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:

- T0283 BH3980, Bacillus halodurans, 112 res
- gi|10176605|dbj|BAB07699.1|_1:112 BH3980 [Bacillus halodurans C-125]
- gi|15616542|ref|NP_244848.1| hypothetical protein BH3980 [Bacillus halodurans C-125]
- gi|89096657|ref|ZP_01169549.1|_1:113 hypothetical protein B14911_13492 [Bacillus sp. NRRL B-14911]
- gi|89088672|gb|EAR67781.1| hypothetical protein B14911_13492 [Bacillus sp. NRRL B-14911]
- gi|51975558|gb|AAU17108.1|_1:109 conserved hypothetical protein [Bacillus cereus E33L]
- gi|52142089|ref|YP_084738.1| hypothetical protein BCZK3151 [Bacillus cereus E33L]
- gi|49329787|gb|AAT60433.1|_1:109 conserved hypothetical protein [Bacillus thuringiensis serovar konkukian str. 97-27]
- gi|49478231|ref|YP_037537.1| hypothetical protein BT9727_3214 [Bacillus thuringiensis serovar konkukian str. 97-27]
- gi|42782501|ref|NP_979748.1|_1:109 hypothetical protein BCE3448 [Bacillus cereus ATCC 10987]
- gi|42738427|gb|AAS42356.1| conserved hypothetical protein [Bacillus cereus ATCC 10987]
- gi|29897095|gb|AAP10372.1|_1:109 hypothetical Cytosolic Protein [Bacillus cereus ATCC 14579]
- gi|30021540|ref|NP_833171.1| hypothetical Cytosolic Protein [Bacillus cereus ATCC 14579]
- gi|47564563|ref|ZP_00235608.1|_1:109 hypothetical protein cytosolic protein [Bacillus cereus G9241]
- gi|47558715|gb|EAL17038.1| hypothetical protein cytosolic protein [Bacillus cereus G9241]
- gi|89209513|ref|ZP_01187915.1|_1:109 conserved hypothetical protein [Bacillus weihenstephanensis KBAB4]
- gi|89152556|gb|EAR72723.1| conserved hypothetical protein [Bacillus weihenstephanensis KBAB4]
- gi|47503929|gb|AAT32605.1|_1:109 conserved hypothetical protein [Bacillus anthracis str. 'Ames Ancestor']
- gi|49180173|gb|AAT55549.1| conserved hypothetical protein [Bacillus anthracis str. Sterne]
- gi|47528781|ref|YP_020130.1| hypothetical protein GBAA3494 [Bacillus anthracis str. 'Ames Ancestor']
- gi|49186246|ref|YP_029498.1| hypothetical protein BAS3241 [Bacillus anthracis str. Sterne]
- gi|30258032|gb|AAP27260.1| conserved hypothetical protein [Bacillus anthracis str. Ames]
- gi|30263397|ref|NP_845774.1| hypothetical protein BA3494 [Bacillus anthracis str. Ames]
- gi|65320729|ref|ZP_00393688.1| COG4817: Uncharacterized protein conserved in bacteria [Bacillus anthracis str. A2012]
- gi|22779009|dbj|BAC15276.1|_2:107 hypothetical conserved protein [Oceanobacillus iheyensis HTE831]
- gi|23100775|ref|NP_694242.1| hypothetical protein OB3320 [Oceanobacillus iheyensis HTE831]
- gi|68205464|ref|ZP_00557666.1|_2:107 conserved hypothetical conserved protein [Desulfitobacterium hafniense DCB-2]
- gi|68170615|gb|EAM98499.1| conserved hypothetical conserved protein [Desulfitobacterium hafniense DCB-2]
- gi|12725109|gb|AAK06155.1|_1:107 UNKNOWN PROTEIN [Lactococcus lactis subsp. lactis Il1403]
- gi|15674039|ref|NP_268214.1| hypothetical protein L127611 [Lactococcus lactis subsp. lactis Il1403]
- gi|62462434|ref|ZP_00381844.1|_1:107 COG4817: Uncharacterized protein conserved in bacteria [Lactococcus lactis subsp. cremoris SK11]
- gi|68205463|ref|ZP_00557665.1|_1:112 Uncharacterised conserved protein UCP029876 [Desulfitobacterium hafniense DCB-2]
- gi|68170614|gb|EAM98498.1| Uncharacterised conserved protein UCP029876 [Desulfitobacterium hafniense DCB-2]
- gi|29343328|gb|AAO81090.1|_1:113 conserved hypothetical protein [Enterococcus faecalis V583]
- gi|29375866|ref|NP_815020.1| hypothetical protein EF1298 [Enterococcus faecalis V583]
- gi|10176601|dbj|BAB07695.1|_3:107 BH3976 [Bacillus halodurans C-125]
- gi|15616538|ref|NP_244844.1| hypothetical protein BH3976 [Bacillus halodurans C-125]
- gi|62462433|ref|ZP_00381843.1|_6:113 COG4817: Uncharacterized protein conserved in bacteria [Lactococcus lactis subsp. cremoris SK11]
- gi|12725110|gb|AAK06156.1|_5:113 UNKNOWN PROTEIN [Lactococcus lactis subsp. lactis Il1403]
- gi|15674040|ref|NP_268215.1| hypothetical protein L127921 [Lactococcus lactis subsp. lactis Il1403]
- gi|46906971|ref|YP_013360.1|_1:106 hypothetical protein LMOf2365_0756 [Listeria monocytogenes str. 4b F2365]
- gi|47095286|ref|ZP_00232897.1| conserved hypothetical protein [Listeria monocytogenes str. 1/2a F6854]
- gi|47091683|ref|ZP_00229479.1| conserved hypothetical protein [Listeria monocytogenes str. 4b H7858]
- gi|47020002|gb|EAL10739.1| conserved hypothetical protein [Listeria monocytogenes str. 4b H7858]
- gi|47016357|gb|EAL07279.1| conserved hypothetical protein [Listeria monocytogenes str. 1/2a F6854]
- gi|16410109|emb|CAC98798.1| lmo0720 [Listeria monocytogenes]
- gi|46880237|gb|AAT03537.1| conserved hypothetical protein [Listeria monocytogenes str. 4b F2365]
- gi|16802762|ref|NP_464247.1| hypothetical protein lmo0720 [Listeria monocytogenes EGD-e]
- gi|16413180|emb|CAC95960.1|_1:106 lin0728 [Listeria innocua]
- gi|16799803|ref|NP_470071.1| hypothetical protein lin0728 [Listeria innocua Clip11262]
- gi|10176602|dbj|BAB07696.1|_1:112 BH3977 [Bacillus halodurans C-125]
- gi|15616539|ref|NP_244845.1| hypothetical protein BH3977 [Bacillus halodurans C-125]

                  10        20        30        40         50        60
                  |         |         |         |          |         |
   1 ...MSFIE.KMIGSLNDKREWKAMEARAKALPKEYHHAYKAIQKYMWTSG.GPTDWQDTKRIFGG
   2 ...MSFIE.KMIGSLNDKREWKAMEARAKALPKEYHHAYKAIQKYMWTSG.GPTDWQDTKRIFGG
   3 ...MSIFE.KIIGSLDDKREWKAMEARAKALPSEYSAAYKAIQKYMWTAGgGPTDWKGTNRIFTG
   4 ...--MLE.IFKKIIGDKKEYRMMMARVAALPEDYQFVFKKIQNYMWNFS.-TGNGMDMLHIQYE
   5 ...--MLE.IFKKLIGDKKEYRMMMARVAALPEDYQFVFKKIQNYMWNFS.-TGNGMDMLHIQYE
   6 ...--MLE.MFKKLIGDKKEYKMMMARVAALPEDYQFVFKKIQNYMWNFS.-AGNGMDMLHIQYE
   7 ...--MLE.MFKKLIGDKKEYKMMMARVEALPEDYQFVFKKIQNYMWNFS.-AGNGMDMLHIQYE
   8 ...--MLE.MFKKLIGDKKEYKMMMARVEALPEDYQFVFKKIQNYMWNFS.-AGNGMDMLHIQYE
   9 ...--MLE.MFKKLIGDKKEYKMMMARVGALPEDYQFVFKKIQNYMWNFS.-AGNGMDMLHIQYE
  10 ...--MLE.IFKKLIGDKKEYRMMMARVAALSEDYQFVFKKIQNYMWNFS.-TGNGMDMLHIQYE
  11 ...M----.RIQDIIEGKKEWRAHKARVKALPKDYQIVYKEIQKYLFKV-.GPVELTDGIGLLSG
  12 ...M----.RIQDIIEGKKEWRGHMARVKALPRDYQIVYKELQKYLFKV-.GPVELTDGMGLLSG
  13 ...M-VLD.KISDLLAEKKDWQEMQNRAKKLPKDFYQAYRSIQKYMFKM-.GATDW----HIFND
  14 ...M-ILE.KISDVLKEKREWQAMENRAKNLPKDFYLAYKAIQKYMFNM-.GETDW----HIFTD
  15 ...MNFWE.KITGS-DMTKEWKAFESRVQKLPADYQAAWEKISLNLWPHS.DFTG-RNLMPILDG
  16 ...MSNFKaLIKKVVGDKKEYKEYKRRIAALPVEYRQVFQEIEKYAWHFS.DHSG-ANMFNALTD
  17 ...MS---.-IKKIIEGKREWRAHVSRVEKLPKDYQIVYKEIQKYLFKV-.GPVELNEGIGLLSE
  18 trqRNIVD.RMIG-LEEKREFREFEERAKNLGPDYYKDYCELKRYVW-IS.GASKWSDFKFIFNQ
  19 aehRNIVD.RMIG-LEEKREFHEFENRAQKLGENYYEDYKELKKYIWH-S.GVTKWADFKFIFGQ
  20 ...--MFN.WYKKYREEKRDYKQYKKRIAALPEDYKTAMKAIETYLWNFA.---KGAGMFEILKN
  21 ...--MFK.WYTKYREEKRDYKQYKKRIDALPEDYKTAMKAIETYLWNFA.---KGAGMFEILKN
  22 ...MNFLE.KITGS-DMTKEMKGFETRAKVLPAEYRAAWEEITSNLWLHS.DFTG-RNLMPILDS


              70        80        90          100          110     
              |         |         |            |            |     
   1 ILDLFEEGAAEGKKVTDLTGEDVAAFCDELMKD..TK.TWMDKYRTKLNDSI...GRD...
   2 ILDLFEEGAAEGKKVTDLTGEDVAAFCDELMKD..TK.TWMDKYRTKLNDSI...GRD...
   3 ILDLFEEGAAEGKKVTDLTGEDVAAFCDELVKD..EK.TWNDKYRKKLNDTI...GRG...
   4 LIDLFEAGAAEGRQVLDITGEDVASFADELVAN..AK.TYVSKYREDLNESI...MKKlrk
   5 LIDLFEAGAAEGRQVLDITGEDVASFADELVAN..AK.TYVSKYREDLNESI...MKKlrk
   6 LIDLFEAGAAEGRQVLDITGEDVASFADELVAN..AK.TYVSKYREDLNESI...MKKlrk
   7 LIDLFEAGAAEGRQVLDITGDDVASFADELVAN..AK.TYVSKYREDLNESI...MKKlrk
   8 LIDLFEAGAAEGRQVLDITGEDVASFADELVAN..AK.TYVSKYREDLNESI...MKKlrk
   9 LIDLFEAGAAEGRQVLEITGEDVASFADELVAN..AK.TYVSKYREDLNESI...MKQlrk
  10 LIDLFEAGAAEGRQVLDITGEDVASFADELVAN..AK.TYVSKYREDLNESI...MKKlrk
  11 IIDLFEKGAHMGKDVLEVTGEDVAAFCDELIKD..SK.TYADLYQESVNQTVneaMKE...
  12 IIDLFEEGAALGKGVLEVTGRDVAAFCDDLIKD..SK.TYADIYQESADQEVckaMKK...
  13 IIELFELAVVDGRSPAEVLGDDVATFADKLLSD..NKeDWRNKYRQALNDYF...AQK...
  14 IIELFELAVIDGRTLAEVLGEDSSAFADELLSE..NKqDWRETYRQELNDYF...AQK...
  15 VLGLLEETAAEGQRVQEVLGDDIKGFCAALAGEegAK.TYRDKWREQLNHNI...AKKlgk
  16 LLDLFEEGAANGTPIKNITGEKVGDFAETIVNEv.AG.KWTDKQKEKLNHQF...SKQ...
  17 ILGFFEEGAAAGKGVLDVTGTDVAAFCDALIGD..SK.TYADLYQESIQQHVdkaMKN...
  18 LLDLLEEAKGQKRKLTDLIGTDVAAFIDEMIDD..-K.GWEKKQKVKLNRAV...KK-...
  19 VLDLLEEAKIQDKELTDLIGPDVATFIDEMMDD..-N.SWGKKQKNKLNKEL...KNGfr.
  20 VLEMFENAAADNLELKAVVGDDLAEFADNLLSEfpEE.TWMDKQRQKLRDSI...K--...
  21 VLEMFENAAADQLELKAVVGDDLAEFADSLLNEypEE.TWMDKQRSKLRNSI...K--...
  22 ALELLEVASADGQSVEEVLGDDIEGFCAALVGDqgAK.TFRDKWRDQLNKNV...ARKlgg