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:

- T0263 1wd6, Escherichia coli
- gi|16129623|ref|NP_416182.1|_1:99 protein ofunknown function; conserved hypothetical protein [Escherichia coli K12]
- gi|24113056|ref|NP_707566.1| orf, conserved hypothetical protein [Shigella flexneri 2a str. 301]
- gi|30063181|ref|NP_837352.1| hypothetical protein S1827 [Shigella flexneri 2a str. 2457T]
- gi|3915430|sp|P77225|YDHR_ECOLI Protein ydhR precursor [Taxonomy]
- gi|7459798|pir||C64924 hypothetical protein b1667 - Escherichia coli (strain K-12) [Taxonomy]
- gi|1549278|gb|AAB47943.1| hypothetical protein [Escherichia coli]
- gi|1787956|gb|AAC74737.1| protein ofunknown function; conserved hypothetical protein [Escherichia coli K12]
- gi|24052027|gb|AAN43273.1| orf, conserved hypothetical protein [Shigella flexneri 2a str. 301]
- gi|30041433|gb|AAP17161.1| hypothetical protein [Shigella flexneri 2a str. 2457T]
- gi|15802079|ref|NP_288101.1|_1:99 orf, hypothetical protein [Escherichia coli O157:H7 EDL933]
- gi|15831628|ref|NP_310401.1| hypothetical protein ECs2374 [Escherichia coli O157:H7]
- gi|25337268|pir||F90925 hypothetical protein ECs2374 [imported] - Escherichia coli (strain O157:H7, substrain RIMD 0509952) [Taxonomy]
- gi|25337270|pir||B85774 hypothetical protein Z2694 [imported] - Escherichia coli (strain O157:H7, substrain EDL933) [Taxonomy]
- gi|12515666|gb|AAG56654.1| orf, hypothetical protein [Escherichia coli O157:H7 EDL933]
- gi|13361841|dbj|BAB35797.1| hypothetical protein [Escherichia coli O157:H7]
- gi|30021302|ref|NP_832933.1|_3:102 Protein ydhR precursor [Bacillus cereus ATCC 14579]
- gi|29896856|gb|AAP10134.1| Protein ydhR precursor [Bacillus cereus ATCC 14579]
- gi|49479518|ref|YP_037301.1|_1:98 conserved hypothetical protein [Bacillus thuringiensis serovar konkukian str. 97-27]
- gi|49331074|gb|AAT61720.1| conserved hypothetical protein [Bacillus thuringiensis serovar konkukian str. 97-27]
- gi|21401104|ref|NP_657089.1|_1:98 hypothetical protein predicted by GeneMark [Bacillus anthracis A2012]
- gi|30263148|ref|NP_845525.1| conserved hypothetical protein [Bacillus anthracis str. Ames]
- gi|47528508|ref|YP_019857.1| conserved hypothetical protein [Bacillus anthracis str. 'Ames Ancestor']
- gi|49185995|ref|YP_029247.1| conserved hypothetical protein [Bacillus anthracis str. Sterne]
- gi|30257782|gb|AAP27011.1| conserved hypothetical protein [Bacillus anthracis str. Ames]
- gi|47503656|gb|AAT32332.1| conserved hypothetical protein [Bacillus anthracis str. 'Ames Ancestor']
- gi|49179922|gb|AAT55298.1| conserved hypothetical protein [Bacillus anthracis str. Sterne]
- gi|46916534|emb|CAG23299.1|_14:113 conserved hypothetical protein [Photobacterium profundum]
- gi|28901461|ref|NP_801116.1|_1:100 conserved hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]
- gi|28810008|dbj|BAC62949.1| conserved hypothetical protein [Vibrio parahaemolyticus]
- gi|47564352|ref|ZP_00235397.1|_1:98 protein ydhR precursor [Bacillus cereus G9241]
- gi|47558504|gb|EAL16827.1| protein ydhR precursor [Bacillus cereus G9241]
- gi|26247914|ref|NP_753954.1|_1:99 Protein ydhR precursor [Escherichia coli CFT073]
- gi|26108317|gb|AAN80519.1| Protein ydhR precursor [Escherichia coli CFT073]
- gi|16762822|ref|NP_458439.1|_3:101 conserved hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi str. CT18]
- gi|16766749|ref|NP_462364.1| putative cytoplasmic protein [Salmonella typhimurium LT2]
- gi|29144309|ref|NP_807651.1| conserved hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi Ty2]
- gi|25337272|pir||AD1003 conserved hypothetical protein STY4337 [imported] - Salmonella enterica subsp. enterica serovar Typhi (strain CT18) [Taxonomy]
- gi|16422018|gb|AAL22323.1| putative cytoplasmic protein [Salmonella typhimurium LT2]
- gi|16505128|emb|CAD08152.1| conserved hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
- gi|29139946|gb|AAO71511.1| conserved hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi Ty2]
- gi|50427139|ref|XP_462181.1|_1:99 unnamed protein product [Debaryomyces hansenii]
- gi|49657851|emb|CAG90671.1| unnamed protein product [Debaryomyces hansenii CBS767]
- gi|16120955|ref|NP_404268.1|_1:99 conserved hypothetical protein [Yersinia pestis]
- gi|22127423|ref|NP_670846.1| hypothetical protein y3549 [Yersinia pestis KIM]
- gi|45442711|ref|NP_994250.1| conserved hypothetical protein [Yersinia pestis biovar Medievalis str. 91001]
- gi|25337271|pir||AH0077 conserved hypothetical protein YPO0629 [imported] - Yersinia pestis (strain CO92) [Taxonomy]
- gi|15978719|emb|CAC89483.1| conserved hypothetical protein [Yersinia pestis CO92]
- gi|21960513|gb|AAM87097.1| hypothetical protein [Yersinia pestis KIM]
- gi|45437577|gb|AAS63127.1| conserved hypothetical protein [Yersinia pestis biovar Medievalis str. 91001]
- gi|25026911|ref|NP_736965.1|_1:99 conserved hypothetical protein [Corynebacterium efficiens YS-314]
- gi|23492191|dbj|BAC17165.1| conserved hypothetical protein [Corynebacterium efficiens YS-314]
- gi|23126908|ref|ZP_00108789.1|_44:143 hypothetical protein [Nostoc punctiforme]
- gi|31195133|ref|XP_306514.1|_1:97 ENSANGP00000001083 [Anopheles gambiae]
- gi|21290078|gb|EAA02223.1| ENSANGP00000001083 [Anopheles gambiae str. PEST]
- gi|38505807|ref|NP_942426.1|_2:102 sll8032 [Synechocystis sp. PCC 6803]
- gi|38423831|dbj|BAD02040.1| sll8032 [Synechocystis sp. PCC 6803]
- gi|39935870|ref|NP_948146.1|_6:88 hypothetical protein RPA2803 [Rhodopseudomonas palustris CGA009]
- gi|39649724|emb|CAE28245.1| hypothetical protein [Rhodopseudomonas palustris CGA009]
- gi|23016338|ref|ZP_00056095.1|_8:88 hypothetical protein Magn0210781 [Magnetospirillum magnetotacticum]
- gi|16126078|ref|NP_420642.1|_28:93 hypothetical protein [Caulobacter crescentus CB15]
- gi|25374740|pir||F87476 hypothetical protein CC1835 [imported] - Caulobacter crescentus [Taxonomy]
- gi|13423274|gb|AAK23810.1| hypothetical protein [Caulobacter crescentus CB15]

              10          20        30        40        50        60   
              |           |         |         |         |         |   
   1 MATLLQLHFAFN.GPFG.DAMAEQLKPLAESINQEPGFLWKVWTESEKNHEAGGIYLFTDEKSAL
   2 MATLLQLHFAFN.GPFG.DAMAEQLKPLAESINQEPGFLWKVWTESEKNHEAGGIYLFTDEKSAL
   3 MATLLQLHFAFN.GPFG.DAMAEQLKPLAESINQEPGFLWKVWTESEKNHEAGGIYLFTDEKSAL
   4 MAYLLQVDFPFE.GPFG.EEMEKGFWDLAKSINEEEGFHWKIWTENEETKEAGGIYVFEEKQDAE
   5 MAYLLQVDFPFE.GPFG.EEMEKGFWDLAKSINEEEGFHWKIWTENQETKEAGGIYVFEEKQDAE
   6 MAYLLQVDFPFE.GPFG.EEMEKGFWDLAKSINEEEGFHWKIWTENQETKEAGGIYVFEEKQDAE
   7 MAKLLQVDFEFN.GPFG.EDMAKAFVELAESINREPGMIWKIWTESAKDKLGGGIYLFEDEASAQ
   8 MAKLLQVDFEFH.GPFG.EEMSNTLVDLAKSINQEPGMIWKVWTESEKDKLGGGIYLFEDEATAQ
   9 MAYVLQVDFPFE.GPFG.EEMEKAFLDLAKSINEEEGFHWKIWTENEETNEAGGIYVFEEKQDAE
  10 MATLLQLHFAFN.GPFG.DAMAEQLKPLAESINQEPGFLWKVWTESEKNHEAGGIYLFSDEKSAL
  11 -KTLLQIHFNFS.GPFG.EEMTQQLVGLAESINEEPGFIWKIWTESEKNQQAGGIYLFESEETAQ
  12 MGYVLQVDFKMN.GPFG.DEMAEQFSGLAKSINEEEGFMWKIWTESPERNEAGGIYVFETKETAE
  13 MSYILQVDFPYT.GPWG.NEMTKAMEGLARSIAEEPGLIWKIWTVNETTNEAGGIYLFSDISAAK
  14 MTTLLVFEFPST.GPFG.ADAETAYADLAHDIAGEAGLIWKVWTEDPQREVAGGVYLFADEASTQ
  15 -SRILQINFKYN.NSTS.D-FRKQMKDVAPRIAKAPGLRWKIWSIDEGNKEASGFYLFEDEKSLN
  16 MPSLLQIHFNFPaELMG.PALTAAAIPLAESITKEPGFISKIWTENPRTCEAGGIYLFEDEASAL
  17 SNLILQINVTYD.CSQA.E-LENVFSHAVGAIAAFPGLTWKIWIINDGTKEAGGLYCFDSETALT
  18 ------VQFHMA.TPISlEEAKKRFESSAPKYQKLPGLIRKYYIRSEDGTTAGGIYLWESREAAE
  19 --------FTLR.KPITrEEARAIFLSTAPKYQAVPGLIRKTYILSEDGTVAGGLYLWNSRAEAE
  20 ------------.----.-----IWGDANPAMQTVPGLRSKTWLSGLNTQSVGGFYEFDSVENAR


              70          80        90       100       110       120   
              |           |         |         |         |         |   
   1 A.YLE..KHTA..RLKNLGVEEVVAKVFDVNEPLSQINQAKLAMATLLQLHFAFNGPFGDAMAEQ
   2 A.YLE..KHTA..RLKNLGVEEVVAKVFDVNEPLSQINQAK------------------------
   3 A.YLE..KHTA..QLKKLGVEEVVAKVFDVNEPLSQINQAK------------------------
   4 K.YAE..MHKS..RLEAAGVKDIRVKIFNINEKLTELNRGYI-----------------------
   5 K.YAE..MHKN..RLEAAGVKDIRVKIFNINEKLTELNRG-------------------------
   6 K.YAE..MHKN..RLEAAGVKDIRVRIFNINEKLTELNRG-------------------------
   7 A.YLQ..MHTA..RLQQMGIGEVRGHIFDINQPLTAINNSPI-----------------------
   8 A.YLE..MHAA..RLRKMGVVEVRGQIFDINVPLTTINQGPI-----------------------
   9 K.YAE..MHKN..RLQTFGVKDIRVRIFAINEKLTKLNRG-------------------------
  10 T.YLE..KHTA..RLKNLGVEEVVAKVFDVNVSLSQFNQAK------------------------
  11 A.YIK..KHTA..RLKNLGVDEVTFTLFGVNDALTKINHGNL-----------------------
  12 K.YLD..MHSK..RLAGFGVTGVNAKIFAINSKLSEITNGP------------------------
  13 A.YLA..MHTA..RLKSFGIPHVNGKIFLVNEALSQLDRAP------------------------
  14 A.YVE..KHTA..RLAGFGITDITATSYEVNEVLSRIDHAV------------------------
  15 N.YVE..NIFNvgMRNNSAISNIVVKKFNILEDPTIVTRGPI-----------------------
  16 A.YAT..MHEQ..RVLAMGASAVQFKLFDVNEPLSRLT---------------------------
  17 A.YVNspIITA..LKANPLLPTVQIKAFEAITALTTQTRGPV-----------------------
  18 SvYGG..EWRA..RVAALYGAEPVMSWFD------------------------------------
  19 AlYTP..EWRA..FVTEKYGTEPVVAYFE------------------------------------
  20 A.YAE..GMLA..GFAKAAGASLTVKLFD------------------------------------


          130       140       150       160       170       180       1
           |         |         |         |         |         |        
   1 LKPLAESINQEPGFLWKVWTESEKNHEAGGIYLFTDEKSALAYLEKHTARLKNLGVEEVVAKVFD
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      90       200  
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   1 VNEPLSQINQAKLA
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