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:

- T0482 PaT3, Pseudomonas aeruginosa, 120 residues
- gi|152985375|ref|YP_001349654.1|_1:120 hypothetical protein PSPA7_4301 [Pseudomonas aeruginosa PA7]
- gi|150960533|gb|ABR82558.1| hypothetical protein PSPA7_4301 [Pseudomonas aeruginosa PA7]
- gi|15596273|ref|NP_249767.1|_1:120 hypothetical protein PA1076 [Pseudomonas aeruginosa PAO1]
- gi|84322068|ref|ZP_00970413.1| hypothetical protein PaerC_01000048 [Pseudomonas aeruginosa C3719]
- gi|84328538|ref|ZP_00976542.1| hypothetical protein Paer2_01000047 [Pseudomonas aeruginosa 2192]
- gi|107100521|ref|ZP_01364439.1| hypothetical protein PaerPA_01001546 [Pseudomonas aeruginosa PACS2]
- gi|116049005|ref|YP_792193.1| hypothetical protein PA14_50500 [Pseudomonas aeruginosa UCBPP-PA14]
- gi|9946992|gb|AAG04465.1|AE004539_7 hypothetical protein PA1076 [Pseudomonas aeruginosa PAO1]
- gi|115584226|gb|ABJ10241.1| hypothetical protein PA14_50500 [Pseudomonas aeruginosa UCBPP-PA14]
- gi|126166143|gb|EAZ51654.1| hypothetical protein PACG_00047 [Pseudomonas aeruginosa C3719]
- gi|126192812|gb|EAZ56875.1| hypothetical protein PA2G_00047 [Pseudomonas aeruginosa 2192]
- gi|49074138|gb|AAT49383.1|_1:120 PA1076 [synthetic construct]
- gi|66044353|ref|YP_234194.1|_1:118 hypothetical protein Psyr_1102 [Pseudomonas syringae pv. syringae B728a]
- gi|71733966|ref|YP_273437.1| hypothetical protein PSPPH_1170 [Pseudomonas syringae pv. phaseolicola 1448A]
- gi|63255060|gb|AAY36156.1| conserved hypothetical protein [Pseudomonas syringae pv. syringae B728a]
- gi|71554519|gb|AAZ33730.1| conserved hypothetical protein [Pseudomonas syringae pv. phaseolicola 1448A]
- gi|146306421|ref|YP_001186886.1|_1:121 hypothetical protein Pmen_1389 [Pseudomonas mendocina ymp]
- gi|145574622|gb|ABP84154.1| hypothetical protein Pmen_1389 [Pseudomonas mendocina ymp]
- gi|28868491|ref|NP_791110.1|_1:118 conserved hypothetical protein [Pseudomonas syringae pv. tomato str. DC3000]
- gi|28851729|gb|AAO54805.1| conserved hypothetical protein [Pseudomonas syringae pv. tomato str. DC3000]
- gi|167032012|ref|YP_001667243.1|_1:122 conserved hypothetical protein [Pseudomonas putida GB-1]
- gi|166858500|gb|ABY96907.1| conserved hypothetical protein [Pseudomonas putida GB-1]
- gi|49077714|gb|AAT49710.1|_1:120 PA2753 [synthetic construct]
- gi|15597949|ref|NP_251443.1|_1:120 hypothetical protein PA2753 [Pseudomonas aeruginosa PAO1]
- gi|84320491|ref|ZP_00968866.1| hypothetical protein PaerC_01001740 [Pseudomonas aeruginosa C3719]
- gi|84327110|ref|ZP_00975134.1| hypothetical protein Paer2_01001933 [Pseudomonas aeruginosa 2192]
- gi|107102290|ref|ZP_01366208.1| hypothetical protein PaerPA_01003348 [Pseudomonas aeruginosa PACS2]
- gi|116050747|ref|YP_790432.1| hypothetical protein PA14_28500 [Pseudomonas aeruginosa UCBPP-PA14]
- gi|9948832|gb|AAG06141.1|AE004703_7 hypothetical protein PA2753 [Pseudomonas aeruginosa PAO1]
- gi|115585968|gb|ABJ11983.1| conserved hypothetical protein [Pseudomonas aeruginosa UCBPP-PA14]
- gi|126167666|gb|EAZ53177.1| hypothetical protein PACG_01673 [Pseudomonas aeruginosa C3719]
- gi|126194587|gb|EAZ58650.1| hypothetical protein PA2G_01898 [Pseudomonas aeruginosa 2192]
- gi|148546278|ref|YP_001266380.1|_1:122 hypothetical protein Pput_1035 [Pseudomonas putida F1]
- gi|148510336|gb|ABQ77196.1| hypothetical protein Pput_1035 [Pseudomonas putida F1]
- gi|67157692|ref|ZP_00418887.1|_1:119 conserved hypothetical protein [Azotobacter vinelandii AvOP]
- gi|67085274|gb|EAM04749.1| conserved hypothetical protein [Azotobacter vinelandii AvOP]
- gi|170723387|ref|YP_001751075.1|_1:122 conserved hypothetical protein [Pseudomonas putida W619]
- gi|169761390|gb|ACA74706.1| conserved hypothetical protein [Pseudomonas putida W619]
- gi|146308273|ref|YP_001188738.1|_1:121 hypothetical protein Pmen_3253 [Pseudomonas mendocina ymp]
- gi|145576474|gb|ABP86006.1| hypothetical protein Pmen_3253 [Pseudomonas mendocina ymp]
- gi|104783400|ref|YP_609898.1|_1:122 hypothetical protein PSEEN4431 [Pseudomonas entomophila L48]
- gi|95112387|emb|CAK17114.1| conserved hypothetical protein [Pseudomonas entomophila L48]
- gi|152983732|ref|YP_001347852.1|_1:121 hypothetical protein PSPA7_2486 [Pseudomonas aeruginosa PA7]
- gi|150958890|gb|ABR80915.1| hypothetical protein PSPA7_2486 [Pseudomonas aeruginosa PA7]
- gi|26987734|ref|NP_743159.1|_21:142 hypothetical protein PP_0998 [Pseudomonas putida KT2440]
- gi|24982424|gb|AAN66623.1|AE016290_1 conserved hypothetical protein [Pseudomonas putida KT2440]
- gi|77460610|ref|YP_350117.1|_1:120 hypothetical protein PflO1_4389 [Pseudomonas fluorescens PfO-1]
- gi|77384613|gb|ABA76126.1| conserved hypothetical protein [Pseudomonas fluorescens PfO-1]
- gi|146306139|ref|YP_001186604.1|_1:121 hypothetical protein Pmen_1105 [Pseudomonas mendocina ymp]
- gi|145574340|gb|ABP83872.1| hypothetical protein Pmen_1105 [Pseudomonas mendocina ymp]
- gi|70731980|ref|YP_261722.1|_3:118 hypothetical protein PFL_4638 [Pseudomonas fluorescens Pf-5]
- gi|68346279|gb|AAY93885.1| conserved hypothetical protein [Pseudomonas fluorescens Pf-5]
- gi|146284288|ref|YP_001174441.1|_1:120 hypothetical protein PST_3976 [Pseudomonas stutzeri A1501]
- gi|145572493|gb|ABP81599.1| conserved hypothetical protein [Pseudomonas stutzeri A1501]

                   10                20        30        40        50  
                   |                 |         |         |         |  
   1 ...M..FEPGHLHLV.SLP...GLD.Q.QD..INIHIRYEVRQNAESGAYVHFDMDGEIDGKPFS
   2 ...M..FEPGHLHLV.SLP...GLD.Q.QD..INIHIRYEVRHNAESGAYVHFDMDGEIDGKPFS
   3 ...M..FEPGHLHLV.SLP...GLD.Q.QD..INIHIRYEVRQNAESGAYVHFDMDGEIDGKPFS
   4 ...M..FEPGHLHLV.SLP...GLD.Q.QD..INIHIRYEVRQNAESGAYVHFDMDGEIDGKPFS
   5 ...M..YEPGHLHLT.HV-...ALQ.P.SDisYDIHLRYNVEEDPKQGTSMHFTMQGEINGKPFE
   6 ...M..FEPGHLHRS.NPP...GLG.G.QPa.YSIDFYYEVRKDSPEGPMLHGRLVGEIDGKAFE
   7 ...M..YEPGHLHIT.HV-...ALQ.P.SEvsYDIHLRYEVNEDPKEGTSMHFTMQGQINDKPFE
   8 ...MaqYHPGHVH-I.ERT...ALN.N.ADhsYDLNIEYEAVSDPREGRGIQFHMHGSIEGKPVE
   9 ...M..FIPGHLHLA.SAS...EVD.R.QA..FDIHLRYRVLEAEARPVAVHFDMEGRIDGQPFS
  10 ...M..FIPGHLHLA.SAS...EVD.R.QA..FDIHLRYRVLEAEARPVAVHFDMEGRIDGQPFS
  11 ...MaqYQPGHVH-I.ERS...ALN.N.ADhsYDLNIEYEAVSDPKEGRGIQFHMHGSIEGKTVE
  12 ...M..FTPGHAHREqKVD...KLN.R.QA..FICDVYYEVREDAREGAMLHMRMEGEIDGRPFA
  13 ...MaqYQPGHVH-I.ERT...ALN.A.NDhsYDLNIEYEATQDPREGRGIQFRLHGSIEGKPVD
  14 ...M..FEPGHLNRK.KQP...GIP.GvPD..FDIDVYYDVRHDPKEGVLLHFRMTGQVNGRSFT
  15 ...MaqYQPGHVH-I.ERT...ALN.T.NDhsYDLNIEYEAATDPKEGRGIQFRMHGHIEGKTVD
  16 ...M..FVPGHLHLA.SAS...EVD.R.QA..FDIHLRYRILEADARPVAVHFDMEGRIDGQPFR
  17 eiaMaqYHSGHVH-I.ERT...ALN.N.ADhsYDLNIEYEAVADPKEGRGIQFHMHGSIEGKPVE
  18 ...MaqFEPGHLH-I.ERH...ALT.D.DDvnYNVHLDYEVFTDPQKGKGIQFTLHGSMQGKEVN
  19 ...M..FTPGHLHRD.NLDrpeGLRlA.PP..FSVDFYYEIRQDPVQGPMLHMRLVGEVSGRHFD
  20 ma.M..FEPGHLH-I.ERH...ALN.K.DDfsYNLCIDYEVAHDPKEGKGMLFTLHGTIEDKSLK
  21 ...M..FGPGHVEIS.RLP...TEA.R.PG..YHLTLDYHVEGAEPRPEWACFHLRVEAPQVHID


            60         70         80         90       100       110    
            |          |          |          |         |         |    
   1 DSFELPRDTAFN.FASDATRVAQKHGLH.P.KFGAITRVHKEYDAMFEDIRAKLHAHPGEPVDLE
   2 DSFELPRDTAFN.FASDATRVAQKHGLH.P.KFGAITRVHKEYDAMFEDIRDKLHAHPGEPVDLE
   3 DSFELPRDTAFN.FASDATRVAQKHGLH.P.KFGAITRVHKEYDAMFEDIRAKLHAHPGEPVDLE
   4 DSFELPRDTAFN.FASDATRVAQKHGLH.P.KFGAITRVHKEYDAMFEDIRAKLHAHPGEPVDLE
   5 EQFQLPRDLAFN.FAHDASRIAIRHGLP.N.SAALPIAQHKDYDRMFADIRDKLHAKSGDPVKPE
   6 EVFEMHRDTAFN.FASVISRLVAKHGLH.P.NNSPIMRAHKEYDAIFEDIRAKLHAKPGEAVNLD
   7 EQFQLTRDLAFN.FAHDASRIAIRHGLP.N.SASLPIAQHKDYDRIFADIRDKLHAKPGDPVKPE
   8 EKFFLPKDQVLPsFLMLLTRKAQSYLAP.PkKFETLSSPHKLYDYMFADIREKLDVKSGDPIKPE
   9 ESFELPRDAAVH.FASRASRLARRHGLR.L.RQGPIVRQRREYDAMFDDLRRRLKLKSGEAIDLD
  10 ESFELPRDAAVH.FASRASRLARRHGLR.L.RQGPIVRQRREYDAMFDDLRRRLKLKSGEAIDLD
  11 EKFFLAKDQALPsFLMLLTRKAQSYLAP.PkKFETLSSPHKLYDHMFADIREKLEVKSGDPIKPE
  12 EECELHRDMAFD.FLNALTRIAVRNGLH.P.RFGPVLREHGEYDAMFRDIRDKLGLRPGDPVDLG
  13 EKFYLPKDQVLPsFLMVLSRKAQSHLPPhK.KFETLGSPHKIYDQMFEDIRAKLDVKSGDSIKPE
  14 DEFEMHRDTAFN.FASRIAKAAVKQGLP.V.NASPIMRSHSEYDAMFADIRRKLEIRTGEPVNFD
  15 EKFFLAKDQVLPsFLMQLSRKAQSYLPP.PkKFENLGSPHKLYDYMFEDIRTKLDVKSGDPIKPE
  16 DSFELPRDAAVH.FASRASRVARRHGLR.L.RQGPIVRQRREYDAMFDDLRRRLKLKAGEAIDLD
  17 EKFFLAKDQVLPsFLMLLTRKAQSYLAP.PkKFETLSSPHKLYDHMFADIREKLDVKSGDPIKPE
  18 EPFFLPKEEAYN.FARNVTQIAEKYGIP.K.SHSQIGSVHKHYDLMFEDIRMKLNMKSGDPVNPE
  19 EEFELHRDVAFN.FASVASRVAARHGLP.P.NASPVMRGHDEYDKVFADIRSKLHARPGEPVNLD
  20 EQFFLAKDLAFD.FARHATRLAQQHGLP.K.SAS-IASMHKYYDEMFEDVRKQLDVKPGDPVKPE
  21 EQFRMHRDVAYN.FLQRIRRCLRDHGVQ.V.RQDILFGFHALYDPLYADLRQQLHLQPGEAVDLD


           120   
            |   
   1 .RIIR.HE...
   2 .RIIR.HE...
   3 .RIIR.HE...
   4 .RIIRhEG...
   5 .HLE-.--...
   6 .HVER.DGl..
   7 .HLE-.--...
   8 .HLE-.--...
   9 .RYLR.GEaga
  10 .RYLR.GEaga
  11 .HLE-.--...
  12 .HLPN.A-...
  13 .HLE-.--...
  14 .NLEK.DGf..
  15 .HLE-.--...
  16 rHLLG.AAgaa
  17 .HLE-.--...
  18 .HFE-.--...
  19 .HVL-.--...
  20 .HLA-.--...
  21 .RFLR.EG...