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:

- T0251 NP_374059, Staphylococcus aureus subsp. aureus N315
- gi|49483097|ref|YP_040321.1|_6:107 conserved hypothetical protein [Staphylococcus aureus subsp. aureus MRSA252]
- gi|49241226|emb|CAG39905.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus MRSA252]
- gi|15923927|ref|NP_371461.1|_1:102 conserved hypothetical protein [Staphylococcus aureus subsp. aureus Mu50]
- gi|15926526|ref|NP_374059.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus N315]
- gi|25338837|pir||B89860 conserved hypothetical protein SA0798 [imported] - Staphylococcus aureus (strain N315) [Taxonomy]
- gi|13700741|dbj|BAB42037.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus N315]
- gi|14246706|dbj|BAB57099.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus Mu50]
- gi|21282548|ref|NP_645636.1|_6:107 conserved hypothetical protein [Staphylococcus aureus subsp. aureus MW2]
- gi|49485713|ref|YP_042934.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus MSSA476]
- gi|21203985|dbj|BAB94684.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus MW2]
- gi|49244156|emb|CAG42582.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus MSSA476]
- gi|27467549|ref|NP_764186.1|_6:102 conserved hypothetical protein [Staphylococcus epidermidis ATCC 12228]
- gi|27315093|gb|AAO04228.1| conserved hypothetical protein [Staphylococcus epidermidis ATCC 12228]
- gi|47092978|ref|ZP_00230758.1|_7:101 conserved hypothetical protein [Listeria monocytogenes str. 4b H7858]
- gi|47018632|gb|EAL09385.1| conserved hypothetical protein [Listeria monocytogenes str. 4b H7858]
- gi|16804431|ref|NP_465916.1|_7:101 similar to B. subtilis YuzD protein [Listeria monocytogenes EGD-e]
- gi|47095872|ref|ZP_00233476.1| conserved hypothetical protein [Listeria monocytogenes str. 1/2a F6854]
- gi|25338840|pir||AI1373 B. subtilis YuzD protein homolog lmo2393 [imported] - Listeria monocytogenes (strain EGD-e) [Taxonomy]
- gi|16411881|emb|CAD00471.1| lmo2393 [Listeria monocytogenes]
- gi|47015749|gb|EAL06678.1| conserved hypothetical protein [Listeria monocytogenes str. 1/2a F6854]
- gi|42784131|ref|NP_981378.1|_25:121 conserved hypothetical protein [Bacillus cereus ATCC 10987]
- gi|42740062|gb|AAS43986.1| conserved hypothetical protein [Bacillus cereus ATCC 10987]
- gi|30022991|ref|NP_834622.1|_1:97 hypothetical protein [Bacillus cereus ATCC 14579]
- gi|29898551|gb|AAP11823.1| hypothetical protein [Bacillus cereus ATCC 14579]
- gi|30264991|ref|NP_847368.1|_4:100 conserved hypothetical protein [Bacillus anthracis str. Ames]
- gi|47530491|ref|YP_021840.1| conserved hypothetical protein [Bacillus anthracis str. 'Ames Ancestor']
- gi|49187810|ref|YP_031063.1| conserved hypothetical protein [Bacillus anthracis str. Sterne]
- gi|49481019|ref|YP_038968.1| conserved hypothetical protein [Bacillus thuringiensis serovar konkukian str. 97-27]
- gi|30259668|gb|AAP28854.1| conserved hypothetical protein [Bacillus anthracis str. Ames]
- gi|47505639|gb|AAT34315.1| conserved hypothetical protein [Bacillus anthracis str. 'Ames Ancestor']
- gi|49181737|gb|AAT57113.1| conserved hypothetical protein [Bacillus anthracis str. Sterne]
- gi|49332575|gb|AAT63221.1| conserved hypothetical protein [Bacillus thuringiensis serovar konkukian str. 97-27]
- gi|47566982|ref|ZP_00237699.1|_4:100 YuzD-like protein [Bacillus cereus G9241]
- gi|47556300|gb|EAL14634.1| YuzD-like protein [Bacillus cereus G9241]
- gi|16080274|ref|NP_391101.1|_7:101 yuzD [Bacillus subtilis]
- gi|7475467|pir||C70026 hypothetical protein yuzD - Bacillus subtilis [Taxonomy]
- gi|2635718|emb|CAB15211.1| yuzD [Bacillus subtilis subsp. subtilis str. 168]
- gi|21397432|ref|NP_653417.1|_4:100 hypothetical protein predicted by GeneMark [Bacillus anthracis A2012]
- gi|23099810|ref|NP_693276.1|_8:102 hypothetical protein OB2355 [Oceanobacillus iheyensis HTE831]
- gi|22778041|dbj|BAC14311.1| hypothetical conserved protein [Oceanobacillus iheyensis HTE831]
- gi|16801554|ref|NP_471822.1|_7:101 similar to B. subtilis YuzD protein [Listeria innocua Clip11262]
- gi|25338838|pir||AG1743 B. subtilis YuzD protein homolog lin2492 [imported] - Listeria innocua (strain Clip11262) [Taxonomy]
- gi|16415014|emb|CAC97719.1| lin2492 [Listeria innocua]
- gi|46908567|ref|YP_014956.1|_7:101 conserved hypothetical protein [Listeria monocytogenes str. 4b F2365]
- gi|46881839|gb|AAT05133.1| conserved hypothetical protein [Listeria monocytogenes str. 4b F2365]
- gi|15615978|ref|NP_244283.1|_7:98 BH3416~unknown conserved protein in B. subtilis [Bacillus halodurans C-125]
- gi|25338835|pir||H84076 hypothetical protein BH3416 [imported] - Bacillus halodurans (strain C-125) [Taxonomy]
- gi|10176039|dbj|BAB07135.1| BH3416 [Bacillus halodurans C-125]
- gi|45531012|ref|ZP_00182095.1|_3:95 COG4837: Uncharacterized protein conserved in bacteria [Exiguobacterium sp. 255-15]

              10        20        30          40        50        60   
              |         |         |           |         |         |   
   1 MVVYGADVICASCVNAPTSKDIYDWLQPLLKRKYPNI..SFKYTYIDITKDNDNLTDHDLQFIER
   2 VIVYGADVICASCVNAPTSKDIYDWLQPLLKRKYPNI..SFKYTYIDITKDNDNLTDHDLQFIER
   3 MVVYGADVICASCVNAPTSKDIYDWLQPLLKRKYPNI..SFKYTYIDITKDNDNLTDHDLQFIER
   4 VVVYGADVICASCVNAPTSKDIYDWLQPLLKRKYPNI..SFKYTYIDITKDNDNLTDHDLQFIER
   5 VVVYGAEVVCASCVNAPTSIDTYQWLQALLLRKFPQH..HFEFTYIDIRNDTENLTDHDMQFIER
   6 LYVYGSTTICASCVGAPSSKETEEWLRAAIGRKFSGQ..PFVVEYVDIFNPPNEKALAD--MANK
   7 LYVYGSTTICASCVGAPSSKETEEWLRAAIGRKFSGQ..PFVVEYVDIFNPPNETALAD--MANK
   8 VQVYGTKVICASCVGMPSSTETFEWLQAAIGRKYEGQenKFNFEYIDFQEEQEDEDKKA--FAER
   9 MQVYGTKVICASCVGMPSSTETFEWLQAAIGRKYEGQenKFNFEYIDFQEEQEDADKKA--FAER
  10 VQVYGTKVICASCVGMPSSTETFEWLQAAIGRKYEGQenKFNFEYIDFQEEQEDEEKKA--FAER
  11 VQVYGTKVICASCVGMPSSTETFEWLQAAIGRKYEGQenKFNFEYIDFQEEQEDENKKA--FAER
  12 LSVYGAENVCASCVNMPTAKDTYEWLEAALKRKYPNQ..PFEMQYIDIHEPPDNEHAKE--LAEK
  13 VQVYGTKVICASCVGMPSSTETFEWLQAAIGRKYEGQenKFNFEYIDFQEXQEDEEKKA--FAER
  14 ITVYGSKQICASCVGAPGSKDTYEWLQAAIGRKYVVD..MVDYTYIDINEPQKELIHQE--FINE
  15 LYVYGSTTICASCVGAPSSKETEEWLRAAIGRKFSGQ..PFVVEYVDIFNPPNEAALAD--MANK
  16 LYVYGSTTICASCVGAPSSKETEEWLRAAIGRKFSGQ..PFVVEYVDIFNPPNEKALAD--MANK
  17 VTVFGAEEKCASCIHLPSAKETMEWLEAAVKRKYPEH..NFRFRYVDINKVAEK---KDQAYADA
  18 IKVYGAAQTCPSCVGAPSSEETYSWLQAVLGRKYETA..-LTFEYVDF-----EAAPVEDEWITA


           70        80        90       100  
           |         |         |         |  
   1 IEQDELFYPLITMNDEYVADGYIQTKQITRFIDQKLVNE
   2 IEQDELFYPLITMNDEYVADGYIQTKQITRFIDQKLVNE
   3 IEQDELFYPLITMNDEYVADGYIQTKQITRFIDQKLVNE
   4 IEQDELFYPLITMNDEYVADGYIQTKQITRFIDQKLVNE
   5 INEDELFYPLVTMNDEYVADGYIQYKQITRFIKS-----
   6 IVEEDYMYPVIVVDGEIIAEGNPRLKDIYQVMTD-----
   7 IVEEDYMYPVIVVDGEIIAEGNPRLKDIYQVMTD-----
   8 VVEEDLFYPVVLVNGEIVGEGNPRLKDVYEEIEK-----
   9 IVEEDLFYPVVLVNGEIVGEGNPRLKDVYEEIEK-----
  10 VVEEDLFYPVVLVNGEIVGEGNPRLKDVYEEIEK-----
  11 VVEEDLFYPVVLVNGEIVGEGNPRLKDVYEEIEK-----
  12 IRNDEYFYPLVLVEDKIVGEGNPKLKDVYEEMEK-----
  13 VVEEDLFYPVVLVNGEIVEEGNPRLKDVYEEIEK-----
  14 MMEEDMFYPIIFINDKIVAEGIPTLKPIYRTLDD-----
  15 IVDEDYMYPVIVVDGEIIAEGNPRLKDIYQVMTD-----
  16 IVEEDYMYPVIVVDDEIIAEGNPRLKDIYQVMTD-----
  17 ILSDEYMYPLVVIEDEVVAEGNPRLKDVYVKI-------
  18 LQDDVYFYPLVLLDGEMVDEGYVQLKKITQAIDRRL---