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:

- T0272 1wj9, Thermus thermophilus
- gi|16766245|ref|NP_461860.1|_123:212 putative cytoplasmic protein [Salmonella typhimurium LT2]
- gi|16421489|gb|AAL21819.1| putative cytoplasmic protein [Salmonella typhimurium LT2]
- gi|15803273|ref|NP_289305.1|_122:212 orf; hypothetical protein [Escherichia coli O157:H7 EDL933]
- gi|15832864|ref|NP_311637.1| hypothetical protein ECs3610 [Escherichia coli O157:H7]
- gi|25391291|pir||B91080 hypothetical protein ECs3610 [imported] - Escherichia coli (strain O157:H7, substrain RIMD 0509952) [Taxonomy]
- gi|25497212|pir||C85925 hypothetical protein Z4065 [imported] - Escherichia coli (strain O157:H7, substrain EDL933) [Taxonomy]
- gi|12517213|gb|AAG57863.1| orf; hypothetical protein [Escherichia coli O157:H7 EDL933]
- gi|13363081|dbj|BAB37033.1| hypothetical protein [Escherichia coli O157:H7]
- gi|16761711|ref|NP_457328.1|_120:230 conserved hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi str. CT18]
- gi|29143195|ref|NP_806537.1| conserved hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi Ty2]
- gi|25512790|pir||AF0857 conserved hypothetical protein STY3066 [imported] - Salmonella enterica subsp. enterica serovar Typhi (strain CT18) [Taxonomy]
- gi|16504012|emb|CAD06045.1| conserved hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
- gi|29138828|gb|AAO70397.1| conserved hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi Ty2]
- gi|29834080|ref|NP_828714.1|_126:217 hypothetical protein SAV7538 [Streptomyces avermitilis MA-4680]
- gi|29611205|dbj|BAC75249.1| hypothetical protein [Streptomyces avermitilis MA-4680]
- gi|48837457|ref|ZP_00294452.1|_100:205 COG0583: Transcriptional regulator [Thermobifida fusca]
- gi|16130663|ref|NP_417236.1|_110:198 orf, hypothetical protein; unknown CDS [Escherichia coli K12]
- gi|6136707|sp|Q46897|YGCH_ECOLI Hypothetical protein ygcH [Taxonomy]
- gi|7466432|pir||H65056 hypothetical protein b2756 - Escherichia coli (strain K-12) [Taxonomy]
- gi|882649|gb|AAA69266.1| ORF_f199 [Taxonomy]
- gi|1789114|gb|AAC75798.1| orf, hypothetical protein; unknown CDS [Escherichia coli K12]
- gi|37524751|ref|NP_928095.1|_132:222 hypothetical protein [Photorhabdus luminescens subsp. laumondii TTO1]
- gi|36784176|emb|CAE13045.1| unnamed protein product [Photorhabdus luminescens subsp. laumondii TTO1]
- gi|41718693|ref|ZP_00147662.1|_73:163 COG1643: HrpA-like helicases [Methanococcoides burtonii DSM 6242]
- gi|23105453|ref|ZP_00091909.1|_116:202 hypothetical protein [Azotobacter vinelandii]
- gi|39996491|ref|NP_952442.1|_111:199 CRISPR-associated protein, CT1974 family [Geobacter sulfurreducens PCA]
- gi|39983372|gb|AAR34765.1| CRISPR-associated protein, CT1974 family [Geobacter sulfurreducens PCA]
- gi|21674785|ref|NP_662850.1|_110:202 hypothetical protein [Chlorobium tepidum TLS]
- gi|21648001|gb|AAM73192.1| hypothetical protein [Chlorobium tepidum TLS]
- gi|23474688|ref|ZP_00129980.1|_123:216 hypothetical protein [Desulfovibrio desulfuricans G20]
- gi|48837463|ref|ZP_00294458.1|_49:139 hypothetical protein Tfus02000666 [Thermobifida fusca]
- gi|48763784|ref|ZP_00268338.1|_128:215 hypothetical protein Rrub02003223 [Rhodospirillum rubrum]
- gi|47104064|ref|YP_015493.1|_98:178 hypothetical protein [Photobacterium profundum SS9]
- gi|46911628|emb|CAG17977.1| hypothetical protein [Photobacterium profundum SS9]
- gi|38234753|ref|NP_940520.1|_170:225 Conserved hypothetical protein [Corynebacterium diphtheriae NCTC 13129]
- gi|38201017|emb|CAE50740.1| Conserved hypothetical protein [Corynebacterium diphtheriae]

              10          20         30        40             50       
              |           |          |         |              |       
   1 ATGKRVALKTPAEKVAWL..ERRLE.EGGFRLLEGERGPWVQILQDTFLEV.....RRKKD....
   2 ---QDIWSYQQQAALTWL..ARQGE.QNGFTLREASVDAYRQ---------.....-QQIR....
   3 --GSDVWLHQQQAALDWL..AAQGE.RSGFTLLDTSVDAYRQ---------.....-QQLR....
   4 -EKERWWELQQQAAQAWL..EQQGQ.QHGFRLIAPEPDDFAMWAGDEYSELq11yqQHRFV....
   5 ---PAVVPLNGAAADEWW..TRQAD.AAGLKPLALHPHPLDAAQGV-----.....---RA....
   6 ---KLTAHLTQRYQKKWL..LQRQD.AAGFRVVEKPAEKRRLPEGDEHELI.....VHNRRdw6s
   7 -KRCRVPLIKEAEQIAWL..QRKLG.NA-------------ARVEDVHPIS.....ERPQY....
   8 ---GKIKAMMENAARNWLlnHRRMQ.QWGIQFDNLL----------DIEGY.....TQHRS....
   9 ----NMPDIVQRKGSEWL..LRKGD.MNGFSINAEQIRVDAY--------Q.....NHKLF....
  10 ---KRRGLLGEAEQLAWL..QRQGE.RHGFAVKAVLVSASDLL--------.....---DS....
  11 -KKCRVPLIREEDLRAWL..KRKLE.--GVAVIEAV---------EVEKRP.....AMNFR....
  12 --GKRVPIKTREEVAAWF..GGKSQtSWGFSVDPARLDVRMLPVMQ-----.....----F....
  13 ---PTRAEIAQEAGTRWL..LARQQ.ALGLSIESAA----ILVEGCKVERF.....VKRAT....
  14 --REYTWALRGAAAEEWW..HSRAA.ANGLELLSTY---------AQTLDD.....VRDPG....
  15 ---PLTVEDRERVALDWL..LDRQQ.GFGVLFERALCSAGGY---------.....-RQVR....
  16 --KKVIEIKDENEQIQWL..QRKLR.GANVTVTALE---------------.....---SV....
  17 ------------------..-----.----------------------REV.....IGTKH....


            60        70        80        90       100   
            |         |         |         |         |   
   1 .GEEAGKLLQVQAVLFEGRLEVVDPERALATLRRGVGPGKALGLGLLSVAP
   2 .RGKDRQMIQFSSVDYTGVLVINEPALFLQRLAQGFGKSRAFGCGMMMIKP
   3 .RENSRQLIQFSSVDYTGMLTVTDPGLFLQRLSQGYGKSRAFGCGLMLIKP
   4 .RKDQETPITFSSVDFSGALCITDAALFKQALFSGLGKSKALGCGMLMV--
   5 .GNGDKQRIRHNRIRFDGSATITDPDLLRQKITEGIGRGKAYGCGLLSIAP
   6 kGARKGRPVSLVTVTFDGRLEVTDPDALRRALISGIGRAKAYGCGLMTLAP
   7 .FSGDGKSGKIQTVCFEGVLTINDAPALIDLVQQGIGPAKSMGCGLLSLAP
   8 .VKKQGQKIQFSSVDFQGLLTITNGELYLEQYAKGFGRAKAMGCGLMLIR-
   9 .KPKGKHHVSFSTVDIVGTLTVTDPDIFRDALFKGIGPAKGFGCGMLLVRP
  10 .RRKGGAPIVLQRVCFEGLLQVVEADALRRALASGIGPAKAFGCGLLSV--
  11 .KAREKRVGKVQAVSFHGVLSVTDPVGLISLINTGIGPAKAFGCGLLSL--
  12 .SKQGDRTVTHGAARVSGMLRVENRDLFIESFNKGIGRGRAFGFGLLQIEP
  13 .RDTRSGVVSLGIMDLQGTAEVKDPQLLLQALFQGVGPAKGFGCGLLLI--
  14 .TADRSRKIRHPAVRFDGEAVISDVDAVRHAVLNGIGRGKSYGCGLLSLA-
  15 .VPRGGKAITFSVIDYEGVFTVRDPGLLGQALVRGIGKAKAYGCGLMLL--
  16 .LVKSRKSFTSRFVCFEGILQVDKPDQIYSVLVMGIGRKKHAGAGLLSL--
  17 .RGGKAASMTIQIDTVDGFGIVEDPELLNELILHGVGRAKAYGCGLLSV--