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|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|28901461|ref|NP_801116.1|_1:101 conserved hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]
- gi|28810008|dbj|BAC62949.1| conserved hypothetical protein [Vibrio parahaemolyticus]
- gi|16129623|ref|NP_416182.1|_1:100 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|16762822|ref|NP_458439.1|_3:102 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|15802079|ref|NP_288101.1|_1:100 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|50427139|ref|XP_462181.1|_1:100 unnamed protein product [Debaryomyces hansenii]
- gi|49657851|emb|CAG90671.1| unnamed protein product [Debaryomyces hansenii CBS767]
- gi|26247914|ref|NP_753954.1|_1:100 Protein ydhR precursor [Escherichia coli CFT073]
- gi|26108317|gb|AAN80519.1| Protein ydhR precursor [Escherichia coli CFT073]
- gi|46916534|emb|CAG23299.1|_14:113 conserved hypothetical protein [Photobacterium profundum]
- 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|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|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|_1:100 conserved hypothetical protein [Corynebacterium efficiens YS-314]
- gi|23492191|dbj|BAC17165.1| conserved hypothetical protein [Corynebacterium efficiens YS-314]
- gi|31195133|ref|XP_306514.1|_1:96 ENSANGP00000001083 [Anopheles gambiae]
- gi|21290078|gb|EAA02223.1| ENSANGP00000001083 [Anopheles gambiae str. PEST]
- gi|23126908|ref|ZP_00108789.1|_44:143 hypothetical protein [Nostoc punctiforme]
- gi|39935870|ref|NP_948146.1|_3:101 hypothetical protein RPA2803 [Rhodopseudomonas palustris CGA009]
- gi|39649724|emb|CAE28245.1| hypothetical protein [Rhodopseudomonas palustris CGA009]
- gi|23016338|ref|ZP_00056095.1|_3:101 hypothetical protein Magn0210781 [Magnetospirillum magnetotacticum]
- gi|38505807|ref|NP_942426.1|_3:102 sll8032 [Synechocystis sp. PCC 6803]
- gi|38423831|dbj|BAD02040.1| sll8032 [Synechocystis sp. PCC 6803]
- gi|23127453|ref|ZP_00109322.1|_5:87 hypothetical protein [Nostoc punctiforme]
- gi|46314079|ref|ZP_00214666.1|_3:94 hypothetical protein Bcepa02003904 [Burkholderia cepacia R18194]
- gi|16126078|ref|NP_420642.1|_12:93 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 MATLLQLHFAFNGPF.GDAMAEQLKPLAESINQEPGFLWKVWTESEKNHEAGGIYLFTDEKSALA
   2 MAYLLQVDFPFEGPF.GEEMEKGFWDLAKSINEEEGFHWKIWTENEETKEAGGIYVFEEKQDAEK
   3 MAKLLQVDFEFHGPF.GEEMSNTLVDLAKSINQEPGMIWKVWTESEKDKLGGGIYLFEDEATAQA
   4 MATLLQLHFAFNGPF.GDAMAEQLKPLAESINQEPGFLWKVWTESEKNHEAGGIYLFTDEKSALA
   5 -KTLLQIHFNFSGPF.GEEMTQQLVGLAESINEEPGFIWKIWTESEKNQQAGGIYLFESEETAQA
   6 MATLLQLHFAFNGPF.GDAMAEQLKPLAESINQEPGFLWKVWTESEKNHEAGGIYLFTDEKSALA
   7 MGYVLQVDFKMNGPF.GDEMAEQFSGLAKSINEEEGFMWKIWTESPERNEAGGIYVFETKETAEK
   8 MATLLQLHFAFNGPF.GDAMAEQLKPLAESINQEPGFLWKVWTESEKNHEAGGIYLFSDEKSALT
   9 MAKLLQVDFEFNGPF.GEDMAKAFVELAESINREPGMIWKIWTESAKDKLGGGIYLFEDEASAQA
  10 MAYLLQVDFPFEGPF.GEEMEKGFWDLAKSINEEEGFHWKIWTENQETKEAGGIYVFEEKQDAEK
  11 MAYLLQVDFPFEGPF.GEEMEKGFWDLAKSINEEEGFHWKIWTENQETKEAGGIYVFEEKQDAEK
  12 MAYVLQVDFPFEGPF.GEEMEKAFLDLAKSINEEEGFHWKIWTENEETNEAGGIYVFEEKQDAEK
  13 MSYILQVDFPYTGPW.GNEMTKAMEGLARSIAEEPGLIWKIWTVNETTNEAGGIYLFSDISAAKA
  14 MTTLLVFEFPSTGPF.GADAETAYADLAHDIAGEAGLIWKVWTEDPQREVAGGVYLFADEASTQA
  15 MPSLLQIHFNFPAELmGPALTAAAIPLAESITKEPGFISKIWTENPRTCEAGGIYLFEDEASALA
  16 -SRILQINFKYNNST.-SDFRKQMKDVAPRIAKAPGLRWKIWSIDEGNKEASGFYLFEDEKSLNN
  17 -TTVVQFHMATPISL.-EEAKKRFESSAPKYQKLPGLIRKYYIRSEDGTTAGGIYLWESREAAES
  18 -STMTTFTLRKPITR.-EEARAIFLSTAPKYQAVPGLIRKTYILSEDGTVAGGLYLWNSRAEAEA
  19 -NLILQINVTYDCSQ.-AELENVFSHAVGAIAAFPGLTWKIWIINDGTKEAGGLYCFDSETALTA
  20 -KVFLYAEYQVSIPF.---SQIDWKSANVEMKKFPGLKSKTWLSALNTNTVGGFYEFDSVENAQN
  21 -TEIVFFKLQPDVDL.-PTLRERYEATAAKWAVNPDLLHKWYFYDAATHEGGGVYVWRTREAAAR
  22 --VYLYAEFQNSAPF.---TKAIWGDANPAMQTVPGLRSKTWLSGLNTQSVGGFYEFDSVENARA


             70          80        90       100 
             |           |         |         | 
   1 .YLE..KHTA..RLKNLGVEEVVAKVFDVNEPLSQINQAKLA
   2 .YAE..MHKS..RLEAAGVKDIRVKIFNINEKLTELNRGYI-
   3 .YLE..MHAA..RLRKMGVVEVRGQIFDINVPLTTINQGPIG
   4 .YLE..KHTA..RLKNLGVEEVVAKVFDVNEPLSQINQAKL-
   5 .YIK..KHTA..RLKNLGVDEVTFTLFGVNDALTKINHGNLC
   6 .YLE..KHTA..QLKKLGVEEVVAKVFDVNEPLSQINQAKL-
   7 .YLD..MHSK..RLAGFGVTGVNAKIFAINSKLSEITNGPV-
   8 .YLE..KHTA..RLKNLGVEEVVAKVFDVNVSLSQFNQAKL-
   9 .YLQ..MHTA..RLQQMGIGEVRGHIFDINQPLTAINNSPI-
  10 .YAE..MHKN..RLEAAGVKDIRVKIFNINEKLTELNRG---
  11 .YAE..MHKN..RLEAAGVKDIRVRIFNINEKLTELNRG---
  12 .YAE..MHKN..RLQTFGVKDIRVRIFAINEKLTKLNRG---
  13 .YLA..MHTA..RLKSFGIPHVNGKIFLVNEALSQLDRAP--
  14 .YVE..KHTA..RLAGFGITDITATSYEVNEVLSRIDHAVL-
  15 .YAT..MHEQ..RVLAMGASAVQFKLFDVNEPLSRL------
  16 .YVE..NIFNvgMRNNSAISNIVVKKFNILEDPTIVTRGPI-
  17 vYGG..EWRA..RVAALYGAEPVMSWFDSPVIVDNADGGTI-
  18 lYTP..EWRA..FVTEKYGTEPVVAYFESPVVVDNLTQQIL-
  19 .YVNspIITA..LKANPLLPTVQIKAFEAITALTTQTRGPV-
  20 .YID..GILI..PFAKQVNGNLTVKLFD--------------
  21 wHGD..DYKA..MVERVYGFPPVIRVLDTVAHVD--------
  22 .YAE..GMLA..GFAKAAGASLTVKLFD--------------