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|_1:104 putative cytoplasmic protein [Salmonella typhimurium LT2]
- gi|16421489|gb|AAL21819.1| putative cytoplasmic protein [Salmonella typhimurium LT2]
- gi|16130663|ref|NP_417236.1|_1:99 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|23474688|ref|ZP_00129980.1|_1:98 hypothetical protein [Desulfovibrio desulfuricans G20]
- gi|15803273|ref|NP_289305.1|_1:103 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|23105453|ref|ZP_00091909.1|_1:115 hypothetical protein [Azotobacter vinelandii]
- gi|39996491|ref|NP_952442.1|_1:100 CRISPR-associated protein, CT1974 family [Geobacter sulfurreducens PCA]
- gi|39983372|gb|AAR34765.1| CRISPR-associated protein, CT1974 family [Geobacter sulfurreducens PCA]
- gi|37524751|ref|NP_928095.1|_1:105 hypothetical protein [Photorhabdus luminescens subsp. laumondii TTO1]
- gi|36784176|emb|CAE13045.1| unnamed protein product [Photorhabdus luminescens subsp. laumondii TTO1]
- gi|47104064|ref|YP_015493.1|_2:96 hypothetical protein [Photobacterium profundum SS9]
- gi|46911628|emb|CAG17977.1| hypothetical protein [Photobacterium profundum SS9]
- gi|29834080|ref|NP_828714.1|_3:117 hypothetical protein SAV7538 [Streptomyces avermitilis MA-4680]
- gi|29611205|dbj|BAC75249.1| hypothetical protein [Streptomyces avermitilis MA-4680]
- gi|48763784|ref|ZP_00268338.1|_24:108 hypothetical protein Rrub02003223 [Rhodospirillum rubrum]

              10            20           30           40        50     
              |             |            |            |         |     
   1 MWLTKLVLNPAS....RAARRDLANP...YEMHRTLSKAVSRALE...EGRERLLWRLEP.ARGL
   2 MYLSRITLHTSElspaQLLHLVERGE...YVMHQWLWDLFPGSKE...RQ---FLYRRE-.-ELQ
   3 MYLSKVII----....--ARAWSRDL...YQLHQGLWHLFPNRPD...AARD-FLFHVEK.RNTP
   4 MWMSKLVLDPR-....---RAVGKNL...YDTHRLLWNLFADAPD...RTRD-FLFREQD.----
   5 MYLSRITLHTGQlspaQLLHLVDRGE...YVMHQWLWDLFPGGKE...RQ---FLYRRE-.-ELQ
   6 MYLTRLTLDPRS....AQARRDLADA...YDMHRTLVRAFVRDER...DAPGRFLWRLEPgADAW
   7 MYLSKVLINGT-....-----ACRNP...YEIHRVLWKLFPEDAD...AERD-FLFRVE-.RSGQ
   8 MYLSKIVLRQSSqtanILAKLSANGV...YTSHQLLWKLFSTDEK...RQ---FLFREE-.IGIM
   9 MYISMVAL----....-----SVIDT...YEQHQAIWELFPNSSE...RKRD-HLFRVEN.INTS
  10 VWLTRIVPDPRS....RDARRDLGGNdsaMGLHRRLMSLYPCDAGpdpRARFGVLFRIE-.-DTP
  11 ------------....----RDQGGT...DGGHRLVWTLFADDPK...ASRD-FVFREA-.----


          60        70        80             90       100       110 
          |         |         |              |         |         | 
   1 EPPVVLVQTLTEPDWSVLDEGYAQVF...PPKPFHPA..LKPGQRLRFRLRANPAKRLAATG
   2 GAFRFFVLSQEQPA-----ASAIFDV...QTRPFAPT..LSAGQTLRFNLRANPTVCKNGK-
   3 EGCHVLLQSAQMPV----STAVATVI...KTKQVEFQ..LQVGVPLYFRLRANPIKTILDN-
   4 EPYTFLTVSRRQPE----DTTGWWSI...QIKPYAPK..LQAGDAVAFSLRVNAVVKRNENG
   5 GAFRFFVLSQERPA-----ESETFTI...ECRSFVPE..LRTGQQLCFNLRANPTICKAG--
   6 ASPTLLVQSCESGDWDVLQGLPGYLQrpaECKALDLEalIRPQWRYRFRLLANPTVTRAG--
   7 QSVEVLLQSRREPT--MAASREVLLM...GSKPYLLS..LQQDQQLRFMLVANPIKTINDE-
   8 GLPVFYVLSKTSPQ----TESPLFEV...ETKAFYPQ..LKEGQRLAFKLRVNPTICITD--
   9 GQVMVLLQSASEPQ----SNVKATVL...QSKLFDPQ..ISQGEYYKFKLLANPTKCLSQ--
  10 AGAHILLQSAHEPDLTRLPDGYGQAItr.PLDPLLDA..LKPGLTIRYRCTASPVRKPGA--
  11 EPGRYLIVSARPPG----DGQGLWRL...ETKPYAPA..FREGQRFGFTLRANPATAVKQAG