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:

- T0569
- gi|116491932|ref|YP_803667.1|_1287:1365 adhesion exoprotein [Pediococcus pentosaceus ATCC 25745]
- gi|116102082|gb|ABJ67225.1| Adhesion exoprotein [Pediococcus pentosaceus ATCC 25745]
- gi|116491932|ref|YP_803667.1|_1679:1757 adhesion exoprotein [Pediococcus pentosaceus ATCC 25745]
- gi|116102082|gb|ABJ67225.1| Adhesion exoprotein [Pediococcus pentosaceus ATCC 25745]
- gi|116491932|ref|YP_803667.1|_1483:1561 adhesion exoprotein [Pediococcus pentosaceus ATCC 25745]
- gi|116102082|gb|ABJ67225.1| Adhesion exoprotein [Pediococcus pentosaceus ATCC 25745]
- gi|116491932|ref|YP_803667.1|_1091:1169 adhesion exoprotein [Pediococcus pentosaceus ATCC 25745]
- gi|116102082|gb|ABJ67225.1| Adhesion exoprotein [Pediococcus pentosaceus ATCC 25745]
- gi|116491932|ref|YP_803667.1|_896:974 adhesion exoprotein [Pediococcus pentosaceus ATCC 25745]
- gi|116102082|gb|ABJ67225.1| Adhesion exoprotein [Pediococcus pentosaceus ATCC 25745]
- gi|116491932|ref|YP_803667.1|_700:779 adhesion exoprotein [Pediococcus pentosaceus ATCC 25745]
- gi|116102082|gb|ABJ67225.1| Adhesion exoprotein [Pediococcus pentosaceus ATCC 25745]
- gi|256852185|ref|ZP_05557571.1|_1066:1141 adhesion exoprotein [Lactobacillus jensenii 27-2-CHN]
- gi|260661782|ref|ZP_05862693.1| adhesion exoprotein [Lactobacillus jensenii 115-3-CHN]
- gi|256615231|gb|EEU20422.1| adhesion exoprotein [Lactobacillus jensenii 27-2-CHN]
- gi|260547529|gb|EEX23508.1| adhesion exoprotein [Lactobacillus jensenii 115-3-CHN]
- gi|282933081|ref|ZP_06338470.1|_1040:1115 putative adhesion exoprotein [Lactobacillus jensenii 208-1]
- gi|281302777|gb|EFA94990.1| putative adhesion exoprotein [Lactobacillus jensenii 208-1]
- gi|227525462|ref|ZP_03955511.1|_1066:1141 possible adhesion exoprotein [Lactobacillus jensenii JV-V16]
- gi|227168816|gb|EEI51134.1| possible adhesion exoprotein [Lactobacillus jensenii JV-V16]
- gi|238855733|ref|ZP_04646028.1|_1409:1484 putative adhesion exoprotein [Lactobacillus jensenii 269-3]
- gi|239633102|ref|ZP_04676133.1| predicted protein [Lactobacillus jensenii 1153]
- gi|282934024|ref|ZP_06339309.1| putative adhesion exoprotein [Lactobacillus jensenii 208-1]
- gi|238831634|gb|EEQ23976.1| putative adhesion exoprotein [Lactobacillus jensenii 269-3]
- gi|239529081|gb|EEQ68082.1| predicted protein [Lactobacillus jensenii 1153]
- gi|281301894|gb|EFA94153.1| putative adhesion exoprotein [Lactobacillus jensenii 208-1]
- gi|238855733|ref|ZP_04646028.1|_1842:1916 putative adhesion exoprotein [Lactobacillus jensenii 269-3]
- gi|239633102|ref|ZP_04676133.1| predicted protein [Lactobacillus jensenii 1153]
- gi|282934024|ref|ZP_06339309.1| putative adhesion exoprotein [Lactobacillus jensenii 208-1]
- gi|238831634|gb|EEQ23976.1| putative adhesion exoprotein [Lactobacillus jensenii 269-3]
- gi|239529081|gb|EEQ68082.1| predicted protein [Lactobacillus jensenii 1153]
- gi|281301894|gb|EFA94153.1| putative adhesion exoprotein [Lactobacillus jensenii 208-1]
- gi|256852185|ref|ZP_05557571.1|_1258:1333 adhesion exoprotein [Lactobacillus jensenii 27-2-CHN]
- gi|260661782|ref|ZP_05862693.1| adhesion exoprotein [Lactobacillus jensenii 115-3-CHN]
- gi|256615231|gb|EEU20422.1| adhesion exoprotein [Lactobacillus jensenii 27-2-CHN]
- gi|260547529|gb|EEX23508.1| adhesion exoprotein [Lactobacillus jensenii 115-3-CHN]
- gi|282933081|ref|ZP_06338470.1|_1232:1307 putative adhesion exoprotein [Lactobacillus jensenii 208-1]
- gi|281302777|gb|EFA94990.1| putative adhesion exoprotein [Lactobacillus jensenii 208-1]
- gi|227525462|ref|ZP_03955511.1|_1265:1340 possible adhesion exoprotein [Lactobacillus jensenii JV-V16]
- gi|227168816|gb|EEI51134.1| possible adhesion exoprotein [Lactobacillus jensenii JV-V16]
- gi|256852185|ref|ZP_05557571.1|_668:743 adhesion exoprotein [Lactobacillus jensenii 27-2-CHN]
- gi|260661782|ref|ZP_05862693.1| adhesion exoprotein [Lactobacillus jensenii 115-3-CHN]
- gi|256615231|gb|EEU20422.1| adhesion exoprotein [Lactobacillus jensenii 27-2-CHN]
- gi|260547529|gb|EEX23508.1| adhesion exoprotein [Lactobacillus jensenii 115-3-CHN]
- gi|282933081|ref|ZP_06338470.1|_642:717 putative adhesion exoprotein [Lactobacillus jensenii 208-1]
- gi|281302777|gb|EFA94990.1| putative adhesion exoprotein [Lactobacillus jensenii 208-1]
- gi|227525462|ref|ZP_03955511.1|_668:743 possible adhesion exoprotein [Lactobacillus jensenii JV-V16]
- gi|227168816|gb|EEI51134.1| possible adhesion exoprotein [Lactobacillus jensenii JV-V16]
- gi|238855733|ref|ZP_04646028.1|_1009:1086 putative adhesion exoprotein [Lactobacillus jensenii 269-3]
- gi|239633102|ref|ZP_04676133.1| predicted protein [Lactobacillus jensenii 1153]
- gi|282934024|ref|ZP_06339309.1| putative adhesion exoprotein [Lactobacillus jensenii 208-1]
- gi|238831634|gb|EEQ23976.1| putative adhesion exoprotein [Lactobacillus jensenii 269-3]
- gi|239529081|gb|EEQ68082.1| predicted protein [Lactobacillus jensenii 1153]
- gi|281301894|gb|EFA94153.1| putative adhesion exoprotein [Lactobacillus jensenii 208-1]
- gi|238855733|ref|ZP_04646028.1|_434:503 putative adhesion exoprotein [Lactobacillus jensenii 269-3]
- gi|239633102|ref|ZP_04676133.1| predicted protein [Lactobacillus jensenii 1153]
- gi|282934024|ref|ZP_06339309.1| putative adhesion exoprotein [Lactobacillus jensenii 208-1]
- gi|238831634|gb|EEQ23976.1| putative adhesion exoprotein [Lactobacillus jensenii 269-3]
- gi|239529081|gb|EEQ68082.1| predicted protein [Lactobacillus jensenii 1153]
- gi|281301894|gb|EFA94153.1| putative adhesion exoprotein [Lactobacillus jensenii 208-1]

                 10        20            30           40        50     
                 |         |             |            |         |     
   1 ...MDEDATITYVDDDKGGAQVG..DIV..TVTGKTDDSTT...YTVTIPDGYEYVGTDGG.VVS
   2 ytaMDEDATITYVDDDKGGAQVG..DIV..TVTGKTDDSTT...YTVTIPDGYEYVGTDGG.VVS
   3 ytaSDEDATVTYVDDDKGGAQVG..DIV..TVTGKTDDSTT...YTVTIPDGYEYVGTDGG.VVS
   4 ytaDDEDATITYVDDDKGGAQVG..DIV..KVTGKTDDSTT...YTVTIPDGYEYVGTDGG.VVS
   5 ytaSNEDATVTYVDDDKGGAQVG..DVV..TVTGKTDDSTT...YTVTIPGGYEYVGTDGG.VVS
   6 ytaNPAVATITYVDDDENGKTVK..TED..T-KGKTDGLGV...YTVKIPDGYEYVGAEGAtFIS
   7 yfiEQATATVTVVDDDEDGAKVG..DVV..TVNGDIDTSKT...TTVTIPDGYEYVGADGNgVVS
   8 ysaNPTNTNVVFVDDNDNGKTVKtvTVD..GTTGGTTPLSS...DDQKIPAGYELV--PGN.TIP
   9 ysaNPTNTNVVFVDDNDNGKTVKtvTVD..GTTGGTTPLSS...DDQKIPAGYELV--PGN.TIP
  10 ysaNPTNTNVVFVDDNDNGKTVKtvTVD..GTTGGTTPLSS...DDQKIPAGYELV--PGN.TIP
  11 ytaNPTNTNVVFVDDNENGKTVK..SVPvnGVTGGTTPLSN...DNQKIPDGYELV--DGN.KVP
  12 ytaNPTNTNVVFVDDNENGKTVK..SVSvnGVTGGTTPLSN...DDQKIPDGYELV--DGN.KVP
  13 ytgNPTNTKVIFVDDNDNGKTIK..TVPvnGVTGGTTPLSS...DDQKIPDGYELV--DGN.KVP
  14 ytgNPTNTKVIFVDDNDNGKTIK..TVPvnGVTGGTTPLSS...DDQKIPDGYELV--DGN.KVP
  15 ytgNPTNTKVIFVDDNDNGKTIK..TVPvnGVTGGTTPLSS...DDQKIPDGYELV--DGN.KVP
  16 ytaNNKTTNIVFKDQDNNNKVVN..TVP..-VDGYTSETVPvdgTKTTIPDGYELV--PGN.QVP
  17 ytaNNKTTNIVFKDQDNNNKVVN..TVP..-VDGYTSETVPvdgTKTTIPDGYELV--PGN.QVP
  18 ytaNNKTTNIVFKDQDNNNKVVN..TVP..-VDGYTSETVPvdgTKTTIPDGYELV--PGN.QVP
  19 ytaNKKTTNIVFKDQDNNNEVVK..TVP..-VNGHTSETVTvdgTKTTIPNGYELVDKDGN.VIP
  20 fiaQDQNITIKYVDDDNNGSQVG..DNQ..TVKGKTDETVK...PEYTIPDGYDYV--SGK.V--


          60           70            
          |            |            
   1 SDGKTVTITFAA.DDS..DNVVIHLKHG...
   2 SDGKTVTITFAA.DDS..DNVVIHLKHGhkd
   3 SDGKTVTITFTA.DDS..DNVVIHLKHGhke
   4 SDGKTVTITFAA.DDS..DNVVIHLKHGhke
   5 SDGKTVTITFTA.DDS..DNVVIHLKHGhkd
   6 CDGKTLKLRFTA.DDS..DNATIHLKHKhkd
   7 SDGKTVTITLTD.DDS..DNVVIHLKHHltp
   8 TE-----IKFNN.DGSqtPNTTIHLKHKtit
   9 TE-----IKFNN.DGSqtPNTTIHLKHKtit
  10 TE-----IKFNN.DGSqtPNTTIHLKHKtit
  11 TE-----IKFNN.DGSqtPDTTIHLKHKttt
  12 TE-----IAFNNsSQT..PDTTIHLKHKivt
  13 TE-----IKFNN.DGSqtPDTTIHLKHKtvd
  14 TE-----IKFNN.DGSqtPDTTIHLKHKtvd
  15 TE-----IKFNN.DGSqtPDTTIHLKHKtvd
  16 T-----TITFAG.GDSttPDIVVYLKHKhti
  17 T-----TITFAG.GDSttPDIVVYLKHKhti
  18 T-----TITFAG.GDSttPDIVVYLKHKhti
  19 T-----TITFTG.GDSttPDTVVYVKHKhdi
  20 -DSHT----MIA.GDN..TVITVHLKHHhdl