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:

- T0581
- gi|15598807|ref|NP_252301.1|_1:136 hypothetical protein PA3611 [Pseudomonas aeruginosa PAO1]
- gi|107103125|ref|ZP_01367043.1| hypothetical protein PaerPA_01004194 [Pseudomonas aeruginosa PACS2]
- gi|116051608|ref|YP_789553.1| hypothetical protein PA14_17600 [Pseudomonas aeruginosa UCBPP-PA14]
- gi|152986620|ref|YP_001346914.1| hypothetical protein PSPA7_1530 [Pseudomonas aeruginosa PA7]
- gi|218890164|ref|YP_002439028.1| putative secreted protein [Pseudomonas aeruginosa LESB58]
- gi|254242309|ref|ZP_04935631.1| hypothetical protein PA2G_03050 [Pseudomonas aeruginosa 2192]
- gi|9949768|gb|AAG06999.1|AE004781_7 hypothetical protein PA3611 [Pseudomonas aeruginosa PAO1]
- gi|115586829|gb|ABJ12844.1| putative secreted protein [Pseudomonas aeruginosa UCBPP-PA14]
- gi|126195687|gb|EAZ59750.1| hypothetical protein PA2G_03050 [Pseudomonas aeruginosa 2192]
- gi|150961778|gb|ABR83803.1| hypothetical protein PSPA7_1530 [Pseudomonas aeruginosa PA7]
- gi|218770387|emb|CAW26152.1| putative secreted protein [Pseudomonas aeruginosa LESB58]
- gi|296387885|ref|ZP_06877360.1|_1:136 putative secreted protein [Pseudomonas aeruginosa PAb1]
- gi|49077260|gb|AAT49656.1|_1:136 PA3611 [synthetic construct]
- gi|71737386|ref|YP_275940.1|_1:138 hypothetical protein PSPPH_3802 [Pseudomonas syringae pv. phaseolicola 1448A]
- gi|257487041|ref|ZP_05641082.1| hypothetical protein PsyrptA_27456 [Pseudomonas syringae pv. tabaci ATCC 11528]
- gi|289625996|ref|ZP_06458950.1| hypothetical protein PsyrpaN_12851 [Pseudomonas syringae pv. aesculi str. NCPPB3681]
- gi|289651488|ref|ZP_06482831.1| hypothetical protein Psyrpa2_27667 [Pseudomonas syringae pv. aesculi str. 2250]
- gi|71557939|gb|AAZ37150.1| conserved hypothetical protein [Pseudomonas syringae pv. phaseolicola 1448A]
- gi|66044629|ref|YP_234470.1|_1:138 hypothetical protein Psyr_1381 [Pseudomonas syringae pv. syringae B728a]
- gi|63255336|gb|AAY36432.1| conserved hypothetical protein [Pseudomonas syringae pv. syringae B728a]
- gi|289674626|ref|ZP_06495516.1|_1:138 hypothetical protein PsyrpsF_15277 [Pseudomonas syringae pv. syringae FF5]
- gi|28871173|ref|NP_793792.1|_1:138 hypothetical protein PSPTO_4030 [Pseudomonas syringae pv. tomato str. DC3000]
- gi|213969157|ref|ZP_03397296.1| conserved hypothetical protein [Pseudomonas syringae pv. tomato T1]
- gi|28854423|gb|AAO57487.1| conserved hypothetical protein [Pseudomonas syringae pv. tomato str. DC3000]
- gi|213926155|gb|EEB59711.1| conserved hypothetical protein [Pseudomonas syringae pv. tomato T1]
- gi|167032247|ref|YP_001667478.1|_1:138 hypothetical protein PputGB1_1235 [Pseudomonas putida GB-1]
- gi|166858735|gb|ABY97142.1| conserved hypothetical protein [Pseudomonas putida GB-1]
- gi|26988365|ref|NP_743790.1|_1:138 hypothetical protein PP_1633 [Pseudomonas putida KT2440]
- gi|24983117|gb|AAN67254.1|AE016352_7 conserved hypothetical protein [Pseudomonas putida KT2440]
- gi|148549290|ref|YP_001269392.1|_1:138 hypothetical protein Pput_4084 [Pseudomonas putida F1]
- gi|148513348|gb|ABQ80208.1| hypothetical protein Pput_4084 [Pseudomonas putida F1]
- gi|7579037|gb|AAF64233.1|AF249735_1_1:138 putative secreted protein [Pseudomonas putida]
- gi|104783100|ref|YP_609598.1|_1:139 hypothetical protein PSEEN4124 [Pseudomonas entomophila L48]
- gi|95112087|emb|CAK16814.1| conserved hypothetical protein; putative signal peptide [Pseudomonas entomophila L48]
- gi|237800186|ref|ZP_04588647.1|_1:138 hypothetical protein Psyrpo1_15222 [Pseudomonas syringae pv. oryzae str. 1_6]
- gi|170723187|ref|YP_001750875.1|_1:138 hypothetical protein PputW619_4026 [Pseudomonas putida W619]
- gi|169761190|gb|ACA74506.1| conserved hypothetical protein [Pseudomonas putida W619]
- gi|254236527|ref|ZP_04929850.1|_1:134 hypothetical protein PACG_02524 [Pseudomonas aeruginosa C3719]
- gi|126168458|gb|EAZ53969.1| hypothetical protein PACG_02524 [Pseudomonas aeruginosa C3719]
- gi|70728617|ref|YP_258366.1|_1:140 hypothetical protein PFL_1235 [Pseudomonas fluorescens Pf-5]
- gi|68342916|gb|AAY90522.1| conserved hypothetical protein [Pseudomonas fluorescens Pf-5]
- gi|226945894|ref|YP_002800967.1|_1:132 hypothetical protein Avin_38510 [Azotobacter vinelandii DJ]
- gi|226720821|gb|ACO79992.1| conserved hypothetical protein [Azotobacter vinelandii DJ]
- gi|146306319|ref|YP_001186784.1|_1:133 hypothetical protein Pmen_1287 [Pseudomonas mendocina ymp]
- gi|145574520|gb|ABP84052.1| hypothetical protein Pmen_1287 [Pseudomonas mendocina ymp]
- gi|77457407|ref|YP_346912.1|_1:140 hypothetical protein Pfl01_1180 [Pseudomonas fluorescens Pf0-1]
- gi|77381410|gb|ABA72923.1| putative exported protein [Pseudomonas fluorescens Pf0-1]
- gi|146281887|ref|YP_001172040.1|_1:130 hypothetical protein PST_1513 [Pseudomonas stutzeri A1501]
- gi|145570092|gb|ABP79198.1| conserved hypothetical protein [Pseudomonas stutzeri A1501]
- gi|229588730|ref|YP_002870849.1|_1:140 hypothetical protein PFLU1192 [Pseudomonas fluorescens SBW25]
- gi|229360596|emb|CAY47453.1| putative exported protein [Pseudomonas fluorescens SBW25]

                 10             20        30        40        50       
                 |              |         |         |         |       
   1 MSRF.MA..LALCFV..LP..TA.AHAASLKDFELSKMLEKVAKESSVGTPRAINEDILDQGYTV
   2 MSRF.MA..LALCFV..LP..TA.AHAASLKDFELSKMLEKVAKESSVGTPRAINEDILDQGYTV
   3 MSRL.MA..LALCFV..LP..TA.AHAASLKDFELSKMLEKVAKESSVGTPRAINEDILDQGYTV
   4 MSRF.MA..LALCFV..LP..TA.AHAASLKDFELSKMLEKVAKESSVGTPRAINEDILDQGYTV
   5 MLRL.IVptLTLLLV..AP..LC.AQAASKQEFELSKMLEKVAKESSVGTPRAINEDILDQGYTV
   6 MLRL.IVptLTLLLV..TP..LC.AQAASKQEFELSKMLEKVAKESSVGTPRAINEDILDQGYTV
   7 MLRL.IVptLTLLLV..AP..LC.AQAASKQEFELSKMLEKVAKESSVGTPRAINEDILDQGYTV
   8 MLRL.IVptLTLLLV..AP..LC.AQAASKQDFELSKMLEKVAKESSVGTPRAINEDILDQGYTV
   9 MLRL.IApaLSLLLA..LP..LA.AQAASKQDYDLNKMLEKVAKESSVGTPRAINEDILDQGYTV
  10 MLRL.IApaLSLLLA..LP..LA.AQAASKQDYDLNTLLQKVAKESSVGTPRAINEDILDQGYTV
  11 MLRL.IApaLSLLLA..LP..LA.AQAASKQDYDLNTLLQKVAKESSVGTPRAINEDILDQGYTV
  12 MLRR.IV..PALCLLlaLP..LA.AQAASKQEYDLNNMLQKVAKESSVGTPRAINEDILDQGYTV
  13 MLRV.IAptLSLLLA..LP..LA.AQAASKQEYELTQMLEKVAKESSVGTPRAINEDILDQGYTV
  14 MLRL.IAptLTLLLV..AP..LC.AQAASKQEFELSKMLEKVAKESSVGTPRAINEDILDQGYTV
  15 MLRL.IVptLSLLLT..LP..LA.AQAASKQEFELNKMLEKVAKESSVGTPRAINEDILDQGYTV
  16 MSRF.MA..LALCFV..LP..TA.AHAASLKDFELSKMLEKVAKESSVGTPRAINEDILDQGYTV
  17 MLRF.TIptVALLLA..LP..LG.AQAASLQEFELGKMLEKVAAESNVGTPREINENILDQGYTV
  18 MLRP.TA..LTLCLL..LP..AT.ALAASLKDYELTRMLEKVAKESSIGTPRAINEDILDQGYTV
  19 MLRY.TL..PALALG..LM..LAtAQAASLKEMELTRTLEQVARQSSEGTPRAINEDILDQGYTV
  20 MLRL.IV..PTAAIL..LAssFS.AQAASLSEQNLNRELRNVAAQSSVGTPRAINEDILDQGYTV
  21 MYRLtTL..LALSLA..LP..V-.AHAASLQEQQLSQLLDQVARESNVGTPRAINEDILDQGYTV
  22 MLRF.VApsVALALV..LP..VC.AQAASLLEAQMNRKLQSVAAESNKDLPREIDEKTLEVAYTV


        60        70        80        90       100       110       120 
        |         |         |         |         |         |         | 
   1 E.GNQLINHLSVRASHAERMRSNPDSVRSQLGDSVCSNTGYRQLLARGAILTYSFTEYKTNQPVA
   2 E.GNQLINHLSVRASHAERMRSNPDSVRSQLGDSVCSNTGYRQLLARGAILTYSFTEYKTNQPVA
   3 E.GNQLINHLSVRASHAERMRSNPDSVRSQLGDSVCSNTGYRQLLARGAILTYSFTEYKTNQPVA
   4 E.GNQLINHLSVRASHAERMRSNPDSVRSQLGDSVCSNTGYRQLLARGAILTYSFTEYKTNQPVA
   5 S.GNELINHLSVREGQAQQMRANPDVMRNQLGNSVCHNNGFRQLMTKGAVLKYQFTEYKTNRPVA
   6 S.GNQLINHLSVREGQAQQMRANPDVMRNQLGNSVCHNNGFRQLMTKGAVLKYQFTEYKTNRPVA
   7 S.GNQLINHLSVREGQAQQMRANPDVMRNQLGNSVCHNNGFRQLMTKGAVLKYQFTEYKTNRPVV
   8 S.GNQLINHLSVREGQAQQMRANPDVMRNQLGNSVCHNNGFRQLMTKGAVLKYQFTEYKTNRPVA
   9 E.GKALVNHLSVRQSHAERMQANPAQVRSQLGDSVCRNSGFRNLMSKGAVMVYRFTVYKTNQPIM
  10 E.GKALVNHLSVRQSHAARMQANPEQVRSQLGDSVCRNNGFRNLMSKGAVMVYRFTVYKTNQPVM
  11 E.GKALVNHLSVRQSHAARMQANPEQVRSQLGDSVCRNNGFRNLMSKGAVMVYRFTVYKTNQPVM
  12 E.GKALVNHLSVRQDHAARMQANPEQVRSQLGDSVCRNSGFRNLMSKGAVMVYRFTVYKTNQPIM
  13 EkGKALVNHLSVRESHAERMRENPQLVRSQLGDSVCRNNGYRQLMSKGAVLVYRFTVYKTNQPVM
  14 T.GNQLINHLSVREGQASQMRANPDVMRNQLGNSVCHNNGFRQLMTKGAVLKYQFTEYKTNRPVA
  15 E.GKALVNHLSVRAEHAARMQQNAEQVRSQLGDSVCRNSGYRNLMSKGAVMVYRFTVYKTNQPVM
  16 E.GNQLINHLSVRASHAERMRSNPDSVRSQLGDSVFSNTGYRQLLARGAILTYSFTEYKTNQPVA
  17 E.GKELINHLSVQSGHAEQMRANPKAVYLQLGASVCRNPNYRKLMAKGAIMRYEFTENRTNRPVA
  18 E.GNELINHLSVRTSHAQQMRAHPDAVRNQLLGSVCSNRGFRQLLAQGAVLRYQFSEYQSNRPVT
  19 E.GHTLINHLSVREAHAAQMRGNPDTVRSQLAASVCRNPGYRSLLAQGAQLRYQFSEYRSNRPVT
  20 E.GTTLVNHLSVQKSHADKMRADPKAVYFQLGASVCNNPSYRKLMAKGAIMRYDFTEVKTNKAIG
  21 E.NNQLVNHLSVQPRHAAQMRDNPADVRSQLAVSVCGNEGLRKLMSQGAVLRYDFSEYQSNKPIA
  22 E.GMQLIDHLSVLPDRAEQMRANPKAVYFQLGQSVCLNKGYRELMAKGAVMRYEITENKTNRPVA


            130                
             |                
   1 TERFDAGSCR..I...Q....GKK.
   2 TERFDAGSCR..I...Q....GKK.
   3 TERFDAGSCR..I...Q....GKK.
   4 TERFDAGSCR..I...Q....GKKg
   5 TQTFQASDCT..V...K....PKK.
   6 TQTFQASDCT..V...K....PKQ.
   7 TQTFQASDCT..V...K....PKQ.
   8 TQTFQASDCT..V...K....AKK.
   9 DQAFDSASCV..A...G....NKKk
  10 DQAFDNASCV..A...G....NKKk
  11 DQAFDNASCL..A...G....NKKk
  12 DQAFDNASCV..A...G....NKKk
  13 DQAFDAASCA..S...G....NKKk
  14 AQTFQASDCA..A...K....PKQ.
  15 DQAFDAASCT..A...G....NKKk
  16 TERFDAGSCR..I...Q....K--.
  17 SARFQESDCP..AqstP....KKK.
  18 TERYRAADCN..L...-....---.
  19 VEVFDKSDCG..L...-....---.
  20 SASYQESDCPkaA...Pa...KKK.
  21 SERYTAADCK..-...-....---.
  22 SVKFVEADCP..A...PaaakKKK.