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:

- T0353 NESG:NeT5, Nitrosomonas europaea, 85 res
- gi|30249642|ref|NP_841712.1|_1:85 hypothetical protein NE1680 [Nitrosomonas europaea ATCC 19718]
- gi|30139005|emb|CAD85591.1| conserved hypothetical protein [Nitrosomonas europaea ATCC 19718]
- gi|71548612|ref|ZP_00668836.1|_1:85 conserved hypothetical protein [Nitrosomonas eutropha C71]
- gi|71485793|gb|EAO18342.1| conserved hypothetical protein [Nitrosomonas eutropha C71]
- gi|82703790|ref|YP_413356.1|_1:84 hypothetical protein Nmul_A2677 [Nitrosospira multiformis ATCC 25196]
- gi|82411855|gb|ABB75964.1| conserved hypothetical protein [Nitrosospira multiformis ATCC 25196]
- gi|49082516|gb|AAT50658.1|_1:85 PA0940 [synthetic construct]
- gi|76883122|gb|ABA57803.1|_1:86 conserved hypothetical protein [Nitrosococcus oceani ATCC 19707]
- gi|77164808|ref|YP_343333.1| hypothetical protein Noc_1304 [Nitrosococcus oceani ATCC 19707]
- gi|9946845|gb|AAG04329.1|_1:84 hypothetical protein PA0940 [Pseudomonas aeruginosa PAO1]
- gi|53727416|ref|ZP_00347862.1| hypothetical protein Paer03002666 [Pseudomonas aeruginosa UCBPP-PA14]
- gi|15596137|ref|NP_249631.1| hypothetical protein PA0940 [Pseudomonas aeruginosa PAO1]
- gi|84322524|ref|ZP_00970609.1| hypothetical protein Paer2_01006191 [Pseudomonas aeruginosa 2192]
- gi|107100396|ref|ZP_01364314.1| hypothetical protein PaerPA_01001421 [Pseudomonas aeruginosa PACS2]
- gi|94417961|ref|ZP_01297777.1|_1:84 hypothetical protein PaerP_01000110 [Pseudomonas aeruginosa PA7]
- gi|84316549|ref|ZP_00965022.1|_1:84 hypothetical protein PaerC_01005677 [Pseudomonas aeruginosa C3719]
- gi|91203409|emb|CAJ71062.1|_1:85 conserved hypothetical protein [Candidatus Kuenenia stuttgartiensis]
- gi|91203128|emb|CAJ72767.1| conserved hypothetical protein [Candidatus Kuenenia stuttgartiensis]
- gi|88712477|ref|ZP_01106563.1|_1:87 hypothetical protein FB2170_11031 [Flavobacteriales bacterium HTCC2170]
- gi|88709015|gb|EAR01249.1| hypothetical protein FB2170_11031 [Flavobacteriales bacterium HTCC2170]
- gi|90591352|ref|ZP_01246995.1|_1:86 conserved hypothetical protein [Flavobacterium johnsoniae UW101]
- gi|90432738|gb|EAS58104.1| conserved hypothetical protein [Flavobacterium johnsoniae UW101]
- gi|71147824|gb|AAZ28297.1|_1:79 conserved hypothetical protein [Colwellia psychrerythraea 34H]
- gi|71282084|ref|YP_271542.1| hypothetical protein CPS_4903 [Colwellia psychrerythraea 34H]
- gi|88860299|ref|ZP_01134937.1|_1:79 hypothetical protein PTD2_14782 [Pseudoalteromonas tunicata D2]
- gi|88817497|gb|EAR27314.1| hypothetical protein PTD2_14782 [Pseudoalteromonas tunicata D2]

              10        20           30           40        50        6
              |         |            |            |         |         
   1 MQIHVYDTYVKAKDGHVMHFDVFTDVR..D.DK..K.AIEFAKQWLSSIGEEGATVTSEECRFCH
   2 MQIHVYDTYVKAKDGHVMHFDVFTDVR..D.DK..K.AIEFAKQWLSSIGEEGATVTSEECRFCH
   3 MQIHVYDTYVKSKRGHTMHFDVFTDVR..D.DK..K.AIEFAKEWLASIGEEDATVTSEECRFCH
   4 MEMHVYDTWVKAKDGRTMHFDVFTNTR..D.DK..K.AIEYAKQWLTSVGEGDATVSNRECRFCH
   5 MEVKIFDTHVRTRDGRYLHFDVLVTEE..L.GA..R.AGEFARRWLAGRGIDEADISQGHCSYCH
   6 MQIDVFDTYVTTTEGKRLHFDVFLPTG..K.QG..ElARQYAKEWLESIGIHAKDVQQESCAYCH
   7 MEVKIFDTHVRTRDGRYLHFDVLVTEE..L.GA..R.AGEFARRWLAGRGIDEADISQGHCSYCH
   8 MEVKVFDTHVRTRDGRYLHFDVLVTEE..M.GA..R.AGEFARRWLAGKGIDDADISQGHCSYCH
   9 MEVKIFDTHVRTRDGRYLHFDVLVTEE..L.GA..R.AGEFARRWLAGRGIDEADISQGHCSYCH
  10 MKVSVYDTHVVKKNGLTMHFDIIVPDD..QtHE..K.VLQFGLEYLKRVGQEGQPLTTKECRFCH
  11 MKVSVWDTYVKRKDGTTMHFDILVPSNlkN.EH..S.IYGYGKEYLKGKSFKTNDLTTKECRFCH
  12 MKVAVWDTYVTRKDGKIMHFDILVDEN..T.DDanQ.VFEYGKEYLKTVLQEGQPLTSKECRFCH
  13 MQIHVFDTHVMTDSGQYIHFDVLVNNE..N.IK..E.VEQYAKQYLASLGVKIDNIKQSRCNFCH
  14 MHVHIYDTHVTTRTGQYLHFDVLVDDA..N.VP..H.VARFAEAYLKSLGIIDSQISQSRCNFCH


      0        70        80     
     |         |         |     
   1 SQKAPDEVIEAIKQNGYFIYKMEGCN
   2 SQKAPDEVIEAIKQNGYFIYKMEGCN
   3 SQKAPDEVIEAIKQKGYYIYKMEGCD
   4 SEKAPANVEEAINKDGYFIYKMEGC-
   5 SEIATAEVAEAIRLHGHYILPLEGCG
   6 SEAANPKVQQHIKQHGYYIYQMEGCP
   7 SEIATAEVAEAIRLHGHYILPLEGC-
   8 SEIATTEVAEAIRLHGHYILPLEGC-
   9 SEIATAEIAEAIRLHGHYILPLEGC-
  10 MEEASEDIEKAIKESGYYIYEMEGC-
  11 IEQATEEIILSVEEKGFAVIEMENCN
  12 IDKAPADIENQILKNGFSIIEMENC-
  13 SELADLEVQDNIANQGHSII------
  14 SEMANPEVQLAIQNQGHSIL------