 349 :E Number of specific fragments extracted= 21 number of extra gaps= 0 total=1200 Number of alignments=94 # 1vl6A read from 1vl6A/merged-good-all-a2m # found chain 1vl6A in template set T0294 5 :RLMKVFVTR 1vl6A 58 :NTVAVVSDG T0294 14 :RIP 1vl6A 74 :NIG T0294 17 :AEGRVALARAADCEVEQWDSD 1vl6A 85 :EGKAFLFKAFADIDAFPICLS T0294 39 :PIPAKELERG 1vl6A 106 :ESEEEKIISI T0294 68 :LDAAGANLKVISTMSVGIDHLA 1vl6A 116 :VKSLEPSFGGINLEDIGAPKCF T0294 90 :LDEIKKR 1vl6A 140 :LQRLSEE T0294 97 :GIRVGY 1vl6A 148 :NIPVFH T0294 108 :TDTTAELAVSLLLTTCR 1vl6A 156 :QQGTAVVVSAAFLNALK T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQ 1vl6A 173 :LTEKKIEEVKVVVNGIGAAGYNIVKFLLDLGVKNVVAVDRK T0294 194 :E 1vl6A 239 :E T0294 198 :EFV 1vl6A 240 :RLS T0294 201 :STPELAAQSDFIVVACSLT 1vl6A 244 :DLETALEGADFFIGVSRGN T0294 225 :LCNKDFFQKMKETAVFINISRGDV 1vl6A 263 :ILKPEWIKKMSRKPVIFALANPVP T0294 249 :VNQDDLYQ 1vl6A 288 :IDPELARE T0294 260 :SG 1vl6A 296 :AG T0294 263 :IAAAGLD 1vl6A 298 :AFIVATG T0294 271 :TSPEPLPTNHPLL 1vl6A 305 :RSDHPNQVNNLLA T0294 296 :SATHRTR 1vl6A 320 :GIMKGAV T0294 303 :NTMSLLAANNLLAGL 1vl6A 334 :KNMLLSAVEAIARSC Number of specific fragments extracted= 19 number of extra gaps= 0 total=1219 Number of alignments=95 # 1vl6A read from 1vl6A/merged-good-all-a2m # found chain 1vl6A in template set T0294 44 :ELERGVAGAHGLLCLLSDHVDKRILD 1vl6A 88 :AFLFKAFADIDAFPICLSESEEEKII T0294 70 :AAGANLKVISTMSVGIDHL 1vl6A 118 :SLEPSFGGINLEDIGAPKC T0294 89 :ALDEIKK 1vl6A 139 :ILQRLSE T0294 96 :RGIRVGY 1vl6A 147 :MNIPVFH T0294 108 :TDTTAELAVSLLLTTCRR 1vl6A 156 :QQGTAVVVSAAFLNALKL T0294 147 :CGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1vl6A 174 :TEKKIEEVKVVVNGIGAAGYNIVKFLLDLGV T0294 178 :QRFLYTGRQ 1vl6A 206 :NVVAVDRKG T0294 188 :RPEE 1vl6A 216 :LNEN T0294 195 :FQAEFVSTPELAAQSDFIVVACSLT 1vl6A 238 :PERLSGDLETALEGADFFIGVSRGN T0294 225 :LCNKDFFQKMKETAVFINISRG 1vl6A 263 :ILKPEWIKKMSRKPVIFALANP T0294 247 :DVVNQDDLYQ 1vl6A 286 :PEIDPELARE T0294 261 :GKIAAAGLD 1vl6A 296 :AGAFIVATG T0294 277 :PTNH 1vl6A 305 :RSDH T0294 303 :NTMSLLAANNLLAGL 1vl6A 334 :KNMLLSAVEAIARSC Number of specific fragments extracted= 14 number of extra gaps= 0 total=1233 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a4iA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0294 read from 1a4iA/merged-good-all-a2m # 1a4iA read from 1a4iA/merged-good-all-a2m # found chain 1a4iA in training set Warning: unaligning (T0294)P104 because of BadResidue code BAD_PEPTIDE in next template residue (1a4iA)D142 Warning: unaligning (T0294)D105 because of BadResidue code BAD_PEPTIDE at template residue (1a4iA)D142 Warning: unaligning (T0294)V106 because of BadResidue code BAD_PEPTIDE at template residue (1a4iA)C143 Warning: unaligning (T0294)R318 because last residue in template chain is (1a4iA)E296 T0294 3 :PVRLMKV 1a4iA 32 :PGFTPRL T0294 10 :FVTRRIPAEGRVALA 1a4iA 40 :ILQVGNRDDSNLYIN T0294 25 :RAADCEVEQWDSDEPIPAKELERGV 1a4iA 61 :EEIGIKATHIKLPRTTTESEVMKYI T0294 50 :AGAHGLLCL 1a4iA 92 :STVHGFLVQ T0294 59 :LSDHVD 1a4iA 105 :SENSIN T0294 65 :KRILDAAGA 1a4iA 112 :EEVINAIAP T0294 84 :GIDHLA 1a4iA 123 :DVDGLT T0294 90 :LDEIKKR 1a4iA 132 :AGRLARG T0294 102 :YT 1a4iA 139 :DL T0294 107 :LTDTTAELAVSLL 1a4iA 144 :FIPCTPKGCLELI T0294 124 :R 1a4iA 157 :K T0294 146 :LCGYGLTQSTVGIIGLGR 1a4iA 158 :ETGVPIAGRHAVVVGRSK T0294 164 :IGQAIARRLKPFGV 1a4iA 177 :VGAPMHDLLLWNNA T0294 179 :RFLYTGRQ 1a4iA 191 :TVTTCHSK T0294 199 :FVSTPELAAQSDFIVVAC 1a4iA 199 :TAHLDEEVNKGDILVVAT T0294 221 :ATEGLCNKDF 1a4iA 217 :GQPEMVKGEW T0294 234 :MKETAVFINISRG 1a4iA 227 :IKPGAIVIDCGIN T0294 247 :DVVNQDDL 1a4iA 254 :GDVAYDEA T0294 260 :SG 1a4iA 262 :KE T0294 284 :TLK 1a4iA 264 :RAS T0294 289 :VILPHIGSATHRTRNTMSLLAANNLLAGL 1a4iA 267 :FITPVPGGVGPMTVAMLMQSTVESAKRFL Number of specific fragments extracted= 21 number of extra gaps= 1 total=1254 Number of alignments=97 # 1a4iA read from 1a4iA/merged-good-all-a2m # found chain 1a4iA in training set Warning: unaligning (T0294)P104 because of BadResidue code BAD_PEPTIDE in next template residue (1a4iA)D142 Warning: unaligning (T0294)D105 because of BadResidue code BAD_PEPTIDE at template residue (1a4iA)D142 Warning: unaligning (T0294)V106 because of BadResidue code BAD_PEPTIDE at template residue (1a4iA)C143 Warning: unaligning (T0294)G246 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a4iA)K251 Warning: unaligning (T0294)R318 because last residue in template chain is (1a4iA)E296 T0294 2 :RPVRLMKVFVTRRIP 1a4iA 33 :GFTPRLAILQVGNRD T0294 17 :AEGRVALARAA 1a4iA 50 :NLYINVKLKAA T0294 28 :DCEVEQWDSDEPIPAKELERGV 1a4iA 64 :GIKATHIKLPRTTTESEVMKYI T0294 50 :AGAHGLLCL 1a4iA 92 :STVHGFLVQ T0294 59 :LSDHVD 1a4iA 105 :SENSIN T0294 65 :KRILDAAGA 1a4iA 112 :EEVINAIAP T0294 83 :VGIDHLA 1a4iA 122 :KDVDGLT T0294 90 :LDEIKKRG 1a4iA 132 :AGRLARGD T0294 103 :T 1a4iA 140 :L T0294 107 :LTDTTAELAVSLL 1a4iA 144 :FIPCTPKGCLELI T0294 124 :R 1a4iA 157 :K T0294 146 :LCGYGLTQSTVGIIG 1a4iA 158 :ETGVPIAGRHAVVVG T0294 162 :GRIGQAIARRLKPFGV 1a4iA 175 :KIVGAPMHDLLLWNNA T0294 179 :RFLYTGRQ 1a4iA 191 :TVTTCHSK T0294 199 :FVSTPELAAQSDFIVVAC 1a4iA 199 :TAHLDEEVNKGDILVVAT T0294 221 :ATEGLCNKDF 1a4iA 217 :GQPEMVKGEW T0294 234 :MKETAVFINIS 1a4iA 227 :IKPGAIVIDCG T0294 249 :VNQDDL 1a4iA 256 :VAYDEA T0294 260 :SGKIA 1a4iA 262 :KERAS T0294 289 :VILPHIGSATHRTRNTMSLLAANNLLAGL 1a4iA 267 :FITPVPGGVGPMTVAMLMQSTVESAKRFL Number of specific fragments extracted= 20 number of extra gaps= 1 total=1274 Number of alignments=98 # 1a4iA read from 1a4iA/merged-good-all-a2m # found chain 1a4iA in training set Warning: unaligning (T0294)P104 because of BadResidue code BAD_PEPTIDE in next template residue (1a4iA)D142 Warning: unaligning (T0294)D105 because of BadResidue code BAD_PEPTIDE at template residue (1a4iA)D142 Warning: unaligning (T0294)V106 because of BadResidue code BAD_PEPTIDE at template residue (1a4iA)C143 Warning: unaligning (T0294)D247 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1a4iA)K251 Warning: unaligning (T0294)R318 because last residue in template chain is (1a4iA)E296 T0294 25 :RAADCEVEQWDSDEPIPAKELERGV 1a4iA 61 :EEIGIKATHIKLPRTTTESEVMKYI T0294 50 :AGAHGLLCLLSD 1a4iA 91 :DSTVHGFLVQLP T0294 62 :HVDKRILDAAGAN 1a4iA 108 :SINTEEVINAIAP T0294 83 :VGIDHL 1a4iA 122 :KDVDGL T0294 89 :ALDEIKKRGI 1a4iA 131 :NAGRLARGDL T0294 107 :LTDTTAELAVSLL 1a4iA 144 :FIPCTPKGCLELI T0294 124 :R 1a4iA 157 :K T0294 146 :LCGYGLTQSTVGIIGLGR 1a4iA 158 :ETGVPIAGRHAVVVGRSK T0294 164 :IGQAIARRLKPFGVQRFLYTGR 1a4iA 177 :VGAPMHDLLLWNNATVTTCHSK T0294 199 :FVSTPELAAQSDFIVVACSL 1a4iA 199 :TAHLDEEVNKGDILVVATGQ T0294 220 :P 1a4iA 219 :P T0294 224 :GLCNKDF 1a4iA 220 :EMVKGEW T0294 234 :MKETAVFINISRG 1a4iA 227 :IKPGAIVIDCGIN T0294 289 :VILPHIGSATHRTRNTMSLLAANNLLAGL 1a4iA 267 :FITPVPGGVGPMTVAMLMQSTVESAKRFL Number of specific fragments extracted= 14 number of extra gaps= 1 total=1288 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ww8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ww8A expands to /projects/compbio/data/pdb/1ww8.pdb.gz 1ww8A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0294 read from 1ww8A/merged-good-all-a2m # 1ww8A read from 1ww8A/merged-good-all-a2m # adding 1ww8A to template set # found chain 1ww8A in template set T0294 4 :VRLMKVFVTRRI 1ww8A 62 :KGNLVAVVSDGS T0294 17 :AEG 1ww8A 83 :PLA T0294 20 :RVALARAADCEVEQWDSDEPIP 1ww8A 94 :ALLFKRFGGVDAFPIMIKEQEP T0294 42 :AKELERGVAGAHGLLCLLSD 1ww8A 119 :IDIVKAIAPTFGGINLEDIA T0294 66 :RILDAA 1ww8A 144 :YILERL T0294 93 :IKKRGIRVGY 1ww8A 150 :REELDIPVFH T0294 108 :TDTTAELAVSLLLTTCR 1ww8A 162 :QQGTAAVVLAGLLNALK T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQ 1ww8A 179 :VVGKKISEITLALFGAGAAGFATLRILTEAGVK T0294 179 :RFLYT 1ww8A 214 :NVRVV T0294 184 :GRQPRPEEAAE 1ww8A 229 :TSDLDLEKLFP T0294 195 :F 1ww8A 248 :T T0294 196 :QAEFV 1ww8A 250 :GENIE T0294 201 :STPELAAQSDFIVVACSLTPA 1ww8A 256 :GPQEALKDADVLISFTRPGPG T0294 225 :LCNKDFFQKMKETAVFINISRGDV 1ww8A 277 :VIKPQWIEKMNEDAIVFPLANPVP T0294 249 :VNQDDLYQA 1ww8A 302 :ILPEEAKKA T0294 265 :AAGLDVT 1ww8A 311 :GARIVAT T0294 273 :PE 1ww8A 318 :GR T0294 275 :PLPTNH 1ww8A 372 :IPSPLN T0294 299 :HRTRNTMSLLAANNLLAG 1ww8A 378 :PIVYAREARAVAEEAMKE Number of specific fragments extracted= 19 number of extra gaps= 0 total=1307 Number of alignments=100 # 1ww8A read from 1ww8A/merged-good-all-a2m # found chain 1ww8A in template set T0294 5 :RLMKVFVTRRI 1ww8A 64 :NLVAVVSDGSR T0294 17 :AEGRVALARAADCEVEQWDSDEPIPA 1ww8A 91 :EGKALLFKRFGGVDAFPIMIKEQEPN T0294 43 :KELERGVAGAHGLLCLLSD 1ww8A 120 :DIVKAIAPTFGGINLEDIA T0294 66 :RILDAA 1ww8A 144 :YILERL T0294 93 :IKKRGIRVGY 1ww8A 150 :REELDIPVFH T0294 108 :TDTTAELAVSLLLTTCR 1ww8A 162 :QQGTAAVVLAGLLNALK T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQ 1ww8A 179 :VVGKKISEITLALFGAGAAGFATLRILTEAGVK T0294 179 :RFLYT 1ww8A 214 :NVRVV T0294 184 :GRQPRPEEA 1ww8A 229 :TSDLDLEKL T0294 193 :AE 1ww8A 250 :GE T0294 198 :EFV 1ww8A 252 :NIE T0294 201 :STPELAAQSDFIVVACSLTPA 1ww8A 256 :GPQEALKDADVLISFTRPGPG T0294 225 :LCNKDFFQKMKETAVFINISRGDV 1ww8A 277 :VIKPQWIEKMNEDAIVFPLANPVP T0294 249 :VNQDDLYQ 1ww8A 302 :ILPEEAKK T0294 261 :GKIA 1ww8A 310 :AGAR T0294 266 :AGLDVTSPEPLPTNHPL 1ww8A 314 :IVATGRSDYPNQINNLL T0294 283 :LTL 1ww8A 345 :RTI T0294 298 :T 1ww8A 348 :T T0294 303 :NTMSLLAANNLLAGLRGEP 1ww8A 349 :DSMIIAAAKAIASIVEEPS Number of specific fragments extracted= 19 number of extra gaps= 0 total=1326 Number of alignments=101 # 1ww8A read from 1ww8A/merged-good-all-a2m # found chain 1ww8A in template set T0294 45 :LERGVAGAHGLLCLLSDHVDKRILD 1ww8A 95 :LLFKRFGGVDAFPIMIKEQEPNKFI T0294 70 :AAGANLKVISTMSVGIDHL 1ww8A 124 :AIAPTFGGINLEDIASPKC T0294 89 :ALDEIKK 1ww8A 145 :ILERLRE T0294 96 :RGIRVGY 1ww8A 153 :LDIPVFH T0294 107 :LTDTTAELAVSLLLTTCR 1ww8A 161 :DQQGTAAVVLAGLLNALK T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLK 1ww8A 179 :VVGKKISEITLALFGAGAAGFATLRILT T0294 174 :PFGVQRF 1ww8A 212 :PENVRVV T0294 181 :LYTGRQPRPEE 1ww8A 227 :ILTSDLDLEKL T0294 195 :FQAEFVSTPELAAQSDFIVVACSLTPA 1ww8A 250 :GENIEGGPQEALKDADVLISFTRPGPG T0294 225 :LCNKDFFQKMKETAVFINISRG 1ww8A 277 :VIKPQWIEKMNEDAIVFPLANP T0294 247 :DVVNQDDLYQ 1ww8A 300 :PEILPEEAKK T0294 261 :GKIAAAG 1ww8A 310 :AGARIVA T0294 275 :PLPTNH 1ww8A 317 :TGRSDY T0294 281 :PLLTLK 1ww8A 343 :RARTIT T0294 303 :NTMSLLAANNLLAGLRGEP 1ww8A 349 :DSMIIAAAKAIASIVEEPS Number of specific fragments extracted= 15 number of extra gaps= 0 total=1341 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2d5cA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2d5cA expands to /projects/compbio/data/pdb/2d5c.pdb.gz 2d5cA:# T0294 read from 2d5cA/merged-good-all-a2m # 2d5cA read from 2d5cA/merged-good-all-a2m # adding 2d5cA to template set # found chain 2d5cA in template set Warning: unaligning (T0294)L6 because first residue in template chain is (2d5cA)M1 T0294 7 :MKVFVTRR 2d5cA 2 :LRFAVLGH T0294 15 :IP 2d5cA 11 :VA T0294 17 :AEGRVALARAADC 2d5cA 17 :PAMHAFALESLGL T0294 30 :EVEQWDS 2d5cA 32 :SYEAWDT T0294 41 :PAKEL 2d5cA 39 :PLEAL T0294 65 :KRILDAAGANLKVISTMS 2d5cA 44 :PGRLKEVRRAFRGVNLTL T0294 83 :VGIDHLA 2d5cA 66 :AALAHLD T0294 90 :LDEIKKR 2d5cA 75 :SPEAQRI T0294 100 :VGYT 2d5cA 96 :GFNT T0294 115 :AVSLLLTTCR 2d5cA 100 :DAPGFLEALK T0294 146 :LCGYGLTQ 2d5cA 110 :AGGIPLKG T0294 155 :TVGIIGLGRIGQAIARRLKPFGV 2d5cA 118 :PALVLGAGGAGRAVAFALREAGL T0294 179 :RFLYTGRQPRP 2d5cA 141 :EVWVWNRTPQR T0294 190 :EEAAEFQAEFVSTPE 2d5cA 154 :ALAEEFGLRAVPLEK T0294 206 :AAQSDFIVVAC 2d5cA 169 :AREARLLVNAT T0294 217 :SLTPA 2d5cA 190 :PLPAE T0294 233 :KMKETAVFINISRGDVVNQ 2d5cA 195 :LFPEEGAAVDLVYRPLWTR T0294 254 :LYQALASGKIAA 2d5cA 214 :FLREAKAKGLKV T0294 271 :TSP 2d5cA 226 :QTG T0294 303 :NTMSLLAANNLLAGLRGEPMP 2d5cA 229 :LPMLAWQGALAFRLWTGLLPD Number of specific fragments extracted= 20 number of extra gaps= 0 total=1361 Number of alignments=103 # 2d5cA read from 2d5cA/merged-good-all-a2m # found chain 2d5cA in template set Warning: unaligning (T0294)L6 because first residue in template chain is (2d5cA)M1 T0294 7 :MKVFVTRRIP 2d5cA 2 :LRFAVLGHPV T0294 17 :AEGRVALARAADC 2d5cA 17 :PAMHAFALESLGL T0294 30 :EVEQWD 2d5cA 32 :SYEAWD T0294 40 :IPAKEL 2d5cA 38 :TPLEAL T0294 65 :KRILDAAGANLKVISTMS 2d5cA 44 :PGRLKEVRRAFRGVNLTL T0294 83 :VGIDHLA 2d5cA 66 :AALAHLD T0294 90 :LDEIKKRGI 2d5cA 75 :SPEAQRIGA T0294 99 :RVGYT 2d5cA 95 :FGFNT T0294 108 :TDTT 2d5cA 100 :DAPG T0294 116 :VSLLL 2d5cA 104 :FLEAL T0294 134 :KNGGWTSWK 2d5cA 109 :KAGGIPLKG T0294 155 :TVGIIGLGRIGQAIARRLKPFGV 2d5cA 118 :PALVLGAGGAGRAVAFALREAGL T0294 179 :RFLYTGRQPR 2d5cA 141 :EVWVWNRTPQ T0294 189 :PEEAAEFQAEFVSTPE 2d5cA 153 :LALAEEFGLRAVPLEK T0294 206 :AAQSDFIVVAC 2d5cA 169 :AREARLLVNAT T0294 217 :SLTPA 2d5cA 190 :PLPAE T0294 233 :KMKETAVFINISRGDVVNQ 2d5cA 195 :LFPEEGAAVDLVYRPLWTR T0294 254 :LYQALASGKIAA 2d5cA 214 :FLREAKAKGLKV T0294 271 :TSP 2d5cA 226 :QTG T0294 303 :NTMSLLAANNLLAGLRGEPMP 2d5cA 229 :LPMLAWQGALAFRLWTGLLPD Number of specific fragments extracted= 20 number of extra gaps= 0 total=1381 Number of alignments=104 # 2d5cA read from 2d5cA/merged-good-all-a2m # found chain 2d5cA in template set T0294 23 :LARAADCE 2d5cA 23 :ALESLGLE T0294 31 :VEQWDSDEPIPAKELERG 2d5cA 33 :YEAWDTPLEALPGRLKEV T0294 50 :AGAHGLLCLLSDHVD 2d5cA 51 :RRAFRGVNLTLPLKE T0294 70 :AAGAN 2d5cA 66 :AALAH T0294 85 :IDHL 2d5cA 71 :LDWV T0294 90 :LDEIKKRGIR 2d5cA 75 :SPEAQRIGAV T0294 105 :DVLTDTTAEL 2d5cA 98 :NTDAPGFLEA T0294 133 :VKNGGWTSWK 2d5cA 108 :LKAGGIPLKG T0294 155 :TVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEE 2d5cA 118 :PALVLGAGGAGRAVAFALREAGLEVWVWNRTPQRALA T0294 192 :AAEFQAEFVSTPE 2d5cA 156 :AEEFGLRAVPLEK T0294 206 :AAQSDFIVVAC 2d5cA 169 :AREARLLVNAT T0294 217 :SLTPA 2d5cA 190 :PLPAE T0294 233 :KMKETAVFINISRGDVVNQ 2d5cA 195 :LFPEEGAAVDLVYRPLWTR T0294 254 :LYQALASGKIAA 2d5cA 214 :FLREAKAKGLKV T0294 289 :V 2d5cA 226 :Q T0294 303 :NTMSLLAANNLLAGLRGEPMP 2d5cA 229 :LPMLAWQGALAFRLWTGLLPD Number of specific fragments extracted= 16 number of extra gaps= 0 total=1397 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d4fA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1d4fA expands to /projects/compbio/data/pdb/1d4f.pdb.gz 1d4fA:# T0294 read from 1d4fA/merged-good-all-a2m # 1d4fA read from 1d4fA/merged-good-all-a2m # adding 1d4fA to template set # found chain 1d4fA in template set T0294 1 :SRPVRLMKVFVTRRIPAE 1d4fA 41 :SKPLKGARIAGCLHMTVE T0294 19 :GRVALARAADCEVEQWDSDEPIPAKELERGV 1d4fA 61 :VLIETLVALGAEVRWSSCNIFSTQDHAAAAI T0294 50 :AGAHG 1d4fA 94 :AGIPV T0294 57 :CLLSDHVDKRILDAAG 1d4fA 99 :FAWKGETDEEYLWCIE T0294 74 :NLKVIST 1d4fA 123 :PLNMILD T0294 83 :VGIDHLA 1d4fA 130 :DGGDLTN T0294 92 :EIKKR 1d4fA 137 :LIHTK T0294 97 :GIRVGYTPDVLT 1d4fA 173 :KVPAINVNDSVT T0294 124 :RRLPEAIEEVKNGGWTSWKP 1d4fA 185 :KSKFDNLYGCRESLIDGIKR T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1d4fA 205 :ATDVMIAGKVAVVAGYGDVGKGCAQALRGFGA T0294 179 :RFLYTGRQPRPEE 1d4fA 237 :RVIITEIEPINAL T0294 192 :AAEFQAEFVSTPELAAQSDFIVVAC 1d4fA 251 :AAMEGYEVTTMDEACKEGNIFVTTT T0294 221 :ATEGLCNKDFFQKMKETAVFINISRGDV 1d4fA 276 :GCVDIILGRHFEQMKDDAIVCNIGHFDV T0294 249 :VNQDDL 1d4fA 305 :IDVKWL T0294 259 :ASGKI 1d4fA 311 :NENAV T0294 264 :AAAGLDVTS 1d4fA 320 :IKPQVDRYL T0294 277 :PTNH 1d4fA 329 :LKNG T0294 281 :PL 1d4fA 342 :RL T0294 292 :PHIGSATHRTRNTMSLLAANNLL 1d4fA 351 :GHPSFVMSNSFTNQVMAQIELWT Number of specific fragments extracted= 19 number of extra gaps= 0 total=1416 Number of alignments=106 # 1d4fA read from 1d4fA/merged-good-all-a2m # found chain 1d4fA in template set T0294 7 :MKVFVTR 1d4fA 71 :AEVRWSS T0294 14 :RIPAEGRVALARA 1d4fA 82 :STQDHAAAAIAKA T0294 28 :DCEVEQWD 1d4fA 95 :GIPVFAWK T0294 39 :PIPAKELERGVAG 1d4fA 103 :GETDEEYLWCIEQ T0294 52 :AHGLLCLLS 1d4fA 124 :LNMILDDGG T0294 66 :RILDAA 1d4fA 133 :DLTNLI T0294 73 :ANLKVISTMS 1d4fA 147 :SGIRGISEET T0294 90 :LDEIKKR 1d4fA 160 :VHNLYKM T0294 97 :G 1d4fA 170 :G T0294 98 :IRVGYTPDV 1d4fA 174 :VPAINVNDS T0294 107 :LTDTTAELAVSLLLT 1d4fA 190 :NLYGCRESLIDGIKR T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1d4fA 205 :ATDVMIAGKVAVVAGYGDVGKGCAQALRGFGA T0294 179 :RFLYTGRQPR 1d4fA 237 :RVIITEIEPI T0294 189 :PEEAAEFQAEFVSTPELAAQSDFIVVAC 1d4fA 248 :ALQAAMEGYEVTTMDEACKEGNIFVTTT T0294 221 :ATEGLCNKDFFQKMKETAVFINISRGDV 1d4fA 276 :GCVDIILGRHFEQMKDDAIVCNIGHFDV T0294 249 :VNQDDLY 1d4fA 305 :IDVKWLN Number of specific fragments extracted= 16 number of extra gaps= 0 total=1432 Number of alignments=107 # 1d4fA read from 1d4fA/merged-good-all-a2m # found chain 1d4fA in template set T0294 36 :SDEPIPAKELERGVAGAHGL 1d4fA 100 :AWKGETDEEYLWCIEQTLHF T0294 56 :LCLLSDHVDKRILDAAGA 1d4fA 126 :MILDDGGDLTNLIHTKHP T0294 74 :NLKVISTMS 1d4fA 148 :GIRGISEET T0294 90 :LDEIKK 1d4fA 160 :VHNLYK T0294 96 :RG 1d4fA 169 :NG T0294 98 :IRVGYTPDVLT 1d4fA 174 :VPAINVNDSVT T0294 109 :DTTAELAVSLLLTTC 1d4fA 192 :YGCRESLIDGIKRAT T0294 148 :GYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEEAAEFQAEFVSTPELAAQSDFIVVACS 1d4fA 207 :DVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIEPINALQAAMEGYEVTTMDEACKEGNIFVTTTG T0294 222 :TEGLCNKDFFQKMKETAVFINISRGDV 1d4fA 277 :CVDIILGRHFEQMKDDAIVCNIGHFDV T0294 249 :VNQDDL 1d4fA 305 :IDVKWL Number of specific fragments extracted= 10 number of extra gaps= 0 total=1442 Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1np3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1np3A expands to /projects/compbio/data/pdb/1np3.pdb.gz 1np3A:# T0294 read from 1np3A/merged-good-all-a2m # 1np3A read from 1np3A/merged-good-all-a2m # adding 1np3A to template set # found chain 1np3A in template set T0294 153 :QSTVGIIGLGRIGQAIARRLKPFGV 1np3A 16 :GKKVAIIGYGSQGHAHACNLKDSGV T0294 179 :RFLYTGRQPRP 1np3A 41 :DVTVGLRSGSA T0294 190 :EEAAEFQAEFVSTPELAAQSDFIVVACS 1np3A 54 :AKAEAHGLKVADVKTAVAAADVVMILTP T0294 221 :ATEGLCNKDFFQK 1np3A 83 :EFQGRLYKEEIEP T0294 234 :MKETAVFI 1np3A 97 :LKKGATLA T0294 243 :ISRG 1np3A 105 :FAHG T0294 247 :DV 1np3A 123 :DV T0294 249 :VNQDDLYQALASGKIAAAGLDVTSPE 1np3A 131 :APGHTVRSEFVKGGGIPDLIAIYQDA T0294 298 :THRTRNTMS 1np3A 188 :ETDLFGEQA T0294 307 :LLAANNLLAGLRGEP 1np3A 204 :ELVKAGFETLVEAGY Number of specific fragments extracted= 10 number of extra gaps= 0 total=1452 Number of alignments=109 # 1np3A read from 1np3A/merged-good-all-a2m # found chain 1np3A in template set T0294 153 :QSTVGIIGLGRIGQAIARRLKPFGV 1np3A 16 :GKKVAIIGYGSQGHAHACNLKDSGV T0294 179 :RFLYTGRQPR 1np3A 41 :DVTVGLRSGS T0294 189 :PEEAAEFQAEFVSTPELAAQSDFIVVACS 1np3A 53 :VAKAEAHGLKVADVKTAVAAADVVMILTP T0294 223 :EGLCNKDFF 1np3A 85 :QGRLYKEEI T0294 232 :QKMKETAVFI 1np3A 95 :PNLKKGATLA T0294 243 :ISRG 1np3A 105 :FAHG T0294 247 :DV 1np3A 123 :DV T0294 249 :VNQDDLYQALASGKIAAAGLDVTSPE 1np3A 131 :APGHTVRSEFVKGGGIPDLIAIYQDA T0294 298 :THRTRNTMS 1np3A 188 :ETDLFGEQA T0294 307 :LLAANNLLAGLRGEP 1np3A 204 :ELVKAGFETLVEAGY Number of specific fragments extracted= 10 number of extra gaps= 0 total=1462 Number of alignments=110 # 1np3A read from 1np3A/merged-good-all-a2m # found chain 1np3A in template set T0294 153 :QSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPR 1np3A 16 :GKKVAIIGYGSQGHAHACNLKDSGVDVTVGLRSGSA T0294 189 :PEEAAEFQAEFVSTPELAAQSDFIVVACS 1np3A 53 :VAKAEAHGLKVADVKTAVAAADVVMILTP T0294 221 :ATEGLCNKDFFQ 1np3A 83 :EFQGRLYKEEIE T0294 233 :KMKETAVFINI 1np3A 96 :NLKKGATLAFA T0294 249 :VNQDDLYQALASGKIAAAGLDVTSPEPL 1np3A 131 :APGHTVRSEFVKGGGIPDLIAIYQDASG Number of specific fragments extracted= 5 number of extra gaps= 0 total=1467 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bw9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bw9A expands to /projects/compbio/data/pdb/1bw9.pdb.gz 1bw9A:Skipped atom 69, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 71, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 73, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 75, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 402, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 404, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 406, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 416, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 418, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 551, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 652, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 830, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 832, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 1892, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 1894, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 1896, because occupancy 0.500 <= existing 0.500 in 1bw9A Skipped atom 1898, because occupancy 0.500 <= existing 0.500 in 1bw9A # T0294 read from 1bw9A/merged-good-all-a2m # 1bw9A read from 1bw9A/merged-good-all-a2m # adding 1bw9A to template set # found chain 1bw9A in template set T0294 7 :MKV 1bw9A 74 :MGG T0294 10 :FVTRR 1bw9A 80 :VIALP T0294 15 :IPAEGRVALARA 1bw9A 90 :IDPSTWARILRI T0294 45 :LERG 1bw9A 102 :HAEN T0294 68 :LDAAGAN 1bw9A 106 :IDKLSGN T0294 81 :MSVGID 1bw9A 113 :YWTGPD T0294 87 :HLALDEIKKR 1bw9A 120 :NTNSADMDTL T0294 97 :GI 1bw9A 144 :GG T0294 104 :PDVLTDTTAELAVSLLLTTCR 1bw9A 146 :AGSSAFTTAVGVFEAMKATVA T0294 146 :LCGY 1bw9A 167 :HRGL T0294 150 :GLTQSTVGIIGLGRIGQAIARRLKPFGV 1bw9A 172 :SLDGLTVLVQGLGAVGGSLASLAAEAGA T0294 179 :RFLYTGRQP 1bw9A 200 :QLLVADTDT T0294 188 :RPEEAAEFQAEFVSTPELAAQ 1bw9A 210 :RVAHAVALGHTAVALEDVLST T0294 209 :SDFIVVACSLT 1bw9A 232 :CDVFAPCAMGG T0294 225 :LCNKDFFQKMK 1bw9A 243 :VITTEVARTLD T0294 238 :AVFINISRGDVVNQDDLYQALASGKIAAA 1bw9A 254 :CSVVAGAANNVIADEAASDILHARGILYA Number of specific fragments extracted= 16 number of extra gaps= 0 total=1483 Number of alignments=112 # 1bw9A read from 1bw9A/merged-good-all-a2m # found chain 1bw9A in template set T0294 9 :VFVTR 1bw9A 80 :VIALP T0294 15 :IPAEGRVALARAA 1bw9A 90 :IDPSTWARILRIH T0294 42 :AKELERGVAGAHG 1bw9A 103 :AENIDKLSGNYWT T0294 59 :LSDHVDKRILDAA 1bw9A 117 :PDVNTNSADMDTL T0294 95 :KRGI 1bw9A 142 :ERGG T0294 104 :PDVLTDTTAELAVSLLLTTCRR 1bw9A 146 :AGSSAFTTAVGVFEAMKATVAH T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1bw9A 168 :RGLGSLDGLTVLVQGLGAVGGSLASLAAEAGA T0294 179 :RFLYTGRQPR 1bw9A 200 :QLLVADTDTE T0294 189 :PEEAAEFQAEFVSTPELAAQ 1bw9A 211 :VAHAVALGHTAVALEDVLST T0294 209 :SDFIVVACSLT 1bw9A 232 :CDVFAPCAMGG T0294 225 :LCNKDFFQKMK 1bw9A 243 :VITTEVARTLD T0294 238 :AVFINISRGDVVNQDDLYQALASGKIAAA 1bw9A 254 :CSVVAGAANNVIADEAASDILHARGILYA T0294 296 :SATHRTRNTMSLLAANNLLAGL 1bw9A 302 :GWSESVVHERAVAIGDTLNQVF Number of specific fragments extracted= 13 number of extra gaps= 0 total=1496 Number of alignments=113 # 1bw9A read from 1bw9A/merged-good-all-a2m # found chain 1bw9A in template set T0294 36 :SDEPIPAKELERGVAG 1bw9A 86 :PRHSIDPSTWARILRI T0294 64 :DKRILDAAGAN 1bw9A 102 :HAENIDKLSGN T0294 81 :MSVGID 1bw9A 113 :YWTGPD T0294 87 :HLALDEIK 1bw9A 120 :NTNSADMD T0294 95 :K 1bw9A 131 :D T0294 96 :RGI 1bw9A 143 :RGG T0294 104 :PDVLTDTTAELAVSLLLTTCRR 1bw9A 146 :AGSSAFTTAVGVFEAMKATVAH T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEEAAEFQAEFVSTPELAAQ 1bw9A 168 :RGLGSLDGLTVLVQGLGAVGGSLASLAAEAGAQLLVADTDTERVAHAVALGHTAVALEDVLST T0294 209 :SDFIVVACSL 1bw9A 232 :CDVFAPCAMG T0294 224 :GLCNKDFFQKMK 1bw9A 242 :GVITTEVARTLD T0294 238 :AVFINISRGDVVNQDDLYQALASGKIAAA 1bw9A 254 :CSVVAGAANNVIADEAASDILHARGILYA Number of specific fragments extracted= 11 number of extra gaps= 0 total=1507 Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v8bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1v8bA expands to /projects/compbio/data/pdb/1v8b.pdb.gz 1v8bA:# T0294 read from 1v8bA/merged-good-all-a2m # 1v8bA read from 1v8bA/merged-good-all-a2m # adding 1v8bA to template set # found chain 1v8bA in template set T0294 1 :SRPVRLMKVFVTRRIPAE 1v8bA 41 :DQPLKNAKITGCLHMTVE T0294 19 :GRVALARAADCEVEQWDSDEPIPAKELERGVAGA 1v8bA 61 :LLIETLQKLGAQIRWCSCNIYSTADYAAAAVSTL T0294 53 :HGLLCLLSDHVDKRILDAA 1v8bA 96 :NVTVFAWKNETLEEYWWCV T0294 73 :A 1v8bA 125 :D T0294 74 :NLKVIST 1v8bA 127 :GPDMIVD T0294 83 :VGIDHLAL 1v8bA 134 :DGGDATLL T0294 91 :DEIKKR 1v8bA 150 :KLYEEK T0294 98 :IRVGYTPDVLT 1v8bA 219 :FTAINVNDAVT T0294 109 :DTTAELAVSLLLTT 1v8bA 236 :VYGCRHSLPDGLMR T0294 146 :LCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1v8bA 250 :ATDFLISGKIVVICGYGDVGKGCASSMKGLGA T0294 179 :RFLYTGRQPRPEEAAEF 1v8bA 282 :RVYITEIDPICAIQAVM T0294 196 :QAEFVSTPELAAQSDFIVVAC 1v8bA 300 :GFNVVTLDEIVDKGDFFITCT T0294 221 :ATEGLCNKDFFQKMKETAVFINISRGDV 1v8bA 321 :GNVDVIKLEHLLKMKNNAVVGNIGHFDD T0294 249 :VNQDDLY 1v8bA 350 :IQVNELF T0294 261 :GKI 1v8bA 359 :KGI T0294 264 :AAAGLDVTS 1v8bA 366 :VKPQVDRIT T0294 276 :LPTNH 1v8bA 375 :LPNGN T0294 291 :LPHIGSATHRTRNTMSLLAA 1v8bA 396 :TGHPAFVMSFSFCNQTFAQL T0294 312 :NLLAGLRGEPMPSELK 1v8bA 416 :DLWQNKDTNKYENKVY Number of specific fragments extracted= 19 number of extra gaps= 0 total=1526 Number of alignments=115 # 1v8bA read from 1v8bA/merged-good-all-a2m # found chain 1v8bA in template set T0294 18 :EGRVALARAAD 1v8bA 29 :PGLMRIREEYG T0294 36 :SDE 1v8bA 40 :KDQ T0294 48 :GVAGAHGLLCLLSD 1v8bA 43 :PLKNAKITGCLHMT T0294 66 :RILDAA 1v8bA 64 :ETLQKL T0294 74 :NLKVISTMSVGIDHLA 1v8bA 70 :GAQIRWCSCNIYSTAD T0294 90 :LDEIKKR 1v8bA 88 :AAAVSTL T0294 97 :GIRVGYTPDVLTDTTAELAVS 1v8bA 96 :NVTVFAWKNETLEEYWWCVES T0294 118 :LLLTTCRRLPEAIEEVKNGGWTSWKP 1v8bA 137 :DATLLVHKGVEYEKLYEEKNILPDPE T0294 146 :L 1v8bA 163 :K T0294 151 :LTQSTVGIIGLGRIGQAIARRLKPFGV 1v8bA 255 :ISGKIVVICGYGDVGKGCASSMKGLGA T0294 179 :RFLYTGRQPR 1v8bA 282 :RVYITEIDPI T0294 189 :PEEAAEFQAEFVSTPELAAQSDFIVVAC 1v8bA 293 :AIQAVMEGFNVVTLDEIVDKGDFFITCT T0294 221 :ATEGLCNKDFFQKMKETAVFINISR 1v8bA 321 :GNVDVIKLEHLLKMKNNAVVGNIGH T0294 246 :GDVVNQDDLY 1v8bA 347 :DDEIQVNELF T0294 291 :LPHIGSATHRTRN 1v8bA 396 :TGHPAFVMSFSFC T0294 305 :MSLLAANNLLAGLRGEPMPSE 1v8bA 409 :NQTFAQLDLWQNKDTNKYENK Number of specific fragments extracted= 16 number of extra gaps= 0 total=1542 Number of alignments=116 # 1v8bA read from 1v8bA/merged-good-all-a2m # found chain 1v8bA in template set T0294 45 :LERGVAGA 1v8bA 175 :LLKNSILK T0294 64 :DKRILDAAGANLKVISTMS 1v8bA 183 :NPKKWTNIAKKIIGVSEET T0294 90 :LDEIKK 1v8bA 205 :VLRLKK T0294 96 :RG 1v8bA 214 :QN T0294 98 :IRVGYTPDVLT 1v8bA 219 :FTAINVNDAVT T0294 109 :DTTAELAVSLLLTTC 1v8bA 236 :VYGCRHSLPDGLMRA T0294 147 :CGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEEAAEFQAEFVSTPELAAQSDFIVVACSLTP 1v8bA 251 :TDFLISGKIVVICGYGDVGKGCASSMKGLGARVYITEIDPICAIQAVMEGFNVVTLDEIVDKGDFFITCTGNVD T0294 225 :LCNKDFFQKMKETAVFINISR 1v8bA 325 :VIKLEHLLKMKNNAVVGNIGH T0294 246 :GDVVNQDDLY 1v8bA 347 :DDEIQVNELF T0294 280 :H 1v8bA 358 :Y T0294 292 :PHIGSATHR 1v8bA 397 :GHPAFVMSF T0294 302 :RNTMSLLAANNLLAGLRGEPMPSEL 1v8bA 406 :SFCNQTFAQLDLWQNKDTNKYENKV Number of specific fragments extracted= 12 number of extra gaps= 0 total=1554 Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uufA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0294 read from 1uufA/merged-good-all-a2m # 1uufA read from 1uufA/merged-good-all-a2m # found chain 1uufA in training set T0294 115 :AVSLLLTTCRRL 1uufA 159 :AGITTYSPLRHW T0294 148 :GY 1uufA 171 :QA T0294 151 :LTQSTVGIIGLGRIGQAIARRLKPFGV 1uufA 173 :GPGKKVGVVGIGGLGHMGIKLAHAMGA T0294 179 :RFLYTGRQP 1uufA 200 :HVVAFTTSE T0294 188 :RPEEAAEFQAEFV 1uufA 210 :KREAAKALGADEV T0294 213 :VV 1uufA 223 :VN T0294 225 :LCNKDFFQKMKETAVFINISRGDVVNQDDLY 1uufA 225 :SRNADEMAAHLKSFDFILNTVAAPHNLDDFT T0294 281 :PLLTLKNCVIL 1uufA 256 :TLLKRDGTMTL T0294 296 :SATHRTRN 1uufA 295 :GGIPETQE T0294 305 :MSLLAANN 1uufA 303 :MLDFCAEH Number of specific fragments extracted= 10 number of extra gaps= 0 total=1564 Number of alignments=118 # 1uufA read from 1uufA/merged-good-all-a2m # found chain 1uufA in training set T0294 151 :LTQSTVGIIGLGRIGQAIARRLKPFGV 1uufA 173 :GPGKKVGVVGIGGLGHMGIKLAHAMGA T0294 179 :RFLYTGRQPR 1uufA 200 :HVVAFTTSEA T0294 189 :PEEAAEFQAEFV 1uufA 211 :REAAKALGADEV T0294 225 :LCNKDFFQKMKETAVFINISRGDVVNQDDLY 1uufA 225 :SRNADEMAAHLKSFDFILNTVAAPHNLDDFT T0294 281 :PLLTLKNCVIL 1uufA 256 :TLLKRDGTMTL T0294 296 :SATHRTRNTMSLLAANN 1uufA 294 :IGGIPETQEMLDFCAEH Number of specific fragments extracted= 6 number of extra gaps= 0 total=1570 Number of alignments=119 # 1uufA read from 1uufA/merged-good-all-a2m # found chain 1uufA in training set T0294 115 :AVSLLLTTCRRL 1uufA 159 :AGITTYSPLRHW T0294 149 :YGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEE 1uufA 171 :QAGPGKKVGVVGIGGLGHMGIKLAHAMGAHVVAFTTSEAKREA T0294 202 :TPEL 1uufA 214 :AKAL T0294 208 :QSDFIVV 1uufA 218 :GADEVVN T0294 225 :L 1uufA 225 :S T0294 227 :NKDFFQKMKETAVFINISRGDVVNQDDLY 1uufA 227 :NADEMAAHLKSFDFILNTVAAPHNLDDFT T0294 281 :PLLTLKNCVIL 1uufA 256 :TLLKRDGTMTL Number of specific fragments extracted= 7 number of extra gaps= 0 total=1577 Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pjbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1pjbA expands to /projects/compbio/data/pdb/1pjb.pdb.gz 1pjbA:# T0294 read from 1pjbA/merged-good-all-a2m # 1pjbA read from 1pjbA/merged-good-all-a2m # adding 1pjbA to template set # found chain 1pjbA in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1pjbA)M1 Warning: unaligning (T0294)L218 because of BadResidue code BAD_PEPTIDE in next template residue (1pjbA)P241 Warning: unaligning (T0294)T219 because of BadResidue code BAD_PEPTIDE at template residue (1pjbA)P241 T0294 8 :KVFVTRR 1pjbA 2 :EIGVPKE T0294 15 :IPAEGRVALAR 1pjbA 18 :LSPSSVRTLVE T0294 27 :ADCEVEQWDSD 1pjbA 29 :AGHTVFIETQA T0294 39 :PIPAKELERG 1pjbA 44 :GFADQDYVQA T0294 51 :GAHGL 1pjbA 54 :GAQVV T0294 56 :LCLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDV 1pjbA 69 :MVVKVKEPLPAEYDLMQKDQLLFTYLHLAAARELTEQLMRVGLTAIAYETV T0294 107 :LTDTTAELAVSLLLTTCRRLPE 1pjbA 128 :LLTPMSIIAGRLSVQFGARFLE T0294 138 :WTSWKPLWLCGY 1pjbA 150 :RQQGGRGVLLGG T0294 150 :GLTQSTVGIIGLGRIGQAIARRLKPFGV 1pjbA 164 :GVKPGKVVILGGGVVGTEAAKMAVGLGA T0294 179 :RFLYTGR 1pjbA 192 :QVQIFDI T0294 188 :RPEEAAE 1pjbA 199 :NVERLSY T0294 196 :QAEFV 1pjbA 213 :RVELL T0294 201 :S 1pjbA 220 :N T0294 202 :TPELAAQSDFIVVACS 1pjbA 224 :IETAVAEADLLIGAVL T0294 220 :PA 1pjbA 242 :GR T0294 222 :TEGLCNKDFFQKMKETAVFINISRGDV 1pjbA 245 :APILVPASLVEQMRTGSVIVDVAVDQG T0294 270 :VTSPEPLPTNHPLLTLKNCVILP 1pjbA 274 :VETLHPTSHTQPTYEVFGVVHYG T0294 293 :HIGSATHRTRNTMSLLAANNLLAGL 1pjbA 300 :MPGAVPWTATQALNNSTLPYVVKLA Number of specific fragments extracted= 18 number of extra gaps= 1 total=1595 Number of alignments=121 # 1pjbA read from 1pjbA/merged-good-all-a2m # found chain 1pjbA in template set Warning: unaligning (T0294)M7 because first residue in template chain is (1pjbA)M1 Warning: unaligning (T0294)S217 because of BadResidue code BAD_PEPTIDE at template residue (1pjbA)P241 T0294 8 :KVFVTRR 1pjbA 2 :EIGVPKE T0294 15 :IPAEGRVALARA 1pjbA 18 :LSPSSVRTLVEA T0294 28 :DCEVEQWDS 1pjbA 30 :GHTVFIETQ T0294 39 :PIPAKELERG 1pjbA 44 :GFADQDYVQA T0294 51 :GAHGL 1pjbA 54 :GAQVV T0294 56 :LCLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDV 1pjbA 69 :MVVKVKEPLPAEYDLMQKDQLLFTYLHLAAARELTEQLMRVGLTAIAYETV T0294 107 :LTDTTAELAVSLLLTT 1pjbA 128 :LLTPMSIIAGRLSVQF T0294 130 :IEEVKNGGWTSWKPLWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGV 1pjbA 144 :GARFLERQQGGRGVLLGGVPGVKPGKVVILGGGVVGTEAAKMAVGLGA T0294 179 :RFLYTGRQPR 1pjbA 192 :QVQIFDINVE T0294 191 :EA 1pjbA 202 :RL T0294 193 :AEFQAEFVS 1pjbA 212 :SRVELLYSN T0294 202 :TPELAAQSDFIVVAC 1pjbA 224 :IETAVAEADLLIGAV T0294 218 :LTPATE 1pjbA 242 :GRRAPI T0294 225 :LCNKDFFQKMKETAVFINIS 1pjbA 248 :LVPASLVEQMRTGSVIVDVA T0294 245 :RGDVV 1pjbA 270 :QGGCV T0294 271 :TSPEPLPTNHPLLTLKNCVILP 1pjbA 275 :ETLHPTSHTQPTYEVFGVVHYG T0294 293 :HIGSATHRTRNTMSLLAANNLLAGL 1pjbA 300 :MPGAVPWTATQALNNSTLPYVVKLA Number of specific fragments extracted= 17 number of extra gaps= 1 total=1612 Number of alignments=122 # 1pjbA read from 1pjbA/merged-good-all-a2m # found chain 1pjbA in template set Warning: unaligning (T0294)L218 because of BadResidue code BAD_PEPTIDE in next template residue (1pjbA)P241 Warning: unaligning (T0294)T219 because of BadResidue code BAD_PEPTIDE at template residue (1pjbA)P241 T0294 24 :ARAADCEVEQWDSDE 1pjbA 24 :RTLVEAGHTVFIETQ T0294 39 :PIPAKELERGV 1pjbA 44 :GFADQDYVQAG T0294 53 :HGL 1pjbA 55 :AQV T0294 56 :LCLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTP 1pjbA 69 :MVVKVKEPLPAEYDLMQKDQLLFTYLHLAAARELTEQLMRVGLTAIAYE T0294 105 :DVLTDTTAELAVSLLLTTCRRLPEA 1pjbA 126 :LPLLTPMSIIAGRLSVQFGARFLER T0294 137 :GWTSWKPLWLCGYGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGR 1pjbA 151 :QQGGRGVLLGGVPGVKPGKVVILGGGVVGTEAAKMAVGLGAQVQIFDIN T0294 189 :PEE 1pjbA 200 :VER T0294 192 :AAEFQAEFVS 1pjbA 211 :GSRVELLYSN T0294 202 :TPELAAQSDFIVVACS 1pjbA 224 :IETAVAEADLLIGAVL T0294 220 :PA 1pjbA 242 :GR T0294 225 :LCNKDFFQKMKETAVFINISRGD 1pjbA 248 :LVPASLVEQMRTGSVIVDVAVDQ T0294 262 :KI 1pjbA 271 :GG T0294 270 :VTSPEPLPTNHPLLTLKNCVILP 1pjbA 274 :VETLHPTSHTQPTYEVFGVVHYG T0294 293 :HIGSATHRTRNTMSLLAANNLLAGL 1pjbA 300 :MPGAVPWTATQALNNSTLPYVVKLA Number of specific fragments extracted= 14 number of extra gaps= 1 total=1626 Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sc6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sc6A expands to /projects/compbio/data/pdb/1sc6.pdb.gz 1sc6A:Skipped atom 1168, because occupancy 0.500 <= existing 0.500 in 1sc6A Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 1sc6A Skipped atom 1172, because occupancy 0.500 <= existing 0.500 in 1sc6A Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 1sc6A Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 1sc6A Skipped atom 1178, because occupancy 0.500 <= existing 0.500 in 1sc6A Skipped atom 1180, because occupancy 0.500 <= existing 0.500 in 1sc6A Skipped atom 1182, because occupancy 0.500 <= existing 0.500 in 1sc6A Skipped atom 1184, because occupancy 0.500 <= existing 0.500 in 1sc6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0294 read from 1sc6A/merged-good-all-a2m # 1sc6A read from 1sc6A/merged-good-all-a2m # adding 1sc6A to template set # found chain 1sc6A in template set Warning: unaligning (T0294)P3 because first residue in template chain is (1sc6A)E7 Warning: unaligning (T0294)V4 because of BadResidue code BAD_PEPTIDE at template residue (1sc6A)K8 Warning: unaligning (T0294)T139 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sc6A)S146 Warning: unaligning (T0294)G148 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sc6A)S146 Warning: unaligning (T0294)V270 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sc6A)D275 Warning: unaligning (T0294)H280 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sc6A)D275 Warning: unaligning (T0294)P292 because of BadResidue code BAD_PEPTIDE in next template residue (1sc6A)H292 Warning: unaligning (T0294)H293 because of BadResidue code BAD_PEPTIDE at template residue (1sc6A)H292 T0294 5 :RLMKVFVTRRIPAEGRVALARA 1sc6A 9 :DKIKFLLVEGVHQKALESLRAA T0294 28 :DC 1sc6A 31 :GY T0294 30 :EVEQW 1sc6A 34 :NIEFH T0294 37 :DEPIPAKELERGVAGAHGLLCLLSDHVDKRILDAA 1sc6A 39 :KGALDDEQLKESIRDAHFIGLRSRTHLTEDVINAA T0294 73 :ANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGW 1sc6A 74 :EKLVAIGAFAIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLLLLRGVPEANAKAHRGVG T0294 149 :YGLTQSTVGIIGLGRIGQAIARRLKPFGV 1sc6A 147 :FEARGKKLGIIGYGHIGTQLGILAESLGM T0294 179 :RFLYTGRQPRP 1sc6A 176 :YVYFYDIENKL T0294 195 :FQAEFV 1sc6A 189 :GNATQV T0294 201 :STPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLD 1sc6A 196 :HLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVVDIPALADALASKHLAGAAID T0294 281 :PLLTLKNCVIL 1sc6A 280 :PLAEFDNVLLT T0294 294 :IGSATHRTRNTMSLLAANNLLAGLRGEPMPSE 1sc6A 293 :IGGSTQEAQENIGLEVAGKLIKYSDNGSTLSA Number of specific fragments extracted= 11 number of extra gaps= 1 total=1637 Number of alignments=124 # 1sc6A read from 1sc6A/merged-good-all-a2m # found chain 1sc6A in template set Warning: unaligning (T0294)P3 because first residue in template chain is (1sc6A)E7 Warning: unaligning (T0294)V4 because of BadResidue code BAD_PEPTIDE at template residue (1sc6A)K8 Warning: unaligning (T0294)T139 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sc6A)S146 Warning: unaligning (T0294)G148 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sc6A)S146 Warning: unaligning (T0294)V270 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sc6A)D275 Warning: unaligning (T0294)L276 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sc6A)D275 Warning: unaligning (T0294)P292 because of BadResidue code BAD_PEPTIDE in next template residue (1sc6A)H292 Warning: unaligning (T0294)H293 because of BadResidue code BAD_PEPTIDE at template residue (1sc6A)H292 T0294 5 :RLMKVFVTRRIPAEGRVALARA 1sc6A 9 :DKIKFLLVEGVHQKALESLRAA T0294 28 :DC 1sc6A 31 :GY T0294 30 :EVEQW 1sc6A 34 :NIEFH T0294 37 :DEPIPAKELERGVAGAHGLLCLLSDHVDKRILDAA 1sc6A 39 :KGALDDEQLKESIRDAHFIGLRSRTHLTEDVINAA T0294 73 :ANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGW 1sc6A 74 :EKLVAIGAFAIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLLLLRGVPEANAKAHRGVG T0294 149 :YGLTQSTVGIIGLGRIGQAIARRLKPFGV 1sc6A 147 :FEARGKKLGIIGYGHIGTQLGILAESLGM T0294 179 :RFLYTGRQPR 1sc6A 176 :YVYFYDIENK T0294 189 :P 1sc6A 187 :P T0294 194 :EFQAEFV 1sc6A 188 :LGNATQV T0294 201 :STPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLD 1sc6A 196 :HLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVVDIPALADALASKHLAGAAID T0294 277 :PTNHPLLTLKNCVIL 1sc6A 276 :PFTSPLAEFDNVLLT T0294 294 :IGSATHRTRNTMSLLAANNLLAGLRGEPMPSE 1sc6A 293 :IGGSTQEAQENIGLEVAGKLIKYSDNGSTLSA Number of specific fragments extracted= 12 number of extra gaps= 1 total=1649 Number of alignments=125 # 1sc6A read from 1sc6A/merged-good-all-a2m # found chain 1sc6A in template set Warning: unaligning (T0294)T139 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sc6A)S146 Warning: unaligning (T0294)G148 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sc6A)S146 Warning: unaligning (T0294)V270 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sc6A)D275 Warning: unaligning (T0294)H280 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sc6A)D275 Warning: unaligning (T0294)P292 because of BadResidue code BAD_PEPTIDE in next template residue (1sc6A)H292 Warning: unaligning (T0294)H293 because of BadResidue code BAD_PEPTIDE at template residue (1sc6A)H292 T0294 19 :GRVALARAADCEVEQWDSDEPIPAKELERGVAGAHGLLCLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPDVLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGW 1sc6A 20 :HQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLRSRTHLTEDVINAAEKLVAIGAFAIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLLLLRGVPEANAKAHRGVG T0294 149 :YGLTQSTVGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEE 1sc6A 147 :FEARGKKLGIIGYGHIGTQLGILAESLGMYVYFYDIENKLPLG T0294 195 :FQAEFVSTPELAAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLYQALASGKIAAAGLD 1sc6A 190 :NATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVVDIPALADALASKHLAGAAID T0294 281 :PLLTLKNCVIL 1sc6A 280 :PLAEFDNVLLT T0294 294 :IGSATHRTRNTMSLLAANNLLAGLRGEPMPSELKL 1sc6A 293 :IGGSTQEAQENIGLEVAGKLIKYSDNGSTLSAVNF Number of specific fragments extracted= 5 number of extra gaps= 1 total=1654 Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ygyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0294/1ygyA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0294/1ygyA/merged-good-all-a2m.gz for input Trying 1ygyA/merged-good-all-a2m Error: Couldn't open file 1ygyA/merged-good-all-a2m or 1ygyA/merged-good-all-a2m.gz for input # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 126 Done printing distance constraints # command: