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|_1:82 hypothetical protein MMP0046 [Methanococcus maripaludis S2]
- gi|45047169|emb|CAF29602.1| conserved hypothetical protein [Methanococcus maripaludis S2]
- gi|134046660|ref|YP_001098145.1|_1:82 hypothetical protein MmarC5_1634 [Methanococcus maripaludis C5]
- gi|132664285|gb|ABO35931.1| conserved hypothetical protein [Methanococcus maripaludis C5]
- gi|159905288|ref|YP_001548950.1|_1:82 hypothetical protein MmarC6_0903 [Methanococcus maripaludis C6]
- gi|159886781|gb|ABX01718.1| conserved hypothetical protein [Methanococcus maripaludis C6]
- gi|150402966|ref|YP_001330260.1|_1:82 hypothetical protein MmarC7_1043 [Methanococcus maripaludis C7]
- gi|150033996|gb|ABR66109.1| conserved hypothetical protein [Methanococcus maripaludis C7]
- gi|150399806|ref|YP_001323573.1|_1:82 hypothetical protein Mevan_1061 [Methanococcus vannielii SB]
- gi|150012509|gb|ABR54961.1| conserved hypothetical protein [Methanococcus vannielii SB]
- gi|15669050|ref|NP_247854.1|_4:88 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|163798965|ref|ZP_02192872.1|_1:87 conserved hypothetical protein [Methanococcus voltae A3]
- gi|158972972|gb|EDP40440.1| conserved hypothetical protein [Methanococcus voltae A3]

                 10           20        30           40        50      
                 |            |         |            |         |      
   1 ...MKIPKIYVEG.EL.NDGDRVA.IEKDGNAIIFLEKDE...EYSGNGKLLYQVIYDDLAKYMS
   2 ...MKIPKIYVEG.EL.NDGDRVA.IEKDGNAIIFLEKDE...EYSGNGKLLYQVIYDDLAKYMS
   3 ...MKIPKIYVEG.EL.NDGDRVA.IEKDGNAIIFLEENE...EYSGNGKLLYRVIYDDLAKYLS
   4 ...MKIPKIYVEG.EL.NDGDRVA.IEKDGNAIIFLEENE...EYSGNGKLLYQVIYDDLAKYLS
   5 ...MKIPKIYVEG.EL.NDGERVA.IENNGKIIIFLEENE...EYSGNGKLLYTVIYDDLVKYLS
   6 ...MKIPKIYIEG.EL.NDNNKVV.IENEGKKIIFLEKED...EYFGDGKVLYQVIYDDLSKYLV
   7 mniMRIPRLYVENaEK.HEGRKVV.IENGGKVIKFLDKDE...EYEGDGKVLYQVIYDDFDNYVL
   8 ...MKIPKLYVEN.NIfEDNEPCEkIAVSEKEIIFLDSDEvvdNYKNTHKILYKVRYDDIRSYID


        60          70        80     
        |           |         |     
   1 LDTLKKDVLIQYP..DKHTLTYLKAGTK...
   2 LDTLKKDVLIQYP..DKHTFTYLKAGTKlis
   3 LDELKKDVLIQYP..DKHTFTYLKAGTKlvs
   4 LDKLKKDVLIQYP..DKHTFTYLKAGIKlvs
   5 LNKLKKDVLIQYP..DKHTVTYLKTGTElis
   6 LNKLKKDIFIKFP..DNRTFSYIKKGTElil
   7 MGTVTKDMIIEYEvgGVRQITYIKKGTKlle
   8 NDVLKKDIFVKYP..GNHTFTHIKAGTYitc