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:

- T0344 Hypothetical protein PF2046, Pyrococcus furiosus, 229 res
- gi|57159905|dbj|BAD85835.1|_1:176 hypothetical protein, conserved [Thermococcus kodakarensis KOD1]
- gi|57641581|ref|YP_184059.1| hypothetical protein TK1646 [Thermococcus kodakarensis KOD1]
- gi|18894260|gb|AAL82170.1|_1:176 hypothetical protein [Pyrococcus furiosus DSM 3638]
- gi|18978418|ref|NP_579775.1| hypothetical protein PF2046 [Pyrococcus furiosus DSM 3638]
- gi|5457507|emb|CAB48998.1|_1:178 Hypothetical protein [Pyrococcus abyssi GE5]
- gi|14520292|ref|NP_125767.1| hypothetical protein PAB2293 [Pyrococcus abyssi GE5]
- gi|33359253|ref|NP_142085.2|_11:186 hypothetical protein PH0067 [Pyrococcus horikoshii OT3]
- gi|3256453|dbj|BAA29136.1|_3:178 184aa long hypothetical protein [Pyrococcus horikoshii OT3]

              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 MRIVAADTGGAVLDETFEPIGLIATVAVLVEKPYRSAKEVMVKYANPYDYDLTGRQAIRDEVLLA
   2 MRIVAADTGGALLDDAYNPLGLIATVAVLVEKPYRTASLSRVKYADPFNYDMSGRQAIRDEAYLA
   3 MRIVAADTGGAVLDETFEPIGLIATVAVLVEKPYRSAKEVMVKYANPYDYDLTGRQAIRDEVLLA
   4 MRIVAADTGGAVLDESLQPIGLISTVAVLVEKPYNTAKEFLVKFSDPYNYDLSGRQAILDEINLA
   5 MRIVAADTGGAVLDESFQPVGLIATVAVLVEKPYKTSKRFLVKYADPYNYDLSGRQAIRDEIELA
   6 MRIVAADTGGAVLDESFQPVGLIATVAVLVEKPYKTSKRFLVKYADPYNYDLSGRQAIRDEIELA


         70        80        90       100       110       120       130
         |         |         |         |         |         |         |
   1 IELARKVKPDVIHLDSTLGGIELRKLDEPTIDALGISDKGKEVWKELSKDLQPLARKFWEETNIE
   2 VELAREVKPDVVHLDSTIGGIEVRKLDEPTIEALGITDRGKEVWKDLSRDLQPLAKKLWEETGIE
   3 IELARKVKPDVIHLDSTLGGIELRKLDEPTIDALGISDKGKEVWKELSKDLQPLARKFWEETNIE
   4 IELAKRTKPDVVHLDSTLGGIEVRKLDEPTIEALSISDKGKEVWKDLSKDVQPLAKKFWEETGIE
   5 IELAREVSPDVIHLDSTLGGIEVRKLDESTIDALQISDRGKEIWKELSKDLQPLAKKFWEETGIE
   6 IELAREVSPDVIHLDSTLGGIEVRKLDESTIDALQISDRGKEIWKELSKDLQPLAKKFWEETGIE


             140       150       160         170      
              |         |         |           |      
   1 IVAIGKSSVPVRIAEIYAGIYSAKWGIENVEK..EGHLIIGLPRYMEV
   2 IIAIGKWSVPVRIAEIYSGIYTAKWAIEYARK..NGKVLVGLPRYMRV
   3 IVAIGKSSVPVRIAEIYAGIYSAKWGIENVEK..EGHLIIGLPRYMEV
   4 ILAIGKSSVPVRIAEIYSGIFSVKWAIEEVKKghKDHLIIGLPRYMGV
   5 IIAIGKSSVPVRIAEIYAGIFSVKWALDNVKE..KGGLLVGYPGIWRL
   6 IIAIGKSSVPVRIAEIYAGIFSVKWALDNVKE..KGGLLVGYPGIWRL