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:

- T0464 XfR39, Xylella fastidiosa 9a5c, 89 residues
- gi|166712591|ref|ZP_02243798.1|_1:89 hypothetical protein Xoryp_14340 [Xanthomonas oryzae pv. oryzicola BLS256]
- gi|78048386|ref|YP_364561.1|_1:89 hypothetical protein XCV2830 [Xanthomonas campestris pv. vesicatoria str. 85-10]
- gi|78036816|emb|CAJ24509.1| conserved hypothetical protein [Xanthomonas campestris pv. vesicatoria str. 85-10]
- gi|21243409|ref|NP_642991.1|_1:89 hypothetical protein XAC2680 [Xanthomonas axonopodis pv. citri str. 306]
- gi|21108959|gb|AAM37527.1| conserved hypothetical protein [Xanthomonas axonopodis pv. citri str. 306]
- gi|58582834|ref|YP_201850.1|_1:89 hypothetical protein XOO3211 [Xanthomonas oryzae pv. oryzae KACC10331]
- gi|84624701|ref|YP_452073.1| hypothetical protein XOO_3044 [Xanthomonas oryzae pv. oryzae MAFF 311018]
- gi|188577673|ref|YP_001914602.1| conserved hypothetical protein [Xanthomonas oryzae pv. oryzae PXO99A]
- gi|58427428|gb|AAW76465.1| conserved hypothetical protein [Xanthomonas oryzae pv. oryzae KACC10331]
- gi|84368641|dbj|BAE69799.1| conserved hypothetical protein [Xanthomonas oryzae pv. oryzae MAFF 311018]
- gi|188522125|gb|ACD60070.1| conserved hypothetical protein [Xanthomonas oryzae pv. oryzae PXO99A]
- gi|21231937|ref|NP_637854.1|_1:89 hypothetical protein XCC2504 [Xanthomonas campestris pv. campestris str. ATCC 33913]
- gi|66767936|ref|YP_242698.1| hypothetical protein XC_1612 [Xanthomonas campestris pv. campestris str. 8004]
- gi|188991053|ref|YP_001903063.1| Conserved hypothetical protein [Xanthomonas campestris pv. campestris]
- gi|21113666|gb|AAM41778.1| conserved hypothetical protein [Xanthomonas campestris pv. campestris str. ATCC 33913]
- gi|66573268|gb|AAY48678.1| conserved hypothetical protein [Xanthomonas campestris pv. campestris str. 8004]
- gi|167732813|emb|CAP51007.1| Conserved hypothetical protein [Xanthomonas campestris pv. campestris]
- gi|15839262|ref|NP_299950.1|_1:89 hypothetical protein XF2673 [Xylella fastidiosa 9a5c]
- gi|9107909|gb|AAF85470.1|AE004073_5 hypothetical protein XF_2673 [Xylella fastidiosa 9a5c]
- gi|28199898|ref|NP_780212.1|_1:89 hypothetical protein PD2037 [Xylella fastidiosa Temecula1]
- gi|71275274|ref|ZP_00651561.1| Protein of unknown function DUF343 [Xylella fastidiosa Dixon]
- gi|71899957|ref|ZP_00682103.1| Protein of unknown function DUF343 [Xylella fastidiosa Ann-1]
- gi|71900140|ref|ZP_00682281.1| Protein of unknown function DUF343 [Xylella fastidiosa Ann-1]
- gi|170731276|ref|YP_001776709.1| conserved hypothetical protein [Xylella fastidiosa M12]
- gi|182682648|ref|YP_001830808.1| protein of unknown function DUF343 [Xylella fastidiosa M23]
- gi|28058019|gb|AAO29861.1| conserved hypothetical protein [Xylella fastidiosa Temecula1]
- gi|71164083|gb|EAO13798.1| Protein of unknown function DUF343 [Xylella fastidiosa Dixon]
- gi|71730089|gb|EAO32179.1| Protein of unknown function DUF343 [Xylella fastidiosa Ann-1]
- gi|71730244|gb|EAO32329.1| Protein of unknown function DUF343 [Xylella fastidiosa Ann-1]
- gi|167966069|gb|ACA13079.1| conserved hypothetical protein [Xylella fastidiosa M12]
- gi|182632758|gb|ACB93534.1| protein of unknown function DUF343 [Xylella fastidiosa M23]
- gi|190011525|emb|CAQ45143.1|_1:89 CONSERVED HYPOTHETICAL PROTEIN [Stenotrophomonas maltophilia K279a]
- gi|114319435|ref|YP_741118.1|_3:91 protein of unknown function DUF343 [Alkalilimnicola ehrlichei MLHE-1]
- gi|114225829|gb|ABI55628.1| protein of unknown function DUF343 [Alkalilimnicola ehrlichei MLHE-1]
- gi|121997789|ref|YP_001002576.1|_1:85 protein of unknown function DUF343 [Halorhodospira halophila SL1]
- gi|121589194|gb|ABM61774.1| protein of unknown function DUF343 [Halorhodospira halophila SL1]
- gi|88810847|ref|ZP_01126104.1|_3:86 hypothetical protein NB231_17243 [Nitrococcus mobilis Nb-231]
- gi|88792477|gb|EAR23587.1| hypothetical protein NB231_17243 [Nitrococcus mobilis Nb-231]
- gi|32477481|ref|NP_870475.1|_2:88 hypothetical protein RB12383 [Rhodopirellula baltica SH 1]
- gi|32448035|emb|CAD77552.1| hypothetical protein [Rhodopirellula baltica SH 1]
- gi|186455585|ref|ZP_02965899.1|_131:212 hypothetical protein CflavDRAFT_1015 [bacterium Ellin514]
- gi|184207663|gb|EDU04708.1| hypothetical protein CflavDRAFT_1015 [bacterium Ellin514]

                 10        20        30        40        50        60  
                 |         |         |         |         |         |  
   1 ...MDRKLLHLLCSPDTRQPLSLLESKGLEALNKAIASGTVQRADGSIQNQSLHEALITRDRKQV
   2 ...MDRKLLDLLCSPDTRQPLSLLDVKGLEALNAAIAGGTLRRADGTAQTQPLREALITRDRKQI
   3 ...MDRKLLDLLCSPDTRQPLSLLDGKGLEALNAAIAGGTLQRADGTAQTQPLREALITRDRKQI
   4 ...MDRKLLDLLCSPDTRQPLSLLDGKGLEALNAAIAGGALQRADGAAQTQPLREALITRDRKQI
   5 ...MDRKLLDLLCSPDTRQPLSLLDVKGLEVLNATIAGGTLQRADGTAQTQPLREALITRDRKQI
   6 ...MDRKLLDLLCSPDTRQPLSLLDGKGLEALNRAIAAGTLQRVDGAVQDQPLREALITRDRKQI
   7 ...MDRKLLHLLCSPDTRQPLSLLESKGLEALNKAIASGTVQRADGSIQNQSLHEALITRDRKQV
   8 ...MDRKLLHLLCSPDTRQPLSLLESKGLEALNKAIVSGTVQRADGSIQNQSLHEALITRDRKQV
   9 ...MDRKLLDLLVSPDTRQPLSLLDGKGLEALNKAISAGAVNKADGNPLAQPLREALVTRDRKQV
  10 ms.LDKKLLDILCCPVTKQPVRLLEADALKRLNQRIEQGEVRHMDDSPVETPLREALITENDQRI
  11 ...MDRKLLDILCCPITKRPLQPLSTQELEALNRHIADGQARYLDDTVVDTPLDEGLITDNGSRI
  12 ma.LDRKLLDILCCPISKIPIRPLKRDELQRINEAIANGHLRYLDNSTVEAELDEGLITDNAERV
  13 m..ITPDILPILRCPSNGGQLTLADESLIQRVNQAIRDGNARDQLDERVTDPIEGGLINSPADRL
  14 ssvVDPELLRILCCPETYQDIKVAEAAVIEKINQQIFTGALRNRRGQVIREVIEGGLVRADGRYL


            70        80         
            |         |         
   1 FRIEDSIPVLLPEEAIATIQIANFPDK
   2 FRVDDGIPVLLAEEAIATTQIADFPEK
   3 FRVDDGIPVLLAEEAIATAQIADFPEK
   4 FRVDDGIPVLLAEEAIATAQIADFPEK
   5 FRVDDGIPVLLAEEAIATTQIADFPEK
   6 FRVDDGIPVLLAEEAINPSQIADFPEK
   7 FRIEDSIPVLLPEEAIATIQIANFPDK
   8 FRIEDSIPVLLPEEAIATIQIANFPDK
   9 FRVDDGIPVLLAEEAIPTAQIADFPAA
  10 YPVEDGIPIMLEERAIPASAARPTTEA
  11 YRVDDGIPVMLEERSIPGTAAGRD---
  12 YRVDDGIPIMLEERAISVRSLRLK---
  13 YPIRGGIPTLIVDEAIGLTGISEAE--
  14 YPIRHNIPIMLVDEAIPLIG-------