a2m2html output for file 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, 1999.
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:

- T0086 Chorismate lyase, E. coli
- gi|136659|sp|P26602|UBIC_ECOLI_2:165 CHORISMATE--PYRUVATE LYASE (Escherichia coli)
- gi|43231|emb|CAA47181.1| (X66619) chorismate-pyruvate lyase [Escherichia coli] (Escherichia coli)
- gi|148100|gb|AAA24711.1| (M93136) chorismate lyase [Escherichia coli] (Escherichia coli)
- gi|148107|gb|AAA24716.1| (M93413) chorismate lyase [Escherichia coli] (Escherichia coli)
- gi|347888|gb|AAA17027.1| (M96268) chorismate lyase [Escherichia coli] (Escherichia coli)
- gi|450008|prf||1920311A chorismate-pyruvate lyase [Escherichia coli] (Escherichia coli)
- gi|281803|pir||S25660_39:202 4-hydroxybenzoate synthetase - Escherichia coli (Escherichia coli)
- gi|43234|emb|CAA40681.1| (X57434) 4-hydroxybenzoate synthetase [Escherichia coli] (Escherichia coli)
- gi|396374|gb|AAC43133.1| (U00006) chorismate lyase [Escherichia coli] (Escherichia coli)
- gi|1790472|gb|AAC77009.1| (AE000477) chorismate lyase [Escherichia coli] (Escherichia coli)
- gi|6014666|gb|AAF01449.1|AF187880_4_5:176 (AF187880) unknown [Pseudomonas sp. YH102] (Pseudomonas sp. YH102)
- gi|7225962|gb|AAF41147.1|_5:151 (AE002428) hypothetical protein [Neisseria meningitidis] (Neisseria meningitidis)
- gi|7379648|emb|CAB84215.1|_5:151 (AL162754) hypothetical protein NMA0944 [Neisseria meningitidis] (Neisseria meningitidis)

              10         20        30        40         50        60   
              |          |         |         |          |         |   
   1 SHPALTQLRA.LRYCKEIPALDPQLLDWLLLEDSMTKRFEQQ.GKTVSVTMIREGFVEQNEIPEE
   2 SHPALTQLRA.LRYCKEIPALDPQLLDWLLLEDSMTKRFEQQ.GKTVSVTMIREGFVEQNEIPEE
   3 SHPALTQLRA.LRYCKEIPALDPQLLDWLLLEDSMTKRFEQQ.GKTVSVTMIREGFVEQNEIPEE
   4 YRFSQPHLEW.NSYGHWRSSIAATQREWLFDRSSLTRRLRTLsDNEFEVIPLREA--AGPMLPEE
   5 FGKWLPDLPAaISDGISLPMV------RLLHTRSLTAALRAL.PHTFSVELLKLGELE-------
   6 FEEWLPDLPAdVSDGIGLPMS------RLLKARSLTAALRAL.PHLFSVELLKLGELE-------


              70        80        90       100       110       120     
              |         |         |         |         |         |     
   1 L...PLLPKESRYWLREILLCADGEPWLAGRTVVPVSTLSGPELALQKLGKTPLGRYLFTSS.TL
   2 L...PLLPKESRYWLREILLCADGEPWLAGRTVVPVSTLSGPELALQKLGKTPLGRYLFTSS.TL
   3 L...PLLPKESRYWLREILLCADGEPWLAGRTVVPVSTLSGPELALQKLGKTPLGRYLFTSS.TL
   4 CrvlGLQPGVTG-WIREVYLAGFGRPWVYARSVISHCDVEGSDSALLQLGNIPLGSLLFGEN.PY
   5 -...---TECGGRLVREVLLKLDRIPVVEARSECRIG--SAFWQNILDCGTRPLGERLFQADlEG
   6 -...---TECGGRLVREVLLKLDGIPVVAARSECRIG--SAFWQNILDCGTRPLGERLFQADlEG


         130                 140       150       160    
          |                   |         |         |    
   1 TRDFIEI.....GRD.....AGLWGRRSRLRLSGKPLLLTELFLPASPLY
   2 TRDFIEI.....GRD.....AGLWGRRSRLRLSGKPLLLTELFLPASPLY
   3 TRDFIEI.....GRD.....AGLWGRRSRLRLSGKPLLLTELFLPASPLY
   4 KRSEIEV.....CRYp11paYPLWARRSVFSRRQSRVLVHEMFLPA----
   5 ARSAFEFavageGCG.....RYFAARRSRFSRHGEEMLLTEYFLP-----
   6 ARSAFEFavfgeGCG.....RYFAARRSRFSHHGEEMLLTEYFLP-----