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:

- T0254 AAF93879, Vibrio cholerae O1 biovar eltor str. N16961
- gi|42522456|ref|NP_967836.1|_5:113 conserved hypothetical protein [Bdellovibrio bacteriovorus HD100]
- gi|39574988|emb|CAE78829.1| conserved hypothetical protein [Bdellovibrio bacteriovorus HD100]
- gi|15640733|ref|NP_230363.1|_1:107 hypothetical protein VC0714 [Vibrio cholerae O1 biovar eltor str. N16961]
- gi|11345665|pir||C82288 hypothetical protein VC0714 [imported] - Vibrio cholerae (strain N16961 serogroup O1) [Taxonomy]
- gi|9655157|gb|AAF93879.1| hypothetical protein [Vibrio cholerae O1 biovar eltor str. N16961]
- gi|46914488|emb|CAG21267.1|_20:130 conserved hypothetical protein [Photobacterium profundum]
- gi|28897337|ref|NP_796942.1|_1:110 conserved hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]
- gi|28805546|dbj|BAC58826.1| conserved hypothetical protein [Vibrio parahaemolyticus]
- gi|19704072|ref|NP_603634.1|_1:109 Hypothetical protein [Fusobacterium nucleatum subsp. nucleatum ATCC 25586]
- gi|19714272|gb|AAL94933.1| Hypothetical protein [Fusobacterium nucleatum subsp. nucleatum ATCC 25586]
- gi|34763474|ref|ZP_00144419.1|_1:109 hypothetical protein [Fusobacterium nucleatum subsp. vincentii ATCC 49256]
- gi|27886865|gb|EAA23992.1| hypothetical protein [Fusobacterium nucleatum subsp. vincentii ATCC 49256]
- gi|24373938|ref|NP_717981.1|_1:109 conserved hypothetical protein [Shewanella oneidensis MR-1]
- gi|24348369|gb|AAN55425.1| conserved hypothetical protein [Shewanella oneidensis MR-1]
- gi|30019177|ref|NP_830808.1|_1:107 hypothetical protein [Bacillus cereus ATCC 14579]
- gi|29894720|gb|AAP08009.1| hypothetical protein [Bacillus cereus ATCC 14579]
- gi|49477840|ref|YP_036822.1|_1:107 conserved hypothetical protein [Bacillus thuringiensis serovar konkukian str. 97-27]
- gi|49329396|gb|AAT60042.1| conserved hypothetical protein [Bacillus thuringiensis serovar konkukian str. 97-27]
- gi|47564350|ref|ZP_00235395.1|_24:130 conserved hypothetical protein protein [Bacillus cereus G9241]
- gi|47558502|gb|EAL16825.1| conserved hypothetical protein protein [Bacillus cereus G9241]
- gi|48844224|ref|ZP_00298549.1|_15:114 hypothetical protein Gmet02003277 [Geobacter metallireducens GS-15]
- gi|50364843|ref|YP_053268.1|_1:101 unknown protein [Mesoplasma florum L1]
- gi|50363399|gb|AAT75384.1| unknown protein [Mesoplasma florum L1]

              10        20        30        40        50           60  
              |         |         |         |         |            |  
   1 MPHLRFRAVEAHIVESLVPTLLNELSSLLSTARNAFTFELINTQYFAEGGV...YPMVEVLWFGR
   2 MPHIRMRAVKKEHVQLLSDSLAKELAPAMKTPVDNFTFELVQTQFFSGGQQtdsYPFIEVLWFAR
   3 MPHLRFRAVEAHIVESLVPTLLNELSSLLSTARNAFTFELINTQYFAEGGV...YPMVEVLWFGR
   4 MPHLRFRAVEFDTVKVLSTALVDDLQPLMACPREDITLEHIPASFIFDGEVsdaYPFVEVLWFDR
   5 MPHLRFRAVEPQAVQALSKPLTDELQPLMNSPREDFTFEYIYTTFFSEGEVspaYPFVEVLWFDR
   6 MPHLKIRGIEKNLIVENSKEIIDELTKIIGCDRNWFTIEHQNTKYIFDGKIvdgYTFVELYWFAR
   7 MPHLKIRGIEKNLIVENSKEIIDELTKIIGCDRNWFTIEHQNTEYIFDGKIvdgYTFVELYWFAR
   8 MPHISMRGLPQAVVAELSQTLLQSLAAICKGKAESFTLDWIPSISYRNGRIdqrFVQIELLWFPV
   9 MPHIVFRGITTEQLKHISKPLVEELAEICECGTDNFTLELPSSTFVFNGEEieaFPLIEVKWFER
  10 MPHVVFRGITTEQLKHISKPLVEELAEICECGTDNFTLELPSSTFVFNGEEieaFPLIEVKWFER
  11 MPHVVFRGITTEQLKSISKPLVEELADICECGTDNFTLELPSSTFVFNGEEieaFPLIEVKWFKR
  12 MPYLRFKGFDEGFLRKLGPLVVEEFSRVAVVPPEVVKIELLNIVQITATPRs..---LEIFIFPR
  13 MPILKFNGTTEEKVKEYSKKI-NEIADLIVSKPEAILMMVNNNNIFVAKNTnk.RIYVEVDWLKR


            70        80         90       100       
            |         |          |         |       
   1 EQQTQDQIAQVITDQIRQLL.GADSHLAVVFIPLQRTAYYLDGQHF
   2 SQEVQDECASIITRQIKSI-.ADYEDVVIVFQVLAKEAYYENGIHF
   3 EQQTQDQIAQVITDQIRQLL.GADSHLAVVFIPLQRTAYYLDGQHF
   4 GQVIQDQVANIITLAIRSALqDNEQDVAVIFSSLTPSAYYDNGEHY
   5 GQETQDKVAKVITQQVRGVV.GEDIDVAVIFSALSPNAYYDNGEHY
   6 DEKIKKEVADFLTKFIKKI-.NNNKDCCIIFFTLTGDNYCDNGEFF
   7 DEKIKKEVADFLTKFIKKI-.NNNKDCCIIFFTLTGNNYCDNGEFF
   8 DPDIHLKVEQTIRLAVTEAY.PELTQIAVMFLSLTPSASYRGGQH-
   9 GQEIRNRFAKAITTYVMDF-.-GLPEVEVVFTVFTESAYYINGKH-
  10 GQEIRDRFAKAITTYVMDF-.-GLPEVEVVFTVFTESAYYINGKH-
  11 GQEIRDRFAKAITTYVMDF-.-GLPEVEVVFTVFTESAYYINGKH-
  12 DQKKHDAIAATLAGILGRY-.-GYDDVHIFFVLLSPSLYYKEG---
  13 SEESRVLLVQHLTNFFGNQ-.--GVNVSVKFTEINNDLYVNN----