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:

- T0407
- gi|150006007|ref|YP_001300751.1|_241:363 hypothetical protein BVU_3505 [Bacteroides vulgatus ATCC 8482]
- gi|149934431|gb|ABR41129.1| conserved hypothetical protein [Bacteroides vulgatus ATCC 8482]
- gi|29347939|ref|NP_811442.1|_234:356 hypothetical protein BT_2529 [Bacteroides thetaiotaomicron VPI-5482]
- gi|29339841|gb|AAO77636.1| conserved hypothetical protein [Bacteroides thetaiotaomicron VPI-5482]
- gi|88714279|ref|ZP_01108354.1|_252:374 hypothetical protein FB2170_01936 [Flavobacteriales bacterium HTCC2170]
- gi|88707436|gb|EAQ99681.1| hypothetical protein FB2170_01936 [Flavobacteriales bacterium HTCC2170]
- gi|88805944|ref|ZP_01121462.1|_244:366 hypothetical protein RB2501_10377 [Robiginitalea biformata HTCC2501]
- gi|88783553|gb|EAR14724.1| hypothetical protein RB2501_10377 [Robiginitalea biformata HTCC2501]
- gi|182416382|ref|YP_001821448.1|_252:374 PHP domain protein [Opitutus terrae PB90-1]
- gi|177843596|gb|ACB77848.1| PHP domain protein [Opitutus terrae PB90-1]
- gi|119476864|ref|ZP_01617145.1|_295:416 hypothetical protein GP2143_09937 [marine gamma proteobacterium HTCC2143]
- gi|119449671|gb|EAW30908.1| hypothetical protein GP2143_09937 [marine gamma proteobacterium HTCC2143]
- gi|154493744|ref|ZP_02033064.1|_259:359 hypothetical protein PARMER_03085 [Parabacteroides merdae ATCC 43184]
- gi|154086494|gb|EDN85539.1| hypothetical protein PARMER_03085 [Parabacteroides merdae ATCC 43184]
- gi|29345441|ref|NP_808944.1|_252:315 hypothetical protein BT_0031 [Bacteroides thetaiotaomicron VPI-5482]
- gi|29337333|gb|AAO75138.1| Polymerase and histidinol phosphatase [Bacteroides thetaiotaomicron VPI-5482]

              10         20        30        40        50        60    
              |          |         |         |         |         |    
   1 RSLQGIREALDNRRTAAY.FHELLIGREDLLRPFFEKCVKIEEVSRNEQGVTLSITNVTDLVLKL
   2 RSLQGIREALDNRRTAAY.FHELLIGREDLLRPFFEKCVKIEEVSRNEQGVTLSITNVTDLVLKL
   3 RSPEGIREALDNRRTAVY.YRELVIGREEILRPFFEKCVDIKEVKRTEKEVTFSVMNATDLVLKL
   4 KSLKSMKEALFEGRTVAV.YNDLLVGKPEYLNPLLKESIVIESAKYLSKTNVLKVELKNISSSDL
   5 RSIESLREALFAGRTVAV.YKDLLVGREEYLVPLLRASVEIVSASYIPKTQILKVELKNTSSTDL
   6 RSEAALKEALLARRTAVW.FTNTLVGRAEWLDPLLAASLQLTSSRYLPDTSVLELVITNRSDADF
   7 -TADSLREALFEHRTLVW.FNNLLLGRDAEMQELLTAALTVTAANYSGEKNLLNFDIENSSDVDF
   8 -TPESIKEALYAGRSIAY.ADQKLAGKENMLKLFLRSSLKVL--SYEERNGKFHVRLLNESDIPY
   9 RSLDAMRDALENRRTIGYgAGGTLMGQEYLLRQLFMSCVSISPVNGH------NIQLKNPTSLRF


          70          80        90       100       110       120   
          |           |         |         |         |         |   
   1 KKTAHDTLLV..YFRDMTLKPHTRYTVRIGFKQGIKGGDVNFEVTNFIVAPDKGLKYTISL
   2 KKTAHDTLLV..YFRDMTLKPHTRYTVRIGFKQGIKGGDVNFEVTNFIVAPDKGLKYTISL
   3 KKTAHDPSLV..YFREMTLKPHTQHTISVKFDNGIKGGDCNFEVTNFIVAPDKGLDYTIKL
   4 LFENQMDFNF..YDSSPVFEVEAGRTKTVHIKTIEKLTSVQLKLKALGAFTAPKQQPVVEW
   5 LFENAMPYSF..YSSSPVFRIPAGGNYTLQIKTLEKSETIQLALKALGAFTAPGVQPVVNW
   6 ILRNASSYRL..HLHADVLEAKAHQQLKILVKPIQRSPRVVVAFEVLNAVTAPGVHPTIAF
   7 QLYNNSPFTFskNPNQVTIKQHAKTTLVLRTPTRLSAIDLPFSVLNALIAPGQPAQLTL--
   8 LLDNGV----..LS--DRIRIPAHA--VCDMTRPLSQLTQPFRVTNMYIS-----------
   9 IIHPD-----..-------------------------------------------------