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:

- T0287 CagS (HP0534), Helicobacter pylori, 199 res
- gi|46091395|dbj|BAD13840.1|_1:199 cag pathogenicity island protein [Helicobacter pylori]
- gi|12229775|sp|Q9ZLU4|CAGS_HELPJ_1:199 CAG pathogenicity island protein 13 [Taxonomy]
- gi|4155031|gb|AAD06070.1| cag island protein [Helicobacter pylori J99]
- gi|15611549|ref|NP_223200.1| cag island protein [Helicobacter pylori J99]
- gi|46091566|dbj|BAD14005.1|_1:199 cag pathogenicity island protein [Helicobacter pylori]
- gi|46091423|dbj|BAD13867.1|_1:199 cag pathogenicity island protein [Helicobacter pylori]
- gi|46091594|dbj|BAD14032.1|_1:199 cag pathogenicity island protein [Helicobacter pylori]
- gi|37811824|gb|AAR03896.1|_1:199 Cag13 [Helicobacter pylori]
- gi|37811892|gb|AAR03957.1|_1:199 Cag13 [Helicobacter pylori]
- gi|8843983|gb|AAF80204.1|_1:199 CagS [Helicobacter pylori]
- gi|46091622|dbj|BAD14059.1|_1:199 cag pathogenicity island protein [Helicobacter pylori]
- gi|46091537|dbj|BAD13977.1|_1:199 cag pathogenicity island protein [Helicobacter pylori]
- gi|46091367|dbj|BAD13813.1|_1:199 cag pathogenicity island protein [Helicobacter pylori]
- gi|46091509|dbj|BAD13950.1|_1:199 cag pathogenicity island protein [Helicobacter pylori]
- gi|46091452|dbj|BAD13895.1|_1:199 cag pathogenicity island protein [Helicobacter pylori]
- gi|46091339|dbj|BAD13786.1| cag pathogenicity island protein [Helicobacter pylori]
- gi|37811793|gb|AAR03868.1|_1:199 Cag13 [Helicobacter pylori]
- gi|37811858|gb|AAR03926.1|_1:199 Cag13 [Helicobacter pylori]
- gi|46091480|dbj|BAD13922.1|_1:199 cag pathogenicity island protein [Helicobacter pylori]
- gi|15645160|ref|NP_207330.1|_1:196 cag pathogenicity island protein (cag13) [Helicobacter pylori 26695]
- gi|2313649|gb|AAD07600.1| cag pathogenicity island protein (cag13) [Helicobacter pylori 26695]
- gi|2498201|sp|P97227|CAGS_HELPY CAG pathogenicity island protein 13 [Taxonomy]

              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 MSNNMRKLFSMIADSKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKGALDKVL
   2 MSNNMRKLFSMIADSKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKGALDKVL
   3 MSNNMRKLFSMIANSKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKGALDKVL
   4 MSNNMRKLFSMIADSKDKKEKLIESLQENELLNPDEKKKIIDQIKTMHDFFKQMHTNKGALDKVL
   5 MSNNMRKLFSMIADSKDKKERLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKGALDKVL
   6 MSNNMRKLFSMIADSKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKGALDKVL
   7 MSNNMRKLFSMIADSKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKGALDKVL
   8 MSNSMRKLFSMIADSKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKGALDKVL
   9 MGNNMRKLFSMIANSKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKGALDKVL
  10 MSNNMRKLFSMIADSKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKGALDKVL
  11 MSNNMRKLFSMIADSKDKKEKLIESLQENELLNTDEKKKIIDQIKTKHDFFKQMHTNKGALDKVL
  12 MSNNMRKLFSMIADSKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKRALDKVL
  13 MSNNMRKLFSMIADSKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKGSLDKVL
  14 MSNNMRKLFSMIADSKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKGALDKVL
  15 MSNNMRKLFSMIADSKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKGALDKVL
  16 MGNNMRKLFSMIANSKDKKEKLIESLQENELLNTDEKEKIIDQIKTMHDFFKQMHTNKGALDKVL
  17 MSNNMRKLFSMIADSKDKKEKLIESLQENELLNTDEKKKIMDQIKTMHDFFKQMHTNKGALDKVL
  18 MSNNMRKLFSMIADSKDKKEKLIESLQENELLSTDEKKKIIDQIKTMHDFFKQMHTNKGALDKVL


         70        80        90       100       110       120       130
         |         |         |         |         |         |         |
   1 RNYMKDYRAVIKSIGVDKFKKVYRLLESETMELLHAIAENPNFLFSKFDRSILGIFLPFFSKPIM
   2 RNYMKDYRAVIKSIGVDKFKKVYRLLESETMELLHAIAENPNFLFSKFDRSILGIFLPFFSKPIM
   3 RNYMKDYRAVIKSIGVDKFKKVYRLLESETMELLHAIAENPNFLFSKFDRSILGIFLPFFSKPIM
   4 RNYMKDYRAVIKSIGVDKFKKVYRLLESETMELLHAIAENPNFLFSKFDRSILGIFLPFFSKPIM
   5 RNYMKDYRAVIKSIGVDKFKKVYQLLESETMELLHAIAKNPNFLFSKFDRSILGIFLPFFSKPIM
   6 RNYMKDYRAVIKSIGVGKFKKVYRLLESETMELLHAIAENPNFLFSKFDRSILGIFLPFFSKPIM
   7 RNYMKDYRAVIKSIGVDKFKKVYQLLESETMELLHAIAKNPNFLFSKFDRSILGIFLPFFSKPVM
   8 RNYMKDYRAVIKSIGVDKFKKVYQLLESETMELLHAIAKNPNFLFSKFDRSILGIFLPFFSKPIM
   9 RNYMKDYRAVIKSIGVDKFKKVYRLLESETMELLHAIAENPNFLFSKFDRSILGIFLPFFSKPIM
  10 RNYMKDYRAVIKSIGVDKFKKVYRLLESETMELLHAIAENPNFLFSKFDRSILGIFLPFFSKPIM
  11 RNYMKDYRAVIKSIGVDKFKKVYQLLESETMELLHAIAKNPNFLFSKFDRSILGIFLPFFSKPIM
  12 RNYMKDYRAVIKSIGVDKFKKVYRLLESETMELLHAIAENPNFLFSKFDRSILGIFLPFFSKPIM
  13 RNYMKDYRAVIKSIGVGKFKKVYRLLESETMELLHAIAENPNFLFSKFDRSILGIFLPFFSKPIM
  14 RNYMKDYRAVIKSIGVDKFKKVYRLLESETMELLHAITENPNFLFSKFDRSILGIFLPFFSKPIM
  15 RNYMKDYRAVIKSIGVDKFKKVYRLLESETMELLHAITENPNFLFSKFDRSILGIFLPFFSKPIM
  16 RNYMKDYRAVIKSIGVDKFKKVYQLLESETMELLHAIAESPNFLFSKFDRSILGIFLPFFSKPIM
  17 RNYMKDYRAVIKSIGIDKFKKVYRLLENETMELLHAIAKNPNFLFSKFDRSILGIFLPFFSKPIM
  18 RNYMKDYRAVIKSIGVDKFKKVYRLLESETMELLHAIAENPNFLFSKFDRSILGIFLPFFSKPIM


             140       150       160       170       180       190     
              |         |         |         |         |         |     
   1 FKMSIREMDSQIELYGTNLPLLKLFVMTDEEVNFYANLKTIEQYNDYVRDLLMKFDLEKYMKEKG
   2 FKMSIREMDSQIELYGTKLPLLKLFVMTDEEVNFYANLKTIEQYNDYVRDLLMKFDLEKYMKEKG
   3 FKMSIREMDSQIELYGTKLPPLKLFVMTDEEVNFYANLKTIEQYNDYVRDLLMKFDLEKYMEEKG
   4 FKMSIREMDSQIELYGTKLPLLKLFVMTDEEVNFYANLKTIEQYNDYVRDLLMKFDLEKYMKEKG
   5 FKMSIREMDSQIELYGTKLPLLKLFVMTDEEVNFYANLKTIEQYNDYVRDLLMKFDLEKYMKEKG
   6 FKMSIREMDSQIELYGTKLPLLKLFVMTDEEVNFYANLKTIEQYNDYVRDLLMKFDLEKYMEEKG
   7 FKMSIREMDSQIELYGTKLPLLKLFVMTDEEVNFYANLKTIEQYNDYVRDLLMKFDLEKYMKEKG
   8 FKMSIREMDSQIELYGTKLPLLKLFVMTDEEVNFYANLKTIEQYNDYVRDLLMKFDLEKYMKEKG
   9 FKMSIREMDSQIELYGTKLPLLKLFVMTDEEMNFYANLKTIEQYNDYVRDLLMKFDLEKYMEEKG
  10 FKMSIREMDSQIELYGTNLPLLKLFVMTDEEVNFYANLKTIEQYNDYVRDLLMKFDLEKYMKEKG
  11 FKMSIREMDSQIELYGTKLPLLKLFVMTDEEVNFYANLKTIEQYNDYVRDLLMKFDLEKYMKEKG
  12 FKMSIREMDSQIELYGTKLPLLKLFVMTDEEVNFYANLKTIEQYNDYVRDLLMKFDLEKYMKEKG
  13 FKMSIREMDSQIELYGTKLPLLKLFVMTDEEVNFYANLKTIEQYNDYVRDLLMKFDLEKYMKEKG
  14 FKMSIREMDSQIELYGTKLPLLKLFVMTDEEVNFYANLKTIEQYNDYVRDLLMKFDLEKYMKEKG
  15 FKMSIREMDSQIELYGTKLPLLKLFVMTDEEMNFYANLKTIEQYNDYVRDLLMKFDLEKYMKEKG
  16 FKMSIREMDSQIELYGTKLPLLKLFVMTDEEMNFYANLKTIEQYNDYVRDLLMKFDLEKYMKEKG
  17 FKMSIREMDSQIELYDTKLPLLKLFVMTDEEVNFYANLKTIEQYNDYVRDLLMKFDLEKYMEEKG
  18 FKMSIREMDSQIELYGTKLPLLKLFVMTDEEMNFYANLKTIEQYNDYVRDLLMKFDLEKYMKEKG


          
         
   1 VQNA
   2 VQNA
   3 VQNA
   4 VQNA
   5 VQNA
   6 VQNA
   7 VQNA
   8 VQNA
   9 VQNA
  10 VQNA
  11 VQNA
  12 VQNA
  13 VQNA
  14 VQNA
  15 VQNA
  16 VQNA
  17 VQNA
  18 V---