a2m2html output for tmp.a2m

Citations (SAM, SAM-T99, HMMs)

R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: Extension and analysis of the basic method, CABIOS 12:95-107, 1996.
K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting remote protein homologies, Bioinformatics 14(10):846-856, 1998.
A. Krogh et al., Hidden Markov models in computational biology: Applications to protein modeling, JMB 235:1501-1531, Feb 1994.

Sequence numbers correspond to the following labels:

- T0451 YP_322774.1, Anabaena variabilis, 133 residues
- gi|17232498|ref|NP_489046.1|_7:139 hypothetical protein all5006 [Nostoc sp. PCC 7120]
- gi|17134144|dbj|BAB76705.1| all5006 [Nostoc sp. PCC 7120]
- gi|75908478|ref|YP_322774.1|_1:133 hypothetical protein Ava_2261 [Anabaena variabilis ATCC 29413]
- gi|75702203|gb|ABA21879.1| conserved hypothetical protein [Anabaena variabilis ATCC 29413]
- gi|53687088|ref|ZP_00106679.2|_29:159 hypothetical protein Npun02007157 [Nostoc punctiforme PCC 73102]
- gi|186685661|ref|YP_001868857.1|_2:131 conserved hypothetical protein [Nostoc punctiforme PCC 73102]
- gi|186468113|gb|ACC83914.1| conserved hypothetical protein [Nostoc punctiforme PCC 73102]
- gi|119512878|ref|ZP_01631943.1|_4:130 hypothetical protein N9414_16646 [Nodularia spumigena CCY9414]
- gi|119462460|gb|EAW43432.1| hypothetical protein N9414_16646 [Nodularia spumigena CCY9414]
- gi|126435602|ref|YP_001071293.1|_5:128 protein of unknown function DUF1486 [Mycobacterium sp. JLS]
- gi|126235402|gb|ABN98802.1| protein of unknown function DUF1486 [Mycobacterium sp. JLS]
- gi|119869086|ref|YP_939038.1|_5:128 protein of unknown function DUF1486 [Mycobacterium sp. KMS]
- gi|119695175|gb|ABL92248.1| protein of unknown function DUF1486 [Mycobacterium sp. KMS]
- gi|156743446|ref|YP_001433575.1|_99:223 hypothetical protein Rcas_3507 [Roseiflexus castenholzii DSM 13941]
- gi|156234774|gb|ABU59557.1| hypothetical protein Rcas_3507 [Roseiflexus castenholzii DSM 13941]
- gi|118470610|ref|YP_888127.1|_2:130 hypothetical protein MSMEG_3836 [Mycobacterium smegmatis str. MC2 155]
- gi|118171897|gb|ABK72793.1| conserved hypothetical protein [Mycobacterium smegmatis str. MC2 155]
- gi|186898829|ref|ZP_02971793.1|_3:125 conserved hypothetical protein [Cyanothece sp. PCC 7424]
- gi|186694106|gb|EDU18718.1| conserved hypothetical protein [Cyanothece sp. PCC 7424]
- gi|108799974|ref|YP_640171.1|_4:108 hypothetical protein Mmcs_3008 [Mycobacterium sp. MCS]
- gi|108770393|gb|ABG09115.1| conserved hypothetical protein [Mycobacterium sp. MCS]
- gi|119485989|ref|ZP_01620051.1|_7:124 hypothetical protein L8106_05695 [Lyngbya sp. PCC 8106]
- gi|119456764|gb|EAW37892.1| hypothetical protein L8106_05695 [Lyngbya sp. PCC 8106]
- gi|183980382|ref|YP_001848673.1|_4:120 conserved hypothetical protein [Mycobacterium marinum M]
- gi|183173708|gb|ACC38818.1| conserved hypothetical protein [Mycobacterium marinum M]
- gi|118619826|ref|YP_908158.1|_4:120 hypothetical protein MUL_4769 [Mycobacterium ulcerans Agy99]
- gi|118571936|gb|ABL06687.1| conserved hypothetical protein [Mycobacterium ulcerans Agy99]
- gi|24638008|sp|Q9ZAG3|LIMA_RHOER_14:135 Limonene-1,2-epoxide hydrolase [Taxonomy]
- gi|33357516|pdb|1NWW|A Chain A, Limonene-1,2-Epoxide Hydrolase [Taxonomy]
- gi|33357517|pdb|1NWW|B Chain B, Limonene-1,2-Epoxide Hydrolase [Taxonomy]
- gi|4160334|emb|CAA77012.1| limonene-1,2-epoxide hydrolase [Rhodococcus erythropolis]
- gi|12054949|emb|CAC20854.1| limonene-1,2-epoxide hydrolase [Rhodococcus erythropolis]
- gi|159486648|ref|XP_001701350.1|_70:193 ketoacid isomerase-like protein [Chlamydomonas reinhardtii]
- gi|158271745|gb|EDO97558.1| ketoacid isomerase-like protein [Chlamydomonas reinhardtii]
- gi|111022377|ref|YP_705349.1|_5:125 hypothetical protein RHA1_ro05411 [Rhodococcus sp. RHA1]
- gi|110821907|gb|ABG97191.1| conserved hypothetical protein [Rhodococcus sp. RHA1]
- gi|94498797|ref|ZP_01305344.1|_5:122 hypothetical protein SKA58_10240 [Sphingomonas sp. SKA58]
- gi|94421764|gb|EAT06818.1| hypothetical protein SKA58_10240 [Sphingomonas sp. SKA58]
- gi|50121896|ref|YP_051063.1|_36:164 putative hydrolase [Erwinia carotovora subsp. atroseptica SCRI1043]
- gi|49612422|emb|CAG75872.1| putative hydrolase [Erwinia carotovora subsp. atroseptica SCRI1043]
- gi|167647193|ref|YP_001684856.1|_6:124 ketosteroid isomerase-like protein [Caulobacter sp. K31]
- gi|167349623|gb|ABZ72358.1| ketosteroid isomerase-like protein [Caulobacter sp. K31]
- gi|88705726|ref|ZP_01103436.1|_7:132 conserved hypothetical protein [gamma proteobacterium KT 71]
- gi|88700239|gb|EAQ97348.1| conserved hypothetical protein [Congregibacter litoralis KT71]
- gi|33357489|pdb|1NU3|A_14:135 Chain A, Limonene-1,2-Epoxide Hydrolase In Complex With Valpromide [Taxonomy]
- gi|33357490|pdb|1NU3|B Chain B, Limonene-1,2-Epoxide Hydrolase In Complex With Valpromide [Taxonomy]
- gi|149201702|ref|ZP_01878676.1|_24:124 hypothetical protein RTM1035_04160 [Roseovarius sp. TM1035]
- gi|149144750|gb|EDM32779.1| hypothetical protein RTM1035_04160 [Roseovarius sp. TM1035]
- gi|87120218|ref|ZP_01076113.1|_25:130 hypothetical protein MED121_08503 [Marinomonas sp. MED121]
- gi|86164321|gb|EAQ65591.1| hypothetical protein MED121_08503 [Marinomonas sp. MED121]
- gi|159474152|ref|XP_001695193.1|_69:191 ketoacid isomerase-like protein [Chlamydomonas reinhardtii]
- gi|158276127|gb|EDP01901.1| ketoacid isomerase-like protein [Chlamydomonas reinhardtii]
- gi|126729503|ref|ZP_01745316.1|_24:124 hypothetical protein SSE37_03495 [Sagittula stellata E-37]
- gi|126709622|gb|EBA08675.1| hypothetical protein SSE37_03495 [Sagittula stellata E-37]
- gi|182678465|ref|YP_001832611.1|_30:132 conserved hypothetical protein [Beijerinckia indica subsp. indica ATCC 9039]
- gi|182634348|gb|ACB95122.1| conserved hypothetical protein [Beijerinckia indica subsp. indica ATCC 9039]
- gi|115373203|ref|ZP_01460504.1|_19:128 conserved hypothetical protein [Stigmatella aurantiaca DW4/3-1]
- gi|115369804|gb|EAU68738.1| conserved hypothetical protein [Stigmatella aurantiaca DW4/3-1]
- gi|163840464|ref|YP_001624869.1|_4:107 hypothetical protein RSal33209_1719 [Renibacterium salmoninarum ATCC 33209]
- gi|162953940|gb|ABY23455.1| conserved hypothetical protein [Renibacterium salmoninarum ATCC 33209]
- gi|158314412|ref|YP_001506920.1|_15:125 hypothetical protein Franean1_2584 [Frankia sp. EAN1pec]
- gi|158109817|gb|ABW12014.1| conserved hypothetical protein [Frankia sp. EAN1pec]
- gi|111223008|ref|YP_713802.1|_4:117 Delta-5-3-ketosteroid isomerase-like protein (Fragment) (partial match) [Frankia alni ACN14a]
- gi|111150540|emb|CAJ62240.1| Delta-5-3-ketosteroid isomerase-like protein (Fragment) (partial match) [Frankia alni ACN14a]
- gi|37521629|ref|NP_925006.1|_7:118 hypothetical protein glr2060 [Gloeobacter violaceus PCC 7421]
- gi|35212627|dbj|BAC90001.1| glr2060 [Gloeobacter violaceus PCC 7421]
- gi|21241155|ref|NP_640737.1|_12:129 hypothetical protein XAC0381 [Xanthomonas axonopodis pv. citri str. 306]
- gi|21106460|gb|AAM35273.1| conserved hypothetical protein [Xanthomonas axonopodis pv. citri str. 306]
- gi|114773093|ref|ZP_01450377.1|_7:122 transcriptional regulator-related protein [alpha proteobacterium HTCC2255]
- gi|146275684|ref|YP_001165844.1|_6:113 hypothetical protein Saro_3458 [Novosphingobium aromaticivorans DSM 12444]
- gi|145322375|gb|ABP64318.1| hypothetical protein Saro_3458 [Novosphingobium aromaticivorans DSM 12444]
- gi|183982854|ref|YP_001851145.1|_9:93 conserved hypothetical protein [Mycobacterium marinum M]
- gi|183176180|gb|ACC41290.1| conserved hypothetical protein [Mycobacterium marinum M]

              10        20            30        40        50           
              |         |             |         |         |           
   1 MMTHYSDNTLKVAHQGFEFFTQGL....ATGEWQKFLDMLTEDFTFWFPMGEFHGL...NV....
   2 MMEQNSENTLKVAHQGFEFFTQGL....ATGEWQKFLDMLTEDFTFWFPMGKFHGL...NV....
   3 MMTHYSDNTLKVAHQGFEFFTQGL....ATGEWQKFLDMLTEDFTFWFPMGEFHGL...NV....
   4 -MTQNSENTLKVARQAFEHLTYGM....ATGEWEALLDMLTEDFTLWFPMGKFHGL...NV....
   5 --TQNSENTLKVARQAFEHLTYGM....ATGEWEALLDMLTEDFTLWFPMGKFHGL...NV....
   6 ----NSEKTLKIAQQGFDHFTHGL....ATGEWSAFLDMLTEDFTFWFPMGKFHGL...NE....
   7 -------DRRDRAHQAIDRLQQAL....LAHDMSAFADQWAPDGTMSFPFAPPGWPe..LA....
   8 -------DRRDRAHQAIDRLQQAL....LAHDMSAFADQWAPDGTMSFPFAPPGWPe..LA....
   9 -FTPLSPDPRNVAMRAFQHFCTGL....ASGQWEPFLAMLSDDFSFWFPRGKYKGL...NV....
  10 --TPEPDEARTRTHRTIDRLQQAL....LAGDMNTFADEWAPHGTATFPFAPPGWPs..PK....
  11 ---TASPEILETAHLAFKHFTEGL....ATGEWQAFLNMLTSDFTFWFPVGAFKGK...NV....
  12 ------------------------....--HDMSAFADQWAPDGTMSFPFAPPGWPe..LA....
  13 --------TLETAQQAFEHFRHGL....ATGEWEKFIAILSDDFTFSFPAGPYQGL...NQ....
  14 -------FDDPQAELAWMFLQSMC....EGGDLDEGFALLSDDFTYWSIITRSAF-...--....
  15 -------FDDPQAELAWMFLQSTC....EGGDLDEGFALLSDDFTYWSIITRSAF-...--....
  16 --DSAAGAASTPDEKIVLEFMDAL....TSNDAAKLIEYFAEDTMYQ---NMPLPP...AY....
  17 ---SAASGAAATIQEAYGAFGQFA....ATGEYSPLESYFGDGVKWVSTVN-GGYT...GK....
  18 ----------EQNIDLADNFAKVF....STGDVEQILDTLHPDATYWVSGRIDGMSg..SY....
  19 -------------RAIVAAFLDSF....SSGDVEAILEYLTEDATWWVLGNVHGMSg..TI....
  20 --TNTHDIQGLSARKTVEAYLAAF....AEGKLDDIVSLLDDNVVWHIDGEPGVSTvglLQ....
  21 -------------QSIVQRGYDCF....VKGDLDGLFSTMTDDVQWSVVGPPDAFP...LFgers
  22 ----RKSMKTEETRQLVQHWLSLA....GSGNVEGAMALFAEDAVWTNIGSTKFSGdf.VG....
  23 --DSAAGAASTPDEKIVLEFXDAL....TSNDAAKLIEYFAEDTXYQ---NXPLPP...AY....
  24 ------------------------....-----DSLLGLFTDDVIFEFPYAPDGLPkr.LD....
  25 ------------------------....--PQANRFLEMVSDDIEMEFPYAHEGCIkr.IQ....
  26 ----AATGPAATLESAYGAFGSFV....SSGDYSTLDSFFTNDTTWLSNVN-GGFQ...GK....
  27 ------------------------....-----SDLVDLFCEDVVFEFPYAPEGLPrr.LE....
  28 ------------------------....-----EHFFDIITDDTIYEVLYDVPGWPri.IK....
  29 -----------------------L....VTKDMPAWLELFAENAVIEFPYAPSVGTparLE....
  30 ------------------------....-------FAGLWSRDGIIEFPFATANYPqr.VE....
  31 -----------------------M....VAGEGVVFADLFAEAGVLEYPFAMPGQPre.LR....
  32 -------------------YVEAV....RDGDAAVIRDSFAADAVWHYPGSLPISGe..WR....
  33 -------------ERFMQTLQHTE....QSGDVESLVNLFAEDAELSNLVL--TEP...LR....
  34 ---------------LVQAYYAAF....NRGDWDGMLAFLAEDVAHD----LNQGPr..EI....
  35 ----------------FTTFYQEL....SPDNISQLPDIYSEDITLIDPVGTHHGL...NT....
  36 ----------DQMIQFVDDLYAAT....GTGDWDKAASMLTDDFVVTEAPGLPMEGv..YT....
  37 ---------KAEIEQAVRHYTTVVegcsASGDWRPFADLFTEDVVYT---EHHYGV...FH....


           60        70               80        90            100      
           |         |                |         |              |      
   1 GKER.AKEFFTYVSESFHTGI..QISS.....LDRVTSNETTVVFEFRDEGLF.....LGKPYKN
   2 GKER.AKEFFTYVSESFHPGI..QLSS.....LDHVTSNETTVVFEFRDEGLL.....LGKPYKN
   3 GKER.AKEFFTYVSESFHTGI..QISS.....LDRVTSNETTVVFEFRDEGLF.....LGKPYKN
   4 GKQR.AREFFEYVFEAFSPGL..NLTG.....LDRVTSNETTAVFEFRDEGLL.....FGQLYKN
   5 GKQR.AREFFEYVFEAFSPGL..NLTG.....LDRVTSNETTAVFEFRDEGLL.....FGQLYKN
   6 GKDR.AREFFQYVSESFNSGI..QLTS.....LDSVTSNETTVVFEFRDEGLL.....LNQPYKN
   7 GRDA.VREYLANYTDTVDVRA..VTRM.....VRHDTADPDTVILEWAVSGVAvk...TGKPYDI
   8 GRDA.VREYLANYTDTVDVRA..VTRM.....VRHDTADPDTVILEWAVSGVVvk...TGKPYDI
   9 GKDR.AREFFTYVSSVFSEG-..LSVT.....LDRVVGSGSTYIFEFRDEGKL.....RGQPYTN
  10 GRDE.VRTYLSGLSGSVEIRG..IRHQ.....TRHDTADPGTVVLEWGVTGIVra...TGKPYDI
  11 GKEK.AREFFHFVTDKVFTEG..LVLT.....LERVTSSDTTVLFEARSEGKM.....FGFPYQN
  12 GRDA.VREYLANYTDTVDVRA..VTRM.....VRHDTADPDTVILEWAVSGVVvk...TGKPYDI
  13 GKER.MAEFLGYVSEKVFSQG..LVFT.....LERTTFNENTVVFEGTSEGLM.....FGNPYKN
  14 ---E.KDALRRAVEQRKKVFE..INID.....LRRCVNEGETVVIEGQSEGMTa....TGVRYDS
  15 ---E.KDALRRAVEQRKKVFE..INID.....LRRCVNEGETVVIEGQSEGMTa....TGVRYDS
  16 GRDA.VEQTLAGLFTVMSIDA..VETF.....HIGSSNGLVYTERVDVLRALP.....TGKSYNL
  17 GKAD.VARFFTWVRQVNDVSK..FQPV.....KFVEQGNSVAVLVNMAGKGKL.....TGKPYDG
  18 NKEG.LGALLGGVTSVYENGA..LEIT.....PTSAIAQGDKVAVEATSYAKLk....NGKVYQN
  19 DKAT.LGSLLRKVKPLYLDGA..LTIT.....PSSMISEGRQVSAEATSHARLc....DGRVYAN
  20 GPGR.VRRWLQNFPQNFRPLD..FSIS.....DIIAHNDSVLVLGRFRHTVLS.....TGNAVGS
  21 GREG.AAEYFRQLGEILDITS..ISPN.....RFLSDGDTVVVLGHTDGVMRK.....TGEPVRT
  22 LKAI.TEDLLAPLFGALEDGI..HSEV.....ESVIADGEQAVVLSRGAARTR.....SGVEYNN
  23 GRDA.VEQTLAGLFTVXSIDA..VETF.....HIGSSNGLVYTERVDVLRALP.....TGKSYNL
  24 GKAA.LAAHLEKLGPLLIFGP..MELG.....SVHAAGDTVVFEFSCSGAGVN.....TGAPYNQ
  25 GRIA.LEKYLQKVASLIEFGA..MSEP.....LVHHTLNENTVIIEFTCQGRGtk...TGNPYDQ
  26 GKAD.VKRFFAWNLAANAVSS..FRPL.....QFVEQGNKVASLVAMAGSGKA.....TGRPYDT
  27 GLSA.LADHLTRLGPMLELRE..FTLH.....AVHPAGDTVIFEFSCEGKGIA.....TGLPYDQ
  28 GRDD.LMAAFRGYVDGIALQS..ADKL.....IVHRTDDGHVVVIEYEVHGTIla...TGVKYNN
  29 GKAA.ITAYAQGVSSVMRDFV..FSDL.....RVFPAREPHVLFAEVHGEATLpr...TGRPYVQ
  30 GRDA.IENYLCDYPDLADVQT..INDQ.....TVHNTTDPDVVVVEFEVAGVVvr...TGRPYQM
  31 GRET.IRDYFAAAPAPRKVFE..MDGVea...LVRETDDPEVVVAEIEHHGRStv...TGKPYRF
  32 GRDRiVDDFLGGMGSRLQPGAplHIEL.....TDVLAEGPRVVATWISRGTAA.....GGAPYDN
  33 GLAG.ARQFWSDYLGAF--GQ..IRSH.....FERAIAADNAAVLEWVSEGKLh....SGEPIRY
  34 GRNE.FAAFLQRMNDSYREQ-..LRDV.....VVIANDDGTRVGAEYVVHGVYh10eaTGQTYVL
  35 LHNY.FDNLLTGATSSHFVIH..QILPhktpePLQDTSFTVTWTMSFATPKLN.....SGNLIHV
  36 GKNA.LKELYVKVMGLVDVVG..LNRV.....ETTAGKDHAVTILSFQFADPSlp...-----PA
  37 GREA.VREWIVAVMAPFPHMR..FPSD.....WTAYDEDNDAVVLMI------.....-------


       110       120       130   
        |         |         |   
   1 RVAVSFDVRGDKICSYREYFGSDGKSN
   2 RVAVSFDVRGDKICSYREYFGSDGKSN
   3 RVAVSFDVRGDKICSYREYFGSDGKSN
   4 RVAVSFDVRGDKICGYREYFGSDGKS-
   5 RVAVSFDVRGDKICGYREYFGSDGKS-
   6 RVAVSFDVRGEQISGYREYFGSDGK--
   7 DYVAVITVGPDGIVTYRDYWNP-----
   8 DYVAVITVGPDGIVTYRDYWNP-----
   9 RVALALDVRGRQICAYREYFG------
  10 DYVVVITVGDEGIESFRDYWNP-----
  11 QVAISFDIRGDQVCAYREYL-------
  12 DYVAVITVGPDGIVTYRDYWNP-----
  13 QVAVSFDIRGDKICSYREYL-------
  14 PFVCIFETKDGLIVSLREYSDTQ----
  15 PFVCIFETKDGLIVSLREYSDTQ----
  16 SILGVFQLTEGKITGWRDYFD------
  17 YISHFFVVENGKITDFLEVAGA-----
  18 AYHFLFEFRDGKILSVKEYMDTQ----
  19 AYHFRFDLDGDRICSVREYSDTQ----
  20 DMIIHFKVSGSKITRYQMFEDS-----
  21 QWVHVFTLRDDQIASYQEFVDT-----
  22 SYAQVFTVRGGKIVSVREYMDT-----
  23 SILGVFQLTEGKITGWRDYFD------
  24 KYISVVTVREGRIAHYRDYWNP-----
  25 SYISVITLEQGKIKRYQDYWNP-----
  26 VLAHFATVEGGKITEFREVAGS-----
  27 DYISVVTLREGRIARYRDYWNP-----
  28 RFCSIIKIENRKIAHWRDYMDS-----
  29 DYVMRLETDGERIIHYREYWNP-----
  30 RYIAVVTARDSEITRYRDYWSPQAA--
  31 RALGVIRVRGGEIVSYQDYMDP-----
  32 RCLGIFEVRDGRIVSVREYADTD----
  33 RGVSILEIEGDRVRRFRSYYDS-----
  34 VGGAFFDVRGDKITRVTNYYN------
  35 DGITLLKIRDDKIYFHQDYYD------
  36 ELCELFRFRDGKCC-------------
  37 ---------------------------