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:

- T0236 N-RsbU, Bacillus subtilis
- gi|2660752|gb|AAC29507.1|_1:110 putative sigma-B regulator [Bacillus licheniformis]
- gi|16077537|ref|NP_388351.1|_1:110 serine phosphatase (dephosphorylation of RsbV) [Bacillus subtilis]
- gi|2851675|sp|P40399|RSBU_BACSU Phosphoserine phosphatase rsbU (Sigma factor sigB regulation protein rsbU) [Taxonomy]
- gi|7475789|pir||H69701 regulator of sigma-B activity rsbU - Bacillus subtilis [Taxonomy]
- gi|1146194|gb|AAA85083.1| sigma-B regulator [Taxonomy]
- gi|1881280|dbj|BAA19307.1| SIGMA FACTOR SIGB REGULATION PROTEIN RSBU [Bacillus subtilis]
- gi|2632770|emb|CAB12277.1| serine phosphatase [Bacillus subtilis subsp. subtilis str. 168]
- gi|16802933|ref|NP_464418.1|_2:108 highly similar to serine phosphatase RsbU [Listeria monocytogenes EGD-e]
- gi|25514867|pir||AD1186 serine phosphatase RsbU homolog rsbU [imported] - Listeria monocytogenes (strain EGD-e) [Taxonomy]
- gi|16410295|emb|CAC98970.1| rsbU [Listeria monocytogenes]
- gi|47094899|ref|ZP_00232513.1|_2:108 sigma factor B regulator protein [Listeria monocytogenes str. 1/2a F6854]
- gi|47016781|gb|EAL07700.1| sigma factor B regulator protein [Listeria monocytogenes str. 1/2a F6854]
- gi|46907124|ref|YP_013513.1|_2:108 sigma factor B regulator protein [Listeria monocytogenes str. 4b F2365]
- gi|47092100|ref|ZP_00229893.1| sigma factor B regulator protein [Listeria monocytogenes str. 4b H7858]
- gi|46880391|gb|AAT03690.1| sigma factor B regulator protein [Listeria monocytogenes str. 4b F2365]
- gi|47019540|gb|EAL10280.1| sigma factor B regulator protein [Listeria monocytogenes str. 4b H7858]
- gi|26000669|gb|AAN75461.1|_2:108 RsbU [Listeria monocytogenes]
- gi|16799964|ref|NP_470232.1|_2:108 highly similar to serine phosphatase RsbU [Listeria innocua Clip11262]
- gi|25514606|pir||AC1544 serine phosphatase RsbU homolog rsbU [imported] - Listeria innocua (strain Clip11262) [Taxonomy]
- gi|16413341|emb|CAC96123.1| rsbU [Listeria innocua]
- gi|37781581|gb|AAP42790.1|_3:107 RsbU [Staphylococcus aureus]
- gi|1729794|emb|CAA71065.1|_3:107 rsbU [Staphylococcus aureus]
- gi|37781595|gb|AAP42801.1|_3:107 RsbU [Staphylococcus aureus]
- gi|37781590|gb|AAP42797.1|_3:107 RsbU [Staphylococcus aureus]
- gi|15925057|ref|NP_372591.1|_3:107 sigmaB regulation protein [Staphylococcus aureus subsp. aureus Mu50]
- gi|15927642|ref|NP_375175.1| sigmaB regulation protein RsbU [Staphylococcus aureus subsp. aureus N315]
- gi|21283720|ref|NP_646808.1| sigmaB regulation protein RsbU [Staphylococcus aureus subsp. aureus MW2]
- gi|49484293|ref|YP_041517.1| putative sigma factor sigB regulation protein [Staphylococcus aureus subsp. aureus MRSA252]
- gi|49486861|ref|YP_044082.1| putative sigma factor sigB regulation protein [Staphylococcus aureus subsp. aureus MSSA476]
- gi|25506003|pir||A89999 sigmaB regulation protein RsbU [imported] - Staphylococcus aureus (strain N315) [Taxonomy]
- gi|13701862|dbj|BAB43154.1| sigmaB regulation protein RsbU [Staphylococcus aureus subsp. aureus N315]
- gi|14247840|dbj|BAB58229.1| sigmaB regulation protein [Staphylococcus aureus subsp. aureus Mu50]
- gi|21205162|dbj|BAB95856.1| sigmaB regulation protein RsbU [Staphylococcus aureus subsp. aureus MW2]
- gi|49242422|emb|CAG41136.1| putative sigma factor sigB regulation protein [Staphylococcus aureus subsp. aureus MRSA252]
- gi|49245304|emb|CAG43779.1| putative sigma factor sigB regulation protein [Staphylococcus aureus subsp. aureus MSSA476]
- gi|37781585|gb|AAP42793.1|_3:107 RsbU [Staphylococcus aureus]
- gi|15613089|ref|NP_241392.1|_5:111 indirect positive regulator of sigma-B activity (serine phosphatase) [Bacillus halodurans C-125]
- gi|25493121|pir||F83715 indirect positive regulator of sigma-B activity (serine phosphatase) rsbU [imported] - Bacillus halodurans (strain C-125) [Taxonomy]
- gi|10173139|dbj|BAB04245.1| indirect positive regulator of sigma-B activity (serine phosphatase) [Bacillus halodurans C-125]
- gi|23098082|ref|NP_691548.1|_5:111 indirect positive regulator of sigma-B activity [Oceanobacillus iheyensis HTE831]
- gi|22776307|dbj|BAC12583.1| indirect positive regulator of sigma-B activity (serine phosphatase) [Oceanobacillus iheyensis HTE831]
- gi|27468589|ref|NP_765226.1|_3:107 sigmaB regulation protein RsbU [Staphylococcus epidermidis ATCC 12228]
- gi|17226796|gb|AAL37940.1| RsbU [Staphylococcus epidermidis]
- gi|27316136|gb|AAO05270.1| sigmaB regulation protein RsbU [Staphylococcus epidermidis ATCC 12228]
- gi|10834756|gb|AAG23810.1|_3:107 RsbU [Staphylococcus epidermidis]
- gi|49236074|ref|ZP_00330136.1|_3:97 COG2199: FOG: GGDEF domain [Moorella thermoacetica ATCC 39073]

              10        20         30        40        50        60    
              |         |          |         |         |         |    
   1 MDFREVIEQRYHQLLSRYIAELTETSLY.QAQKFSRKTIEHQIPPEEIISIHRKVLKELYPSL..
   2 MDFREVIEQRYRQLLSRYISELTETSLY.QGQKFSRKTIEHQVPPEEIISIHRKVLSELYPDL..
   3 MDFREVIEQRYHQLLSRYIAELTETSLY.QAQKFSRKTIEHQIPPEEIISIHRKVLKELYPSL..
   4 ---EKAFEGKYRDILIQYLEHQDEEILY.TCEKLSREAMEERVSPEEIVHLHRSVLELYGKEL..
   5 ---EKAFEGKYRDILIQYLEHQDEEILY.TCEKLSREAMEERVSPEEIVHLHRSVLELYGKEL..
   6 ---EKAFEGKYRDILIQYLEHQDEEILY.TCEKLSREAMEERVSPEEIVHLHRSVLELYGKEL..
   7 ---EKAFEGKYRDILIQYLEHQDEEILY.TCEKLSREAMEERVSPEEIVHLHRSVLELYGKEL..
   8 ---EKAFEGKYRDILIQYLEHQDEEILY.TCEKLSREAMEERVSSEEIVHLHRSVLELYGKEL..
   9 -----EFKQHYKGLIDESLTCQDKVELIkKCEKYTDEVIRKDVLPEDIVDIHKNYILTLNL-T..
  10 -----EFKQHYKGLIDESLTCQDKVELIkKCEKYTDEVIRKDVLPEDIVDIHKNYILTLNL-T..
  11 -----EFKQHYKGLIDESLTCQDKVELIkKCEKYTDEVIRKDVLPEDIVDIHKNYILTLNL-T..
  12 -----EFKQHYKGLIDESLTCQDKVELIkKCEKYTDEVIRKDVLPEDIVDIHKNYILTLNL-T..
  13 -----EFKQHYKGLIDESLTCQDKVELIkKCEKYTDEVIRKDVLPEDIVDIHKNYILTLNL-T..
  14 -----EFKQHYKGLIDESLTCQDKVELIkKCEKYTDEVIRKDVLPEDIVDIHKNYILTSNL-T..
  15 ---KDLLNEQYRTILTRYLQNKSEQGLY.QAEQLSKQLLEQKVSPEELVSLHRTVLSDLFPSL..
  16 ---IKNNTKRYQDLLDKYIHSQDEEALY.GIEKVSKDFIKKNILPEEIINLHIQAMESLNKDL..
  17 -----EFTKSYKALVKESLITNNKTLLIkKCEAFTNEVIKKDVLPEDIVEIHKDYINTLDL-T..
  18 -----EFTKSYKALVKESLITNNKPLLIkKCEAFTNEVIKKDVLPEDIDEIHKGYINTLDL-T..
  19 ----IQWQETYFKLLHQYSLQQSEAILY.EASKLSKALVEKGVGPEDIVQFHLEALEKLFKDIsp


               70        80        90       100       110
               |         |         |         |         |
   1 ...PEDVFHSLDFLIEVMIGYGMAYQEHQTLRGIQQEIKSEIEIAANVQQT
   2 ...PDHVFHSLDFLIEVMIGYGLAYQEHQTLRGIQQEIKSEIEIAANVQQT
   3 ...PEDVFHSLDFLIEVMIGYGMAYQEHQTLRGIQQEIKSEIEIAANVQQT
   4 ...PDFVRLSFDVLLEIMVGYGLAYMEHLSLRTEQKELRSEIAQAEDMQKT
   5 ...PDFVRLSFDVLLEIMVGYGLAYMEHLSLRTEQKELRSEIAQAKDMQKT
   6 ...PDFVRLSFDVLLEIMVGYGLAYMEHLSLRTEQKELRSEIAQAEDMQKT
   7 ...PDFVRLSFDVLLEIMVGYGLAYMEHLSLRTEQKELRSEIAQAEDMQKT
   8 ...PDFVRLSFDVLLEIMVGYGLAYMEHLSLRTEQKALRSEIAQAEDMQKT
   9 ...REDVFKTLDVLQEIVKGFGYSYRDYQRLVDKLQVHDKEIDLASSLQQT
  10 ...REDVFKTLDVLQEIVKGFGYSYRDYQRLVDKLQVHDKEIDLASSLQQT
  11 ...REDVFKTLDVLQEIVKGFGYSYRDYQRLVDKLQVHDKEIDLASSLQQT
  12 ...REDVFKTLDVLQEIVKGFGYSYRDYQRLVDKLQVHDKEIDLASSLQQT
  13 ...REDVFKTLDVLQEIVKGFGYSYRDYQRLVDKLQVHDKEIDLASSLQQT
  14 ...REDVFKTLDVLQEIVKGFGYSYRDYQRLVDKLQVHDKEIDLASNLQQT
  15 ...SKDVQDSFEFLLEVMVGYGLAYREHQSLRDRQQELESEIDVAANMQQT
  16 ...TEDYKHSMNFLLEAMIFYGLALQEVTNLRQEKDVLTSEIAIAANMQKT
  17 ...EEDILETLDVLQEVVKGFGYSYRDYQRLVNKLQVHDKEMDLASRLQQT
  18 ...EEDILETLDVLPEVDKGFGYSYRDYQRLANKLQVHDKEMDLASRLQQT
  19 lrvPGLILISFDLLLEVMMAYALNFREYLEVKNKL----------------