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:

- T0379 PG0725, Porphyromonas gingivalis W83, 208 res
- gi|29339854|gb|AAO77649.1|_19:90 putative haloacid dehalogenase-like hydrolase [Bacteroides thetaiotaomicron VPI-5482]
- gi|29347952|ref|NP_811455.1| putative haloacid dehalogenase-like hydrolase [Bacteroides thetaiotaomicron VPI-5482]
- gi|60495004|emb|CAH09822.1|_19:90 putative haloacid dehalogenase-type hydrolase [Bacteroides fragilis NCTC 9343]
- gi|52218492|dbj|BAD51085.1| putative haloacid dehalogenase-like hydrolase [Bacteroides fragilis YCH46]
- gi|53715627|ref|YP_101619.1| putative haloacid dehalogenase-like hydrolase [Bacteroides fragilis YCH46]
- gi|60683570|ref|YP_213714.1| putative haloacid dehalogenase-type hydrolase [Bacteroides fragilis NCTC 9343]
- gi|56750549|ref|YP_171250.1|_20:91 hypothetical protein syc0540_c [Synechococcus elongatus PCC 6301]
- gi|81299814|ref|YP_400022.1| HAD-superfamily hydrolase subfamily IA, variant 3 [Synechococcus elongatus PCC 7942]
- gi|56685508|dbj|BAD78730.1| unknown protein [Synechococcus elongatus PCC 6301]
- gi|81168695|gb|ABB57035.1| HAD-superfamily hydrolase subfamily IA, variant 3 [Synechococcus elongatus PCC 7942]
- gi|34540517|ref|NP_904996.1|_15:86 hydrolase, haloacid dehalogenase-like family [Porphyromonas gingivalis W83]
- gi|34396830|gb|AAQ65895.1| hydrolase, haloacid dehalogenase-like family [Porphyromonas gingivalis W83]
- gi|62463546|ref|ZP_00382870.1|_16:87 COG1011: Predicted hydrolase (HAD superfamily) [Lactococcus lactis subsp. cremoris SK11]
- gi|67940717|ref|ZP_00533074.1|_40:111 HAD-superfamily hydrolase, subfamily IA, variant 3:HAD-superfamily hydrolase, subfamily IA, variant 1 [Chlorobium phaeobacteroides BS1]
- gi|67913071|gb|EAM62562.1| HAD-superfamily hydrolase, subfamily IA, variant 3:HAD-superfamily hydrolase, subfamily IA, variant 1 [Chlorobium phaeobacteroides BS1]
- gi|29338275|gb|AAO76077.1|_15:86 haloacid dehalogenase-like hydrolase [Bacteroides thetaiotaomicron VPI-5482]
- gi|29346380|ref|NP_809883.1| haloacid dehalogenase-like hydrolase [Bacteroides thetaiotaomicron VPI-5482]

              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 HLNREESIRRFKAIGVADIEEMLDPYLQKGLFLDLESGRKSEEEFRTELSRYIGKELTYQQVYDA
   2 NLDRERCIENFKKIGFQNIEEKFCTHQLDGIFLQQEKGLITPAEFRDGIREMMGKMVSDKQIDAA
   3 NLDRQRCIENFRKLGLEKVDELLGMYSQQGIFMQHEKGLISSAQFRDSIRGQITQEVTDEQIDAA
   4 DLDYQSTRRAFEELCGCDWHALYSQQQQTALFDDFETGRIDPATFRDSLRQLLGQDLSDRAIDTA
   5 HLNREESIRRFKAIGVADIEEMLDPYLQKGLFLDLESGRKSEEEFRTELSRYIGKELTYQQVYDA
   6 DLGFTRMINSFEQLGVKDFSSYFNPQKQVDFFEELELGLISPDVFYDEFRKATKSQLTDEVIEEN
   7 DIDPQLTFNEFVNLGFKNPEKLMGPEFMEDLAAKFERGILTPEVFRTKLREFLQIDATDQQIDDA
   8 DIDRDKAVQAFIKLGLADADTRLDKYHQTGIFQELEEGKLSADEFRKQLGDLCGRELTMEETKQA


         70  
         |  
   1 LLGFLEE
   2 WNSFLVD
   3 WNSFLVD
   4 WNAMLGG
   5 LLGFLEE
   6 WNLILKD
   7 WNALLFD
   8 WLGFFNE