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:

- TR464 XfR39, Xylella fastidiosa 9a5c, 89 residues
- gi|78048386|ref|YP_364561.1|_18:86 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|166712591|ref|ZP_02243798.1|_18:86 hypothetical protein Xoryp_14340 [Xanthomonas oryzae pv. oryzicola BLS256]
- gi|21231937|ref|NP_637854.1|_18:86 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| hypothetical protein xccb100_1657 [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|21243409|ref|NP_642991.1|_18:86 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|_18:86 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|190573603|ref|YP_001971448.1|_18:86 CONSERVED HYPOTHETICAL PROTEIN [Stenotrophomonas maltophilia K279a]
- gi|190011525|emb|CAQ45143.1| CONSERVED HYPOTHETICAL PROTEIN [Stenotrophomonas maltophilia K279a]
- gi|15839262|ref|NP_299950.1|_18:86 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|_18:86 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|194365147|ref|YP_002027757.1|_18:86 protein of unknown function DUF343 [Stenotrophomonas maltophilia R551-3]
- gi|194347951|gb|ACF51074.1| protein of unknown function DUF343 [Stenotrophomonas maltophilia R551-3]
- gi|121997789|ref|YP_001002576.1|_18:81 hypothetical protein Hhal_0998 [Halorhodospira halophila SL1]
- gi|121589194|gb|ABM61774.1| protein of unknown function DUF343 [Halorhodospira halophila SL1]
- gi|88810847|ref|ZP_01126104.1|_20:82 hypothetical protein NB231_17243 [Nitrococcus mobilis Nb-231]
- gi|88792477|gb|EAR23587.1| hypothetical protein NB231_17243 [Nitrococcus mobilis Nb-231]
- gi|114319435|ref|YP_741118.1|_21:82 hypothetical protein Mlg_0273 [Alkalilimnicola ehrlichei MLHE-1]
- gi|114225829|gb|ABI55628.1| protein of unknown function DUF343 [Alkalilimnicola ehrlichei MLHE-1]
- gi|186455585|ref|ZP_02965899.1|_156:209 hypothetical protein CflavDRAFT_1015 [bacterium Ellin514]
- gi|184207663|gb|EDU04708.1| hypothetical protein CflavDRAFT_1015 [bacterium Ellin514]

              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 LSLLESKGLEALNKAIASGTVQRADGSIQNQSLHEALITRDRKQVFRIEDSIPVLLPEEAIATIQ
   2 LSLLDGKGLEALNAAIAGGTLQRADGTAQTQPLREALITRDRKQIFRVDDGIPVLLAEEAIATAQ
   3 LSLLDVKGLEALNAAIAGGTLRRADGTAQTQPLREALITRDRKQIFRVDDGIPVLLAEEAIATTQ
   4 LSLLDGKGLEALNRAIAAGTLQRVDGAVQDQPLREALITRDRKQIFRVDDGIPVLLAEEAINPSQ
   5 LSLLDGKGLEALNAAIAGGALQRADGAAQTQPLREALITRDRKQIFRVDDGIPVLLAEEAIATAQ
   6 LSLLDVKGLEVLNATIAGGTLQRADGTAQTQPLREALITRDRKQIFRVDDGIPVLLAEEAIATTQ
   7 LSLLDGKGLEALNKAISAGAVNKADGNPLAQPLREALVTRDRKQVFRVDDGIPVLLAEEAIPTAQ
   8 LSLLESKGLEALNKAIASGTVQRADGSIQNQSLHEALITRDRKQVFRIEDSIPVLLPEEAIATIQ
   9 LSLLESKGLEALNKAIVSGTVQRADGSIQNQSLHEALITRDRKQVFRIEDSIPVLLPEEAIATIQ
  10 LSLLDGGGLEALNKAISTGAVNKADGNPLAQPLREALVTRDRKQVFRVDDGIPVLLAEEAIPTAQ
  11 LQPLSTQELEALNRHIADGQARYLDDTVVDTPLDEGLITDNGSRIYRVDDGIPVMLEERSIPGT-
  12 IRPLKRDELQRINEAIANGHLRYLDNSTVEAELDEGLITDNAERVYRVDDGIPIMLEERAISV--
  13 -RLLEADALKRLNQRIEQGEVRHMDDSPVETPLREALITENDQRIYPVEDGIPIMLEERAIPA--
  14 --------IEKINQQIFTGALRNRRGQVIREVIEGGLVRADGRYLYPIRHNIPIMLVDEAIP---


          
         
   1 IANF
   2 IADF
   3 IADF
   4 IADF
   5 IADF
   6 IADF
   7 IADF
   8 IANF
   9 IANF
  10 IADF
  11 ----
  12 ----
  13 ----
  14 ----