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:

- T0314 PaT4, Pseudomonas aeruginosa, 106 res
- gi|26987889|ref|NP_743314.1|_61:166 lipoprotein, putative [Pseudomonas putida KT2440]
- gi|24982595|gb|AAN66778.1| lipoprotein, putative [Pseudomonas putida KT2440]
- gi|82737513|ref|ZP_00900362.1|_1:106 lipoprotein, putative [Pseudomonas putida F1]
- gi|82715488|gb|EAP50553.1| lipoprotein, putative [Pseudomonas putida F1]
- gi|70731880|ref|YP_261622.1|_1:105 hypothetical protein PFL_4538 [Pseudomonas fluorescens Pf-5]
- gi|68346179|gb|AAY93785.1| conserved hypothetical protein [Pseudomonas fluorescens Pf-5]
- gi|95109496|emb|CAK14197.1|_1:104 conserved hypothetical protein [Pseudomonas entomophila L48]
- gi|77384537|gb|ABA76050.1|_1:105 conserved hypothetical protein [Pseudomonas fluorescens PfO-1]
- gi|77460534|ref|YP_350041.1| hypothetical protein Pfl_4313 [Pseudomonas fluorescens PfO-1]
- gi|9947042|gb|AAG04512.1|_1:106 hypothetical protein PA1123 [Pseudomonas aeruginosa PAO1]
- gi|32041133|ref|ZP_00138716.1| hypothetical protein Paer03002848 [Pseudomonas aeruginosa UCBPP-PA14]
- gi|15596320|ref|NP_249814.1| hypothetical protein PA1123 [Pseudomonas aeruginosa PAO1]
- gi|84328597|ref|ZP_00976601.1| hypothetical protein Paer2_01000106 [Pseudomonas aeruginosa 2192]
- gi|84322118|ref|ZP_00970463.1| hypothetical protein PaerC_01000099 [Pseudomonas aeruginosa C3719]
- gi|94415989|ref|ZP_01295821.1|_1:106 hypothetical protein PaerP_01002318 [Pseudomonas aeruginosa PA7]

              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 MSITSTDICQAADALKGFVGFNRKTGRYIVRFSEDSFGMDVADDSITPTSEFVWSSVRDDVMRLG
   2 MAITSQDICNAADQLKGFVGFHGKRGVHIVRFSEDAFGMDVADASITPCSEFVWRPEQGQRMALC
   3 MAITSQDICNAADQLKGFVGFHGKRGVHIVRFSEDAFGMDVADASITPCSEFVWRPEQGLRMVLC
   4 MSITSELICQAADQLKGFVGFNRKTGRYIVRFSEDSFGMDVADDAIVPAHEFVWAPVSDQAMSLK
   5 MAITSQDICNAADQLKGFVGFHGKRGTHIVRFSEDSFGMDVADDSITPCSEFVWRAEGDRRMALC
   6 MRITSQLICQAADDLNGFVGLNRKTGQYIVRFSEDSFGMDVADDGIIPCSEFVWAPATEQTMTLK
   7 MSITSTDICQAADALKGFVGFNRKTGRYIVRFSEDSFGMDVADDSITPTSEFVWSSVRDDVMRLG
   8 MSISSTDICQAADALKGFVGFNRKTGRYIVRFSEDSFGMDVPDDSITPTSEFVWSSVRDDVMRLG


         70        80        90       100      
         |         |         |         |      
   1 REQLQILLEQNINERLNIGEPLLVYLRRQDLPEITAQRQLR
   2 RERLSLLLDQHVDDRLNIGEPLRAYLRRCDLPEIVAQRSLQ
   3 RERLSLLLDQHVDDRLNIGEPLRAYLRRCDLPEIVAQRSLQ
   4 REQIQLLLDQNIDDRINISEPLRVYMRRSDLPEIQAVRSL-
   5 RERLALLFGQHVDDRLNIGEPLRLYLRRTDLPEIVAERS--
   6 RELIQLLLDQNIDDRINITEPLRVYMNKREVPEIEAVRSL-
   7 REQLQILLEQNINERLNIGEPLLVYLRRQDLPEITAQRQLR
   8 REQLQILLEQNINERLNIGEPLLVYLRRQDLPEITAQRQLR