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:

- T0476 PfG1, Pyrococcus furiosus, 108 residues
- gi|14590436|ref|NP_142504.1|_4:111 hypothetical protein PH0535 [Pyrococcus horikoshii OT3]
- gi|3256941|dbj|BAA29624.1| 115aa long hypothetical protein [Pyrococcus horikoshii OT3]
- gi|5458928|emb|CAB50415.1|_1:108 Hypothetical protein [Pyrococcus abyssi GE5]
- gi|33356798|ref|NP_127185.2|_4:111 hypothetical protein PAB1367 [Pyrococcus abyssi GE5]
- gi|18976757|ref|NP_578114.1|_1:108 hypothetical protein PF0385 [Pyrococcus furiosus DSM 3638]
- gi|18892346|gb|AAL80509.1| hypothetical protein [Pyrococcus furiosus DSM 3638]
- gi|57640581|ref|YP_183059.1|_1:107 hypothetical protein TK0646 [Thermococcus kodakarensis KOD1]
- gi|57158905|dbj|BAD84835.1| hypothetical protein, conserved [Thermococcus kodakarensis KOD1]

              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 SAKCPICGSPLKWEELIEEMLIIENFEEIVKDRERFLAQVEEFVFKCPVCGEEFYGKTLPRREAE
   2 MAKCPVCGSTLDWRELIEQMLSMENAREVFSDKERFLKELEEFTFKCPVCGEEFLGKYLPREEGE
   3 MAKCPVCGASLDWRDLIEQMLTLENAEDIFKDREEFLGKLKEFTFKCPVCGEEFLGKYLPMDEAE
   4 MAKCPVCGASLDWRDLIEQMLTLENAEDIFKDREEFLGKLKEFTFKCPVCGEEFLGKYLPMDEAE
   5 MAKCPICGSPLKWEELIEEMLIIENFEEIVKDRERFLAQVEEFVFKCPVCGEEFYGKTLPRREAE
   6 MARCPLCGKALDWAELINQMLEKGVGEDVFKDRDKFMETFNDFVFKCPHCGEEFYGRNLPASETE


         70        80        90       100        
         |         |         |         |        
   1 KVFELLNDFKGGIDWENKRVKLKLNDLLALETMLEEWDRRVKR
   2 KVFELLNDFKGSIDWERRKVRIRLNQLLVLDKMLEEWDRRVKN
   3 KVFELLNDFKGSIDWDNRKVRIRLNQLLALDKMLEEWDRRVKN
   4 KVFELLNDFKGSIDWDNRKVRIRLNQLLALDKMLEEWDRRVKN
   5 KVFELLNDFKGGIDWENKRVKLKLNDLLALETMLEEWDRRVKR
   6 KVFELLNDFKGSIDWDNKRVRLRLNSLLALDSMLENWDRKMS-