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:

- T0397
- gi|45357609|ref|NP_987166.1|_80:150 hypothetical protein MMP0046 [Methanococcus maripaludis S2]
- gi|45047169|emb|CAF29602.1| conserved hypothetical protein [Methanococcus maripaludis S2]
- gi|150399806|ref|YP_001323573.1|_80:150 hypothetical protein Mevan_1061 [Methanococcus vannielii SB]
- gi|150012509|gb|ABR54961.1| conserved hypothetical protein [Methanococcus vannielii SB]
- gi|150402966|ref|YP_001330260.1|_80:150 hypothetical protein MmarC7_1043 [Methanococcus maripaludis C7]
- gi|150033996|gb|ABR66109.1| conserved hypothetical protein [Methanococcus maripaludis C7]
- gi|159905288|ref|YP_001548950.1|_80:150 hypothetical protein MmarC6_0903 [Methanococcus maripaludis C6]
- gi|159886781|gb|ABX01718.1| conserved hypothetical protein [Methanococcus maripaludis C6]
- gi|134046660|ref|YP_001098145.1|_80:150 hypothetical protein MmarC5_1634 [Methanococcus maripaludis C5]
- gi|132664285|gb|ABO35931.1| conserved hypothetical protein [Methanococcus maripaludis C5]
- gi|14591088|ref|NP_143163.1|_112:182 hypothetical protein PH1273 [Pyrococcus horikoshii OT3]
- gi|3257693|dbj|BAA30376.1| 182aa long hypothetical protein [Pyrococcus horikoshii OT3]
- gi|15669050|ref|NP_247854.1|_86:156 hypothetical protein MJ0859 [Methanocaldococcus jannaschii DSM 2661]
- gi|2842577|sp|Q58269|Y859_METJA Uncharacterized protein MJ0859 [Taxonomy]
- gi|1591544|gb|AAB98874.1| hypothetical protein MJ_0859 [Methanocaldococcus jannaschii DSM 2661]
- gi|57641784|ref|YP_184262.1|_94:164 hypothetical protein TK1849 [Thermococcus kodakarensis KOD1]
- gi|57160108|dbj|BAD86038.1| hypothetical protein, conserved [Thermococcus kodakarensis KOD1]
- gi|18977573|ref|NP_578930.1|_94:162 hypothetical protein PF1201 [Pyrococcus furiosus DSM 3638]
- gi|18893288|gb|AAL81325.1| hypothetical protein [Pyrococcus furiosus DSM 3638]
- gi|14521400|ref|NP_126876.1|_94:162 hypothetical protein PAB1584 [Pyrococcus abyssi GE5]
- gi|5458618|emb|CAB50106.1| Hypothetical protein [Pyrococcus abyssi GE5]
- gi|163798965|ref|ZP_02192872.1|_85:155 conserved hypothetical protein [Methanococcus voltae A3]
- gi|158972972|gb|EDP40440.1| conserved hypothetical protein [Methanococcus voltae A3]
- gi|20094210|ref|NP_614057.1|_88:148 hypothetical protein MK0773 [Methanopyrus kandleri AV19]
- gi|19887235|gb|AAM01987.1| Uncharacterized protein conserved in archaea [Methanopyrus kandleri AV19]

              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 GTKLISVPAEGYKVYPIMDFGFRVLKGYRLATLESKKGDLRYVNSPVSGTVIFMNEIPSERANYV
   2 GTKLISVPAEGYKVYPIMDFGFRVLKGYRLATLESKKGDLRYVNSPVSGTVIFMNEIPSERANYV
   3 GTELILVPAEGYKVYPILDFGYRVLKGYRLAGLESKKGDIRYVNSPVNGTVVFMNEIPSERPNYV
   4 GTELISVVAEGYEVYPIMDFGFRVLKGYRLATLKSKKGDLRYVNSPVSGTVIFMNEIPSERANYV
   5 GIKLVSVVAEGYEVYPIMDFGFRVLKGYRLATLKSKKGDLRYVNSPVSGTVIFMNEVPSERANYV
   6 GTKLVSVVAEGYEVYPIMDFGFRVLKGYRLATLKSKKGDLRYANSPISGTVIFMNEIPSERANYV
   7 GDELMLLPVEGYVVTLIADVGNRVRKGDPFAAITTRKGEVHYLKPPKPGTVVYIDEFTNRPHYVY
   8 GTKLLEIPAEGYKVYPIVDFGCRILGGHRIAALQSRKGDIRFVNTPVNGIVLFLKEVPAKRENYV
   9 GDELMILPVEGFTKTLIANVGNRVRTGDAFAAVTTRKGEVHYLKPPKTGTVVFIDEITNRPHYLY
  10 GDELLLLPVEGYVVTLIADVGNRVRKGDAFAAVTTRKGEVHYLKPPKPGTVVYIDEFTNRPHYIY
  11 GDELLLLPVEGYVVTLIADVGNRVRKGDAFAAVTTRKGEVHYLKPPRPGTVVYIDEFTNRPHYVY
  12 GTYITCVLADSKTTYPILDAGSVVLRDGILATLKSNKGVIRYLKSPVSGTVFFMNEIFEGNNSIY
  13 GDRVYQIPVEGYVVTPIADVGDRLRKGDPLAAVTTRSGNVRYVEAPQDCLVVYVCEQPAIR----


         70 
         | 
   1 FYMLEE
   2 FYMLEE
   3 FYILEE
   4 FYMLEE
   5 FYMIEE
   6 FYMLEE
   7 YILPEE
   8 FYILPE
   9 YILPEE
  10 YILP--
  11 YILP--
  12 LFAIVE
  13 ------