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:

- T0321
- gi|68207206|ref|ZP_00559375.1|_1:123 conserved hypothetical protein [Desulfitobacterium hafniense DCB-2]
- gi|68168883|gb|EAM96800.1| conserved hypothetical protein [Desulfitobacterium hafniense DCB-2]
- gi|89335284|dbj|BAE84879.1|_1:123 hypothetical protein [Desulfitobacterium hafniense Y51]
- gi|89895836|ref|YP_519323.1| hypothetical protein DSY3090 [Desulfitobacterium hafniense Y51]
- gi|71492533|gb|EAO24837.1|_1:123 Protein of unknown function DUF364 [Syntrophomonas wolfei subsp. wolfei str. Goettingen]
- gi|71540788|ref|ZP_00662619.1| Protein of unknown function DUF364 [Syntrophomonas wolfei str. Goettingen]
- gi|83590272|ref|YP_430281.1|_1:111 Protein of unknown function DUF364 [Moorella thermoacetica ATCC 39073]
- gi|83573186|gb|ABC19738.1| Protein of unknown function DUF364 [Moorella thermoacetica ATCC 39073]
- gi|71676114|ref|ZP_00673857.1|_7:123 similar to Uncharacterized conserved protein [Trichodesmium erythraeum IMS101]
- gi|71670975|gb|EAO27642.1| similar to Uncharacterized conserved protein [Trichodesmium erythraeum IMS101]
- gi|39934461|ref|NP_946737.1|_188:295 hypothetical protein RPA1387 [Rhodopseudomonas palustris CGA009]
- gi|46425450|emb|CAE26830.2|_176:283 conserved unknown protein [Rhodopseudomonas palustris CGA009]
- gi|68247943|gb|EAN30026.1|_8:120 conserved hypothetical protein [Magnetococcus sp. MC-1]
- gi|69255578|ref|ZP_00605320.1| conserved hypothetical protein [Magnetococcus sp. MC-1]
- gi|67155965|ref|ZP_00417592.1|_24:135 conserved hypothetical protein [Azotobacter vinelandii AvOP]
- gi|67086909|gb|EAM06377.1| conserved hypothetical protein [Azotobacter vinelandii AvOP]
- gi|46200693|ref|ZP_00207804.1|_173:277 COG2014: Uncharacterized conserved protein [Magnetospirillum magnetotacticum MS-1]
- gi|83309251|ref|YP_419515.1|_199:303 hypothetical protein amb0152 [Magnetospirillum magneticum AMB-1]
- gi|82944092|dbj|BAE48956.1| Uncharacterized conserved protein [Magnetospirillum magneticum AMB-1]
- gi|15622183|dbj|BAB66175.1|_5:118 242aa long conserved hypothetical protein [Sulfolobus tokodaii str. 7]
- gi|15921397|ref|NP_377066.1| hypothetical protein ST1140 [Sulfolobus tokodaii str. 7]
- gi|53802964|ref|YP_115228.1|_5:97 hypothetical protein MCA2834 [Methylococcus capsulatus str. Bath]
- gi|53756725|gb|AAU91016.1| conserved hypothetical protein [Methylococcus capsulatus str. Bath]

              10        20        30         40           50        60 
              |         |         |          |            |         | 
   1 MWEIYDAMINGIPEDFLVDELVCGTTHSVIRSGN.GVGLGPNRPFETRMP...MLTQNLLGLPLR
   2 MWEIYDAMINGIPEDFLVDELVCGTTHSVIRSGN.GVGLGPNRPFETRMP...MLTQNLLGLPLR
   3 MWEIYDAMINGIPEDFLVDELVCGTTHSVVRSGN.GVGLGPNRPFETRMP...MLTQNLLGLPLR
   4 MWSIYNDLIDSIPEDLTVLDCMLGLHWTLIKSES.GTGAAMTVNGGQQNS...GEYKELISMPLK
   5 MWEVYDELIAAVPPDLEVEDCIVGLNWILVRSR-.ATGLVMTPLEGHPRI...KLAGEIKGMPVR
   6 -KEIYDLLLEYGNTTTPIKKILIGLTWTLCETE-.GIGLCMSPGTTTRTL...PWSGTLVNKPAK
   7 -PEQLYRDLALGVADDEVRQIACGQRWIMVEGPH.GAGLAYLPRHPRALQ...PRLASLGKQSLR
   8 -PEQLYRDLALGVADDEVRQIACGQRWIMVEGPH.GAGLAYLPRHPRALQ...PRLASLGKQSLR
   9 -YDQLLEQARLAAGEALVAEVIMGPVWTVVRTDDgGMGLAMSPATATRTL...PWSGTLRGRPIV
  10 -YDWLLEHAAGVTRDDPVERVCLGLSWTLAEVGD.SLGFAFGPRQVPRTL...SWAGTLAGQGAE
  11 -PERLYADLANGVEDAPVKRVVVGLNWTMVETET.GLGLAQTPERGTPGCnaaPDAGRRSEAGLK
  12 -PGRLYADLANGVEDCAVKRVVVGLNWTMVETAT.GVGLAQTPERGTPGCnaaPDAGRRGQAGLK
  13 ------EKLISITPEKKVRELVIGLGWTVVLSK-.YAGMAMTYKSNEE-P...RNIESLHEIDTR
  14 -CEIYDLLQDYAGAPVPVGTVVIGLVWTLCEAD-.AVGLSMSPGVQTRTL...PWAGTLRGKTLS


             70        80        90       100       110       120   
             |         |         |         |         |         |   
   1 VAAGCVKSWNYVEASIGLAAINAYYNNPQVAREHGVIFSDAKRVEDRMNDPFIMSQNEVKGK
   2 VAAGCVKSWNYVEASIGLAAINAYYNNPQVAREHGVIFSDAKRVEDRMNDPFIMSQNEVKGK
   3 VAAGCVKSWNYVEASIGLAAINAYYNNPQVAREHGVIFSDAKRVEDRMNDPFIMSQNEVKGK
   4 ELAKAVKSWTMLEASMGLAAINSALNTPKQVSALTGQVFKVSKDSERANAFTCFLPDIKNKK
   5 DLAEYIKSWNNFEAALGLAAINSVLNTPEQVESLCGRPLSSQPQMNAFTCF-----------
   6 ELASWLRSWNSFEATVGMATINAEINRRSAVRKEKLPPTQAEPLSPYGPGNLAVFEYF----
   7 QLAALAMSWDPLETALGIAAINAHYNRYDLAAAAGNGVKTFRHVAGRV--------------
   8 QLAALAMSWDPLETALGIAAINAHYNRYDLAAAAGNGVKTFRHVAGRV--------------
   9 ELIEWVKSWNFHEAAVGMAALNAALGIPMDWAREATPLMTPGSANLAVFDHF----------
  10 RLYPWLLSWNGAEAAVGLAVVNAVVNRASPCLRQAQPLHGAVPGNLSVFEHF----------
  11 ALAGLVHSTNAFDQALGMAACNAHYNRFDLDLPDGNGLESFG--------------------
  12 ALAGLVHSANAFDQALGMAACNAHYNRYDLELPGGNGLESFG--------------------
  13 KLAELLKSWNFLEASIGLAAINSTIPPPKSYKVANALDLAFQESKDKTVTMVGYFPGYVDK-
  14 ELVAWVREFDPYRATVGMAAVNAGINRLGRLPDG----------------------------