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:

- T0351 NESG:SR355, Bacillus subtilis, 117 res
- gi|2633630|emb|CAB13133.1|_1:107 xkdW [Bacillus subtilis subsp. subtilis str. 168]
- gi|1225960|emb|CAA94044.1| xkdW [Bacillus subtilis]
- gi|1722880|sp|P54342|XKDW_BACSU Phage-like element PBSX protein xkdW [Taxonomy]
- gi|16078341|ref|NP_389159.1| hypothetical protein BSU12760 [Bacillus subtilis subsp. subtilis str. 168]
- gi|1303764|dbj|BAA12420.1|_1:108 YqcD [Bacillus subtilis]
- gi|2635039|emb|CAB14535.1| yqcD [Bacillus subtilis subsp. subtilis str. 168]
- gi|1176763|sp|P45939|YQCD_BACSU Hypothetical protein yqcD [Taxonomy]
- gi|16079647|ref|NP_390471.1| hypothetical protein BSU25940 [Bacillus subtilis subsp. subtilis str. 168]
- gi|1217871|dbj|BAA06956.1| ORF129 [Bacillus subtilis]
- gi|52003167|gb|AAU23109.1|_1:95 phage related protein [Bacillus licheniformis ATCC 14580]
- gi|52347830|gb|AAU40464.1| putative protein [Bacillus licheniformis DSM 13]
- gi|52079956|ref|YP_078747.1| phage related protein [Bacillus licheniformis ATCC 14580]
- gi|52785328|ref|YP_091157.1| hypothetical protein BLi01564 [Bacillus licheniformis ATCC 14580]

              10        20          30        40        50        60   
              |         |           |         |         |         |   
   1 MILYDAIMYKYPNAVSRKDFELRNDGNG..SYIEKWNLRAPLPTQAELETWWEELQKNPPYEPPD
   2 MILYDAIMYKYPNAVSRKDFELRNDGNG..SYIEKWNLRAPLPTQAELETWWEELQKNPPYEPPD
   3 MNIGEAILFKYPTADPTKDFIVQNNGDGtpSYIAEWNIRAPIPTEAELKTWWEELQSTSAYEPPV
   4 MNLALAVKYLFPDAIIGEDFIIRDDGDGrgQYIETWRISAPQPSEKELQEAWENYLENPVTDDPQ


           70        80        90       100       110       
           |         |         |         |         |       
   1 QVELLAQELSQEKLARKQLEELNKTLGNELSDIKLSLLSLKGDYAELEHHHHHH
   2 QVELLAQELSQEKLARKQLEELNKTLGNELSDIKLSLLSLKGDY----------
   3 QVDLLARELSQEKLARKQLEELNQTLGSELSKIKLQLLTLQGG-----------
   4 LSYTSQQLL---------------KLGREMSSLKLEILALKGEMT---------