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:

- T0419
- gi|148549168|ref|YP_001269270.1|_238:297 protein of unknown function DUF344 [Pseudomonas putida F1]
- gi|148513226|gb|ABQ80086.1| Polyphosphate:AMP phosphotransferase [Pseudomonas putida F1]
- gi|26988483|ref|NP_743908.1|_238:297 hypothetical protein PP_1752 [Pseudomonas putida KT2440]
- gi|24983246|gb|AAN67372.1|AE016363_4 conserved hypothetical protein [Pseudomonas putida KT2440]
- gi|167032356|ref|YP_001667587.1|_238:297 protein of unknown function DUF344 [Pseudomonas putida GB-1]
- gi|166858844|gb|ABY97251.1| protein of unknown function DUF344 [Pseudomonas putida GB-1]
- gi|77460318|ref|YP_349825.1|_238:297 Protein of unknown function DUF344 [Pseudomonas fluorescens PfO-1]
- gi|77384321|gb|ABA75834.1| Polyphosphate:AMP phosphotransferase [Pseudomonas fluorescens PfO-1]
- gi|152984862|ref|YP_001347056.1|_286:345 hypothetical protein PSPA7_1672 [Pseudomonas aeruginosa PA7]
- gi|150960020|gb|ABR82045.1| conserved hypothetical protein [Pseudomonas aeruginosa PA7]
- gi|146308249|ref|YP_001188714.1|_239:298 protein of unknown function DUF344 [Pseudomonas mendocina ymp]
- gi|145576450|gb|ABP85982.1| protein of unknown function DUF344 [Pseudomonas mendocina ymp]
- gi|170720546|ref|YP_001748234.1|_238:297 protein of unknown function DUF344 [Pseudomonas putida W619]
- gi|169758549|gb|ACA71865.1| protein of unknown function DUF344 [Pseudomonas putida W619]
- gi|15598651|ref|NP_252145.1|_238:297 hypothetical protein PA3455 [Pseudomonas aeruginosa PAO1]
- gi|116051475|ref|YP_789692.1| hypothetical protein PA14_19410 [Pseudomonas aeruginosa UCBPP-PA14]
- gi|9949597|gb|AAG06843.1|AE004766_4 conserved hypothetical protein [Pseudomonas aeruginosa PAO1]
- gi|115586696|gb|ABJ12711.1| conserved hypothetical protein [Pseudomonas aeruginosa UCBPP-PA14]
- gi|84325751|ref|ZP_00973783.1|_238:297 COG2326: Uncharacterized conserved protein [Pseudomonas aeruginosa 2192]
- gi|107102988|ref|ZP_01366906.1| hypothetical protein PaerPA_01004057 [Pseudomonas aeruginosa PACS2]
- gi|126195519|gb|EAZ59582.1| conserved hypothetical protein [Pseudomonas aeruginosa 2192]
- gi|84319700|ref|ZP_00968090.1|_238:297 COG2326: Uncharacterized conserved protein [Pseudomonas aeruginosa C3719]
- gi|126168340|gb|EAZ53851.1| conserved hypothetical protein [Pseudomonas aeruginosa C3719]
- gi|70731681|ref|YP_261423.1|_238:297 pvdS [Pseudomonas fluorescens Pf-5]
- gi|68345980|gb|AAY93586.1| pvdS [Pseudomonas fluorescens Pf-5]
- gi|104780653|ref|YP_607151.1|_237:296 hypothetical protein PSEEN1471 [Pseudomonas entomophila L48]
- gi|95109640|emb|CAK14341.1| conserved hypothetical protein; putative signal peptide [Pseudomonas entomophila L48]
- gi|67155159|ref|ZP_00416787.1|_238:297 Protein of unknown function DUF344 [Azotobacter vinelandii AvOP]
- gi|67086960|gb|EAM06427.1| Protein of unknown function DUF344 [Azotobacter vinelandii AvOP]
- gi|71734554|ref|YP_273769.1|_235:297 hypothetical protein PSPPH_1515 [Pseudomonas syringae pv. phaseolicola 1448A]
- gi|71555107|gb|AAZ34318.1| conserved hypothetical protein [Pseudomonas syringae pv. phaseolicola 1448A]
- gi|66046969|ref|YP_236810.1|_235:297 Protein of unknown function DUF344 [Pseudomonas syringae pv. syringae B728a]
- gi|63257676|gb|AAY38772.1| Protein of unknown function DUF344 [Pseudomonas syringae pv. syringae B728a]
- gi|146282844|ref|YP_001172997.1|_241:300 hypothetical protein PST_2503 [Pseudomonas stutzeri A1501]
- gi|145571049|gb|ABP80155.1| conserved hypothetical protein [Pseudomonas stutzeri A1501]
- gi|28868846|ref|NP_791465.1|_235:297 conserved hypothetical protein [Pseudomonas syringae pv. tomato str. DC3000]
- gi|28852085|gb|AAO55160.1| conserved hypothetical protein [Pseudomonas syringae pv. tomato str. DC3000]
- gi|71909197|ref|YP_286784.1|_237:296 Protein of unknown function DUF344 [Dechloromonas aromatica RCB]
- gi|71848818|gb|AAZ48314.1| Polyphosphate:AMP phosphotransferase [Dechloromonas aromatica RCB]

                       10           20        30        40        50   
                       |            |         |         |         |   
   1 ...K...ERAKRQP...HA...APLVSSLDNRGLLDSLDLGQYLDKDAYKEQLAAEQARLAGLIR
   2 lanN...PKGKHQG...NV...APLGHSIDDRSLLGALDMTLRLDKADYQEQLITEQARLAGLLR
   3 lahN...PKGKHQG...NV...APLGRSIDDRSLLGALDMTLRLDKADYQEQLITEQARLAGLLR
   4 lanN...PKGKHQG...NV...APLGRSIDDRSLLGALDMTLRLDKADYQEQLVTEQARLAGLLR
   5 lkrP...DVHPHEV...NA...APLGTSVDQLNLLDSLDLTQRLEKKDYEEQLITEQARLSGLMR
   6 latK...ERAKRQP...HA...APLVSSLDNRGLLDSLDLGQYLDKDDYKEQLATEQARLAGLIR
   7 aesK...PRVQLQP...HA...APLVSSLDNRGLLDSLDMTQVLGKEDYKEQLAMEQARLSGLMR
   8 lavN...PKGKHQG...NI...APLGRSIDQRSLVGALDMTLRLDKQDYEEQLVTEQARLAGLLR
   9 latK...ERAKRQP...HA...APLVSSLDNRGLLDSLDLGQYLDKDAYKEQLAAEQARLAGLIR
  10 latK...ERAKRQP...HA...APLVSSLDNRGLLDSLDLGQYLDKDAYKEQLAAEQARLAGLIR
  11 latK...ERAKRQP...HA...APLVSSLDNRGLLDSLDLGQYLDKDAYKEQLAAEQARLAGLIR
  12 lnrQ...PLRATQV...NA...APLPPAVDQLSLLDSLDMTQHLDKDDYEEQLITEQARLAGLLR
  13 algN...KPLKHQG...NV...APLGRSIDQKSLLGALDLSKRLDKRDYEEQLVTEQARLAGLLR
  14 lghR...GRPAHRP...HA...APLVSSVDNRALLDSLDMTQALAKPDYQRLLIAEQARLALLMR
  15 ...QaalNKVEPEPaalTV...GPLAIHDNELTLLDSLDLSLHLSKDDYQQQLITEQARLSGNMR
  16 ...QvalNKAEPETaalTV...GPLAIHSNELTLLDSLDLSLNLSKDDYQQQLITEQARLSGNMR
  17 aeqP...GQSVAQP...HS...APLQVDLDHLSLLDSLDLSQKLDKDNYQQQLAEEQARLSRLLR
  18 ...QaalNKVEPES...SAltiGPLAIHNNERTLLDSLDLSLHLSKEDYQHELIAEQARLSGNLR
  19 rlsQ...EGLQRVP...VA...PPIVHPIDEKNVLSELDLTQTLTKKDYESQLAKYQARLSELVR


           60   
           |   
   1 DKRFRQH...
   2 DKRMRRHalv
   3 DKRMRRHalv
   4 DKHMRRHalv
   5 DKRMRRHalv
   6 DKRFRQHslv
   7 DKRMRKHall
   8 HKHMRRHslv
   9 DKRFRQHslv
  10 DKRFRQHslv
  11 DKRFRQHslv
  12 DKRMRKHalv
  13 NKHMRRHalv
  14 DKRIRRHalv
  15 DKRMKSHalv
  16 DKRMKSHall
  17 DRRLRKRgvl
  18 DKRMKSHalv
  19 DPRFVGKrsl