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|_219:363 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|_212:356 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|_231:376 hypothetical protein FB2170_01936 [Flavobacteriales bacterium HTCC2170]
- gi|88707436|gb|EAQ99681.1| hypothetical protein FB2170_01936 [Flavobacteriales bacterium HTCC2170]
- gi|119476864|ref|ZP_01617145.1|_272:416 hypothetical protein GP2143_09937 [marine gamma proteobacterium HTCC2143]
- gi|119449671|gb|EAW30908.1| hypothetical protein GP2143_09937 [marine gamma proteobacterium HTCC2143]
- gi|88805944|ref|ZP_01121462.1|_223:368 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|_230:373 PHP domain protein [Opitutus terrae PB90-1]
- gi|177843596|gb|ACB77848.1| PHP domain protein [Opitutus terrae PB90-1]
- gi|154493744|ref|ZP_02033064.1|_245:369 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|_232:352 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 IQTDYDFEKGEHRTMTFVFAKERSLQGIREALDNRRTAAY.FHELLIGREDLLRPFFEKCVKIE.
   2 IQTDYDFEKGEHRTMTFVFAKERSLQGIREALDNRRTAAY.FHELLIGREDLLRPFFEKCVKIE.
   3 IQTDYDFSKGEHRTMTFVFAKERSPEGIREALDNRRTAVY.YRELVIGREEILRPFFEKCVDIK.
   4 -IDWDYTEKGNHRPITLVFAKEKSLKSMKEALFEGRTVAV.YNDLLVGKPEYLNPLLKESIVIE.
   5 IDWDYKPHEGGHRPVTLVLAENATADSLREALFEHRTLVW.FNNLLLGRDAEMQELLTAALTVTa
   6 -IDWDYTEKGHHRPVTLVFARERSIESLREALFAGRTVAV.YKDLLVGREEYLVPLLRASVEIV.
   7 IDWAHDVPAGGHRPVTLVFAQERSEAALKEALLARRTAVW.FTNTLVGRAEWLDPLLAASLQLT.
   8 ---------KKFRTLTFVFAKENTPESIKEALYAGRSIAY.ADQKLAGKENMLKLFLRSSLKVL.
   9 --FEEYIGRGLRRDMTIILAKDRSLDAMRDALENRRTIGYgAGGTLMGQEYLLRQLFMSCVSIS.


              70        80        90       100       110       120     
              |         |         |         |         |         |     
   1 .E..VSRNEQGVTLSITNVTDLVLKLKKTAHDTLLVYFRDMTLKPHTRYTVRIGFKQGIKGGDVN
   2 .E..VSRNEQGVTLSITNVTDLVLKLKKTAHDTLLVYFRDMTLKPHTRYTVRIGFKQGIKGGDVN
   3 .E..VKRTEKEVTFSVMNATDLVLKLKKTAHDPSLVYFREMTLKPHTQHTISVKFDNGIKGGDCN
   4 .SakYLSKTNVLKVELKNISSSDLLFENQMDFNFYDSSPVFEVEAGRTKTVHIKTIEKLTSVQLK
   5 aN..YSGEKNLLNFDIENSSDVDFQLYNNSPFTFSKNPNQVTIKQHAKTTLVLRTPTRLSAIDLP
   6 .SasYIPKTQILKVELKNTSSTDLLFENAMPYSFYSSSPVFRIPAGGNYTLQIKTLEKSETIQLA
   7 .SsrYLPDTSVLELVITNRSDADFILRNASSYRLHLHADVLEAKAHQQLKILVKPIQRSPRVVVA
   8 .S..YEERNGKFHVRLLNESDIPYLLDNGVLSDRIRIP----------AHAVCDMTRPLSQLTQP
   9 .P..V----NGHNIQLKNPTSLRFIIHPDGKNPIVLPEFSSIILSDKDRGFSVDNAWTGADSFLR


        130       140     
         |         |     
   1 FEVTNFIVAPDKGLKYTISL
   2 FEVTNFIVAPDKGLKYTISL
   3 FEVTNFIVAPDKGLDYTIKL
   4 LKALGAFTAPKQQPVVEWKI
   5 FSVLNALIAPGQPAQLTL--
   6 LKALGAFTAPGVQPVVNWDI
   7 FEVLNAVTAPGVHPTIA---
   8 FRVTNMYISSTERLEIPVS-
   9 I-------------------