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:

- T0327 SR346, Bacillus subtlis, 102 res
- gi|2633549|emb|CAB13052.1|_1:93 yjcQ [Bacillus subtilis subsp. subtilis str. 168]
- gi|16078260|ref|NP_389077.1| hypothetical protein BSU11950 [Bacillus subtilis subsp. subtilis str. 168]
- gi|58253988|gb|AAV42225.1|_23:121 hypothetical protein LBA0333 [Lactobacillus acidophilus NCFM]
- gi|58336671|ref|YP_193256.1| hypothetical protein LBA0333 [Lactobacillus acidophilus NCFM]
- gi|38731447|gb|AAR27377.1|_12:109 putative major head protein [Lactobacillus johnsonii prophage Lj928]
- gi|41179318|ref|NP_958536.1| putative major head protein [Lactobacillus johnsonii prophage Lj928]
- gi|42519307|ref|NP_965237.1| Lj928 prophage major head protein [Lactobacillus johnsonii NCC 533]
- gi|41583595|gb|AAS09203.1| Lj928 prophage major head protein [Lactobacillus johnsonii NCC 533]
- gi|13487834|ref|NP_108712.1|_12:108 unknown [Bacteriophage Tuc2009]
- gi|13346849|gb|AAK19861.1| unknown [Bacteriophage Tuc2009]
- gi|34763367|ref|ZP_00144320.1|_7:103 hypothetical protein [Fusobacterium nucleatum subsp. vincentii ATCC 49256]
- gi|27886981|gb|EAA24100.1| hypothetical protein [Fusobacterium nucleatum subsp. vincentii ATCC 49256]
- gi|75761346|ref|ZP_00741321.1|_29:86 hypothetical protein RBTH_04230 [Bacillus thuringiensis serovar israelensis ATCC 35646]
- gi|74491171|gb|EAO54412.1| hypothetical protein RBTH_04230 [Bacillus thuringiensis serovar israelensis ATCC 35646]

              10        20        30        40        50               
              |         |         |         |         |               
   1 MNKDKLRYAILKEIFEGNTPLSENDIGVTEDQFDDAVNFLKREGYIIGVHY....S...DDRPHL
   2 MNKDKLRYAILKEIFEGNTPLSENDIGVTEDQFDDAVNFLKREGYIIGVHY....S...DDRPHL
   3 KILLYLKYCYENGIEVDPDILSSENIGISEKQFVLTLQMLLEDGYIKGVSLkptiQ...GPTIIC
   4 KILSYLKYCYEEGQNPDLDILDAPTFKISNNQFYKTLMMLMDDGYIKGLKF....T...PTKTGT
   5 KILAYLYHAMKKGEKIDPGVFDPQNYRVSYPYLNDILEELKENGYIKGVSFiet.K...DGKLIT
   6 QILKAIDVAFENQDFNYETTLDLKKLKISKHRLELFIEELVDKNYIKGLTV....RhsiNGNPII
   7 -------------------------------SISKALCYLQDEGFVSIY--....-...EADSIA


      60           70        80        90       100  
      |            |         |         |         |  
   1 YKLG...PELTEKGENYLKENGTWSKAYKTIKEIKDWIKLEHHHHHH
   2 YKLG...PELTEKGENYLKENGTWSKAYKTIKEIKDWI---------
   3 NIQD...TYATSSGLQYLIENSMMHKAYKVSKEVRDWIPL-------
   4 IVSNmdrVYITSDGLQYLEENTMMKKAYKIFKEVRDWLPL-------
   5 GLSD...IKITIKGIEYLDDNSMMKKAYKTLKELKDWIP--------
   6 SIGN...PRLTLDGLDFLENNSSMKKAYKFLKEAKEWIP--------
   7 Y--M...TTLLSAGIAYCEENTLLKKGYKAAKEIKSWMP--------