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:

- T0120-211-end DNA repair protein XRCC4, human
- gi|4507945|ref|NP_003392.1|_211:334 X-ray repair complementing defective repair in Chinese hamster cells 4 (Homo sapiens)
- gi|1151115|gb|AAC50339.1| (U40622) XRCC4 [Homo sapiens] (Homo sapiens)
- gi|5706611|gb|AAD47297.1| (AF055285) DNA repair protein XRCC4 [Homo sapiens] (Homo sapiens)
- gi|1586944|prf||2205251A XRCC4 gene [Homo sapiens] (Homo sapiens)
- gi|5706612|gb|AAD47298.1|_211:336 (AF055285) DNA repair protein XRCC4 [Homo sapiens] (Homo sapiens)
- gi|5706612|gb|AAD47298.1|_211:336 (AF055285) DNA repair protein XRCC4 [Homo sapiens] (Homo sapiens)
- gi|4507945|ref|NP_003392.1|_211:334 X-ray repair complementing defective repair in Chinese hamster cells 4 (Homo sapiens)
- gi|1151115|gb|AAC50339.1| (U40622) XRCC4 [Homo sapiens] (Homo sapiens)
- gi|5706611|gb|AAD47297.1| (AF055285) DNA repair protein XRCC4 [Homo sapiens] (Homo sapiens)
- gi|1586944|prf||2205251A XRCC4 gene [Homo sapiens] (Homo sapiens)
- gi|7488950|pir||S72445_31:155 DNA-binding protein WRKY3 - parsley (Petroselinum crispum)
- gi|1432056|gb|AAC49528.1| (U56834) WRKY3 [Petroselinum crispum] (Petroselinum crispum)
- gi|4680251|gb|AAD27591.1|AF121354_1_31:155 (AF121354) transcription factor; sequence specific DNA-binding protein; WRKY3 [Petroselinum crispum] (Petroselinum crispum)
- gi|7484933|pir||T09887_51:99 DNA-binding protein homolog T22A6.70 - Arabidopsis thaliana (Arabidopsis thaliana)
- gi|5051766|emb|CAB45059.1| (AL078637) putative DNA-binding protein [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|7269274|emb|CAB79334.1| (AL161561) putative DNA-binding protein [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|7484935|pir||T10685_26:79 DNA-binding protein WRKY3 homolog F3L17.120 - Arabidopsis thaliana (Arabidopsis thaliana)
- gi|5262766|emb|CAB45914.1| (AL080283) putaive DNA-binding protein [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|7270058|emb|CAB79873.1| (AL161579) putaive DNA-binding protein [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|4760596|dbj|BAA77358.1|_38:82 (AB020023) DNA-binding protein NtWRKY3 [Nicotiana tabacum] (Nicotiana tabacum)
- gi|7488099|pir||T00500_72:103 probable elicitor response element-binding protein WRKY3 - Arabidopsis thaliana (Arabidopsis thaliana)
- gi|2642432|gb|AAB87100.1| (AC002391) putative WRKY-type DNA-binding protein [Arabidopsis thaliana] (Arabidopsis thaliana)

              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 QEGETAICSEMTADRDPVYDESTDEESENQTDLSGLASAAVSKDDSIISSLDVTDIAPSRKRRQR
   2 QEGETAICSEMTADRDPVYDESTDEESENQTDLSGLASAAVSKDDSIISSLDVTDIAPSRKRRQR
   3 QEGETAICSEMTADRDPVYDESTDEESENQTDLSGLASAAVSKDDSIISSLDVTDIAPSRKRRQR
   4 QEGETAICSEMTADRDPVYDESTDEESENQTDLSGLASAAVSKDDSIISSLDVTDIAPSRKRRQR
   5 QEGETAICSEMTADRDPVYDESTDEESENQTDLSGLASAAVSKDDSIISSLDVTDIAPSRKRRQR
   6 QSVENLIKAISQSNHQTAYLSSSSSSETGDTDYRAVTDVAVNKFKKFISLLDKNRTGHARFRRGP
   7 QSVENLIKAISQSNHQTAYLSSSSSSETGDTDYRAVTDVAVNKFKKFISLLDKNRTGHARFRRGP
   8 -----------------LIGQSQQPTEKSQTEITAVTDVAVNSFKKVISLLGRSRTGHARFRRAP
   9 QSMEHLIRV-----------LSNRPEQQHNVDCSEITDFTVSKFKTVISLLN--RTGHARFRRGP
  10 ----------------------QQQQQPVQLDCREITDFTLSKFKKVVSILD--RTGHARFRRGP
  11 ------------------------------------ADAAVSKFKRVISLLDRTRTGHARFRRAP


         70        80             90       100       110       120     
         |         |              |         |         |         |     
   1 MQRNLGTEPKMAPQENQLQEKE.....NSRPDSSLPETSKKEHISAENMSLETLRNSSPEDLFDE
   2 MQRNLGTEPKMAPQENQLQEKE.....--KPDSSLPETSKKEHISAENMSLETLRNSSPEDLFDE
   3 MQRNLGTEPKMAPQENQLQEKE.....NSRPDSSLPETSKKEHISAENMSLETLRNSSPEDLFDE
   4 MQRNLGTEPKMAPQENQLQEKE.....NSRPDSSLPETSKKEHISAENMSLETLRNSSPEDLFDE
   5 MQRNLGTEPKMAPQENQLQEKE.....--KPDSSLPETSKKEHISAENMSLETLRNSSPEDLFDE
   6 VQEKTGVEMLVNPIQNQIQNHGsdgfqVYRPTAVHPVQP------VQPVQIQPVQLVQPVQRLPP
   7 VQEKTGVEMLVNPIQNQIQNHGsdgfqVYRPTAVHPVQP------VQPVQIQPVQLVQPVQRLPP
   8 A---------------------.....--------------------------------------
   9 VH--------------------.....--------------------------------------
  10 VQVH------------------.....--------------------------------------
  11 VHV-------------------.....--------------------------------------


       
      
   1 I
   2 I
   3 I
   4 I
   5 I
   6 V
   7 V
   8 -
   9 -
  10 -
  11 -