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:

- T0561
- gi|154333008|ref|XP_001562766.1|_401:561 DNA J-binding protein [Leishmania braziliensis MHOM/BR/75/M2904]
- gi|239977116|sp|A4H5X5|JBP1_LEIBR RecName: Full=Thymine dioxygenase JBP1; AltName: Full=J-binding protein 1 [Taxonomy]
- gi|134059769|emb|CAM41892.1| DNA J-binding protein, putative [Leishmania braziliensis]
- gi|74827815|sp|Q9U6M1|JBP1_LEITA_400:561 RecName: Full=Thymine dioxygenase JBP1; AltName: Full=J-binding protein 1 [Taxonomy]
- gi|6018045|gb|AAF01743.1|AF182401_1 J-binding protein [Leishmania tarentolae]
- gi|62361410|gb|AAX81332.1| J-binding protein 1 [Leishmania tarentolae]
- gi|157865226|ref|XP_001681321.1|_400:561 DNA J-binding protein [Leishmania major strain Friedlin]
- gi|75036167|sp|Q4QHM7|JBP1_LEIMA RecName: Full=Thymine dioxygenase JBP1; AltName: Full=J-binding protein 1 [Taxonomy]
- gi|68124616|emb|CAJ03108.1| DNA J-binding protein, putative [Leishmania major]
- gi|146078722|ref|XP_001463611.1|_400:561 DNA J-binding protein [Leishmania infantum JPCM5]
- gi|239977115|sp|A4HU70|JBP1_LEIIN RecName: Full=Thymine dioxygenase JBP1; AltName: Full=J-binding protein 1 [Taxonomy]
- gi|134067697|emb|CAM65977.1| DNA J-binding protein, putative [Leishmania infantum]
- gi|74025708|ref|XP_829420.1|_423:582 chaperone protein DnaJ [Trypanosoma brucei TREU927]
- gi|239977343|sp|Q9U6M3|JBP1_TRYBB RecName: Full=Thymine dioxygenase JBP1; AltName: Full=J-binding protein 1 [Taxonomy]
- gi|70834806|gb|EAN80308.1| J-binding protein [Trypanosoma brucei]
- gi|6018041|gb|AAF01741.1|AF182399_1_423:582 J-binding protein [Trypanosoma brucei]
- gi|261335410|emb|CBH18404.1| j-binding protein, putative [Trypanosoma brucei gambiense DAL972]
- gi|71421637|ref|XP_811851.1|_418:576 DnaJ chaperone protein [Trypanosoma cruzi strain CL Brener]
- gi|122021227|sp|Q4DBW3|JBP1A_TRYCR RecName: Full=Thymine dioxygenase JBP1-A; AltName: Full=J-binding protein 1A [Taxonomy]
- gi|70876562|gb|EAN90000.1| DnaJ chaperone protein, putative [Trypanosoma cruzi]
- gi|71653481|ref|XP_815377.1|_418:576 DnaJ chaperone protein [Trypanosoma cruzi strain CL Brener]
- gi|122024075|sp|Q4DLX9|JBP1B_TRYCR RecName: Full=Thymine dioxygenase JBP1-B; AltName: Full=J-binding protein 1B [Taxonomy]
- gi|70880428|gb|EAN93526.1| DnaJ chaperone protein, putative [Trypanosoma cruzi]
- gi|74827816|sp|Q9U6M2|JBP1_CRIFA_400:559 RecName: Full=Thymine dioxygenase JBP1; AltName: Full=J-binding protein 1 [Taxonomy]
- gi|6018043|gb|AAF01742.1|AF182400_1 J-binding protein [Crithidia fasciculata]

              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 VEKKKYLDSEFLLHCISAQLLDMWKQARARWLELVGKEWAHMLALNPERKDFLWKNQSEMNSAFF
   2 -EKRKYLDSEFLSHCISAQLLDMWKQARARWLELVGKEWKHMLTLNPERKDFLWKNRSEMNSAFF
   3 VEKKKYLDSEFLLHCISAQLLDMWKQARARWLELVGKEWAHMLALNPERKDFLWKNQSEMNSAFF
   4 VEKKKYLNSEFLSHFISAQLLDMWKQARGKWLELVGREWTHMLALNPERKDFLWKNQSEMNSAFF
   5 VEKKKYLNSEFLSHFISAQLLDMWKQARGKWLELVGREWTHMLALNPERKDFLWRNQSEMNSAFF
   6 MNKRHYLDKENLQKMFGEEFVNIWTQSRTHWLQLVKKEWEHQKETNPTRTRFSWNNTSAMNFAFF
   7 MNKRHYLDKENLQKMFGEEFVNIWTQSRTHWLQLVKKEWEHQKETNPTRTRFSWNNTSAMNFAFF
   8 -EKQYFFEEKYLADELGPDLMSMWTQSRAHWLRLVKEDWERLCRRDPERTKFTWNNSSAMNAAFF
   9 -EKQYFFEEKYLADELGPDLMSMWTQSRAHWLRLVKEDWERLCRRDPERTKFTWNNSSAMNAAFF
  10 VEKSKYLERDHLSQCISAELLAMWVEARKHWLRLVATEWARMIATAPERTDFLWKNKSPMNTAFF


         70        80        90       100       110        120       13
         |         |         |         |         |          |         
   1 DLCEVGKQVMLGLLGKEVALPKEEQAFWIMYAVHLSAACAEELHMEV.AMSLRKLNVKLKDFNFG
   2 DLCEVGKQVMLGLLDKEAALPKEEQAFWTMYAVHLSAACAEELHMPHdAMSLRKLNVKLKDFNFG
   3 DLCEVGKQVMLGLLGKEVALPKEEQAFWIMYAVHLSAACAEELHMPEvAMSLRKLNVKLKDFNFG
   4 DLCEVGKQVMLGLLGKEVALPKEEQAFWTMYAVHLNAACAEELHMPHvAMSLRKLNVKLKDFNFG
   5 DLCEVGKQVMLGLLGKEAALPKEEQAFWTMYAVHLNAACAEELNMPHvAMSLRKLNVKLKDFNFG
   6 DLCDVAKQLMCGAFGDREVNKKEEQSFWGMFAAHLDNACINEIGMLQgSMGMHKLNVKLKDYNFG
   7 DLCDVAKQLMCGAFGDREVNKKEEQSFWGMFAAHLDNACINEIGMLQgSMGMHKLNVKLKDYNFG
   8 DLCEVAKQMMIGLLNKETPSSAENHSFWILFAAHLNYACTTENGMPRdAVGMHKLNVKLKDFHFG
   9 DLCEVAKQMMIGLLNKETPSSAENHSFWILFAAHLNYACTTENGMPRdAVGMHKLNVKLKDFHFG
  10 DLCEVAKQVMLGLLDKETATPTEERHFWSVYAAHLHRACAERLMMPEeAMSLRKLNVKLKDFSFG


      0       140       150       160 
     |         |         |         | 
   1 GTRYFKDMPPEEKKRRMERKQRIEEARRHGMP
   2 GTRYFKDMPPEEQQRRMERKQRIEEARRHGMT
   3 GTRYFKDMPPEEKKRRMERKQRIEEARRHGMP
   4 GTRYFKDMPPEEQKRRMERKQRIEEARRHGMS
   5 GTRYFKDMPPEEQKRRMERKQRIEEARRHGMS
   6 GTRYLKDMPPEEQERRRRRRLEIEQARRRA--
   7 GTRYLKDMPPEEQERRRRRRLEIEQARRRA--
   8 GTRYLKDMPPEEQERRLERKKRIEEARRRG--
   9 GTRYLKDMPPEEQERRLERKKRIEEARRRG--
  10 GTRYFKDMPVEEQERRVARKASIEEARRRS--