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, 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:

- T0118 Endodeoxyribonuclease I, Bacteriophage T7
- T0118-active-sites0
- T0118-active-sites1
- T0118-active-sites2
- T0118-active-sites3
- T0118-active-sites4
- T0118-active-sites5
- T0118-active-sites6
- T0118-active-sites7
- T0118-active-sites8
- T0118-active-sites9
- gi|9627444|ref|NP_041972.1|_1:149 gene 3, endonuclease [Bacteriophage T7] (Bacteriophage T7)
- gi|119370|sp|P00641|ENRN_BPT7 ENDODEOXYRIBONUCLEASE I (ENDONUCLEASE) (Bacteriophage T7)
- gi|67296|pir||NEBP37 endodeoxyribonuclease I (EC 3.1.21.-) - phage T7 (Bacteriophage T7)
- gi|15517|emb|CAA24345.1| (V01127) 3 protein [Bacteriophage T7] (Bacteriophage T7)
- gi|15581|emb|CAA24402.1| (V01146) gene 3, endonuclease [Bacteriophage T7] (Bacteriophage T7)
- gi|9634009|ref|NP_052083.1|_3:150 endonuclease [Bacteriophage phiYeO3-12] (Bacteriophage phiYeO3-12)
- gi|6599000|emb|CAB63604.1| (AJ251805) endonuclease [Bacteriophage phiYeO3-12] (Bacteriophage phiYeO3-12)
- gi|9625408|ref|NP_039638.1|_1:149 3 [Bacteriophage T3] (Bacteriophage T3)
- gi|119369|sp|P20314|ENRN_BPT3 ENDODEOXYRIBONUCLEASE I (ENDONUCLEASE) (Bacteriophage T3)
- gi|76916|pir||S07505 endodeoxyribonuclease I (EC 3.1.21.-) - phage T3 (Bacteriophage T3)
- gi|15694|emb|CAA35132.1| (X17255) 3 [Bacteriophage T3] (Bacteriophage T3)
- gi|9964626|ref|NP_064756.1|_15:133 RP Endonuclease I [Roseophage SIO1] (Roseophage SIO1)
- gi|9944317|gb|AAG02601.1|AF189021_20 (AF189021) Roseophage SIO1 complete genome (Roseophage SIO1)

              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 MAGYGAKGIRKVGAFRSGLEDKVSKQLESKGIKFEYEEWKVPYVIPASNHTYTPDFLLPNGIFVE
   2 XXXXXXXXXXXXXXXXXXXEXXXXXXXXXXXXXXEXXXXXXXXXXXXXXXXXXXDXXXXXXXXXE
   3 XXXXXXXXXXXXXXXXXXXEXXXXXXXXXXXXXXEXXXXXXXXXXXXXXXXXXXDXXXXXXXXXE
   4 XXXXXXXXXXXXXXXXXXXEXXXXXXXXXXXXXXEXXXXXXXXXXXXXXXXXXXDXXXXXXXXXE
   5 XXXXXXXXXXXXXXXXXXXEXXXXXXXXXXXXXXEXXXXXXXXXXXXXXXXXXXDXXXXXXXXXE
   6 XXXXXXXXXXXXXXXXXXXEXXXXXXXXXXXXXXEXXXXXXXXXXXXXXXXXXXDXXXXXXXXXE
   7 XXXXXXXXXXXXXXXXXXXEXXXXXXXXXXXXXXEXXXXXXXXXXXXXXXXXXXDXXXXXXXXXE
   8 XXXXXXXXXXXXXXXXXXXEXXXXXXXXXXXXXXEXXXXXXXXXXXXXXXXXXXDXXXXXXXXXE
   9 XXXXXXXXXXXXXXXXXXXEXXXXXXXXXXXXXXEXXXXXXXXXXXXXXXXXXXDXXXXXXXXXE
  10 XXXXXXXXXXXXXXXXXXXEXXXXXXXXXXXXXXEXXXXXXXXXXXXXXXXXXXDXXXXXXXXXE
  11 XXXXXXXXXXXXXXXXXXXEXXXXXXXXXXXXXXEXXXXXXXXXXXXXXXXXXXDXXXXXXXXXE
  12 MAGYGAKGIRKVGAFRSGLEDKVSKQLESKGIKFEYEEWKVPYVIPASNHTYTPDFLLPNGIFVE
  13 -GAYAARGVRKVGAFRSGLEDKVSKQLESKGIKFDYELWRIPYVIPASDHLYTPDFLLPNGIFIE
  14 MAGAYAARCTQGRAFRSGLEDKVSKQLESKGIKFDYELWRIPYVIPESDHLYTPDFLLPNGIFIE
  15 ------------AGYRSGLEEQTAKDLKKRKVLFTYEETKIKWL-DSKVRTYTPDFVLPNGVIIE


         70        80         90       100       110       120       13
         |         |          |         |         |         |         
   1 TKGLWESDDRKKHLLIREQHPEL.DIRIVFSSSRTKLYKGSPTSYGEFCEKHGIKFADKLIPAEW
   2 XXXXXXXXDXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
   3 XXXXXXXXDXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
   4 XXXXXXXXDXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
   5 XXXXXXXXDXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
   6 XXXXXXXXDXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
   7 XXXXXXXXDXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
   8 XXXXXXXXDXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
   9 XXXXXXXXDXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
  10 XXXXXXXXDXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
  11 XXXXXXXXDXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
  12 TKGLWESDDRKKHLLIREQHPEL.DIRIVFSSSRTKLYKGSPTSYGEFCEKHGIKFADKLIPAEW
  13 TKGLWDSDDRKKHLLIREQHPEL.DIRLVFSSSRSKLYKGSPTSYAEWCEKHGILFADKLIPVEW
  14 TKGLWDSDDRKKHLLIREQHPEL.DIRLVFSSSRSKLYKGSPTSYGEWCEKHGILFADKLIPVAG
  15 TKGRFVAADRRKHLEIQKQFGTLyDIRFVFTNSKAKLYKGAKSSYADWCNKHGFLYADKTIPEDW


      0       140         
     |         |         
   1 IKEPKKEVPFDRLKRKGGKK
   2 XXXXXXXXXXXRLKRKGGKK
   3 XXXXXXXXXXXRLKRKGGKK
   4 XXXXXXXXXXXRLKRKGGKK
   5 XXXXXXXXXXXRLKRKGGKK
   6 XXXXXXXXXXXRLKRKGGKK
   7 XXXXXXXXXXXRLKRKGGKK
   8 XXXXXXXXXXXRLKRKGGKK
   9 XXXXXXXXXXXRLKRKGGKK
  10 XXXXXXXXXXXRLKRKGGKK
  11 XXXXXXXXXXXRLKRKGGKK
  12 IKEPKKEVPFDRLKRKGGKK
  13 LKEPKKEVPFDKFKTKKGVK
  14 VKEPKKEVPFDKFKTKKGVK
  15 LN------------------