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:

- T0621
- gi|268679874|ref|YP_003304305.1|_19:190 hypothetical protein Sdel_1248 [Sulfurospirillum deleyianum DSM 6946]
- gi|268617905|gb|ACZ12270.1| hypothetical protein Sdel_1248 [Sulfurospirillum deleyianum DSM 6946]
- gi|268679625|ref|YP_003304056.1|_19:190 hypothetical protein Sdel_0992 [Sulfurospirillum deleyianum DSM 6946]
- gi|268617656|gb|ACZ12021.1| hypothetical protein Sdel_0992 [Sulfurospirillum deleyianum DSM 6946]
- gi|194292144|ref|YP_002008051.1|_25:175 conserved hypothetical protein, putative exported protein [Cupriavidus taiwanensis]
- gi|193226048|emb|CAQ71995.1| conserved hypothetical protein, putative exported protein [Cupriavidus taiwanensis]
- gi|268679628|ref|YP_003304059.1|_20:162 hypothetical protein Sdel_0995 [Sulfurospirillum deleyianum DSM 6946]
- gi|268617659|gb|ACZ12024.1| hypothetical protein Sdel_0995 [Sulfurospirillum deleyianum DSM 6946]
- gi|268679631|ref|YP_003304062.1|_20:157 hypothetical protein Sdel_0998 [Sulfurospirillum deleyianum DSM 6946]
- gi|268617662|gb|ACZ12027.1| hypothetical protein Sdel_0998 [Sulfurospirillum deleyianum DSM 6946]

              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 NPNPISIPIDLSQAGSVVEKEVKIEESWSYHLILQFAVHDRKEDGGLDGKRVWKFLGFNSYDPRD
   2 NPNPISIPIDLSQAGSVVEKEVKIEESWSYHLILQFAVHDRKEDGGLDGKRVWKFLGFNSYDPRD
   3 NPDPISIPIDLSQAGSVVEREVKIEETWAYDLFLEFAVLDRKEDGGLDGKKVRKFLGFNSYNPYD
   4 GTPPFTVPLDPSKAGSRIEREFRIPERQLYAFIVGFKYRERDQADRARARRLSGSYERDK-----
   5 PTPYYTMPIDLSKTGNVAETDIRIDKEYRTGIALNYDFRRQKNKMTRNEYNNIKVFFGNSY----
   6 PTPYYKMPIDLSKAGNVTETDIRIDEKYSVYVELYYDYRKQKISGDRYGEIIDKYFGRHKLFP--


         70        80        90       100       110       120          
         |         |         |         |         |         |          
   1 GKQVGYVDYRLAKSELGDLIDETYDCDGTVVPIKITIHQINQDNTKKLIADNLYMTK....GNGS
   2 GKQVGYVDYRLAKSELGDLIDETYDCDGTVVPIKITIHQINQDNTKKLIADNLYMTK....GNGS
   3 GKKLGFGDYEQAKRKLGDLIDETYDCDGTIAPIKLTIHQINKDNTKKLIVDNLYMTK....GYSS
   4 --------------------NGKIITPGVAFSLRVTVVKTSPEGESTVIDREINVEEialfSWSK
   5 -------------------------TSGTAIPVKLKIEKIMDKNETTILNDIIIVDN....NGGH
   6 -----------------------------IFPIKLTVLKYEKTGT-TMVVDKIYYTN....SLGR


       130       140        150       160       170  
        |         |          |         |         |  
   1 GAYTRDITTISLDKG.KYIFRIENIEAFSEMIGRKVDFTIYINKRDK
   2 GAYTRDITTISLDKG.KYIFRIENIEAFSEMIGRKVDFTIYINKRDK
   3 GAYERDIAIISLDKG.KYIFRIENIEAFQEMNARKVNFIIRIHKRDK
   4 DEFDKEMAALPLEKG.RYRIVVETTKAAPEMKGAPIIFSVHRAYRGK
   5 ELHSSLIKEIALSQG.KYRIKVETTEDFSELSDLSVLVEIYYIRAPK
   6 TYSSREIDEFKLQEGsKYHIKVETVEDYPELAELNVEVVIGYIK---