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|_3:103 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|_1:101 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|_1:101 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|_1:101 protein ydhR precursor [Bacillus cereus G9241]
- gi|47558504|gb|EAL16827.1| protein ydhR precursor [Bacillus cereus G9241]
- gi|16129623|ref|NP_416182.1|_1:101 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|_1:102 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|_1:101 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|26247914|ref|NP_753954.1|_1:101 Protein ydhR precursor [Escherichia coli CFT073]
- gi|26108317|gb|AAN80519.1| Protein ydhR precursor [Escherichia coli CFT073]
- 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|46916534|emb|CAG23299.1|_14:114 conserved hypothetical protein [Photobacterium profundum]
- gi|49657851|emb|CAG90671.1|_1:101 unnamed protein product [Debaryomyces hansenii]
- gi|16120955|ref|NP_404268.1|_1:100 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|31195133|ref|XP_306514.1|_1:98 ENSANGP00000001083 [Anopheles gambiae]
- gi|21290078|gb|EAA02223.1| ENSANGP00000001083 [Anopheles gambiae str. PEST]
- gi|25026911|ref|NP_736965.1|_1:101 conserved hypothetical protein [Corynebacterium efficiens YS-314]
- gi|23492191|dbj|BAC17165.1| conserved hypothetical protein [Corynebacterium efficiens YS-314]
- gi|39935870|ref|NP_948146.1|_2:102 hypothetical protein RPA2803 [Rhodopseudomonas palustris CGA009]
- gi|39649724|emb|CAE28245.1| hypothetical protein [Rhodopseudomonas palustris CGA009]
- gi|23126908|ref|ZP_00108789.1|_43:144 hypothetical protein [Nostoc punctiforme]
- gi|38505807|ref|NP_942426.1|_1:103 sll8032 [Synechocystis sp. PCC 6803]
- gi|38423831|dbj|BAD02040.1| sll8032 [Synechocystis sp. PCC 6803]
- gi|23016338|ref|ZP_00056095.1|_2:102 hypothetical protein Magn0210781 [Magnetospirillum magnetotacticum]
- gi|16126078|ref|NP_420642.1|_9:106 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]
- gi|39935686|ref|NP_947962.1|_2:100 unknown protein [Rhodopseudomonas palustris CGA009]
- gi|39649539|emb|CAE28061.1| unknown protein [Rhodopseudomonas palustris CGA009]
- gi|37522314|ref|NP_925691.1|_2:102 hypothetical protein gll2745 [Gloeobacter violaceus PCC 7421]
- gi|35213314|dbj|BAC90686.1| gll2745 [Gloeobacter violaceus PCC 7421]
- gi|23127453|ref|ZP_00109322.1|_3:100 hypothetical protein [Nostoc punctiforme]
- gi|46314079|ref|ZP_00214666.1|_2:101 hypothetical protein Bcepa02003904 [Burkholderia cepacia R18194]

                   10          20          30        40        50      
                   |           |           |         |         |      
   1 ...MA.TL.LQLHFAFNGPF.G.DAMAEQLKPLA.E.SINQEPGFLWKVWTESEKNHEAGGIYLF
   2 mk.MA.YL.LQVDFPFEGPF.G.EEMEKGFWDLA.K.SINEEEGFHWKIWTENEETKEAGGIYVF
   3 ...MA.YL.LQVDFPFEGPF.G.EEMEKGFWDLA.K.SINEEEGFHWKIWTENQETKEAGGIYVF
   4 ...MA.YL.LQVDFPFEGPF.G.EEMEKGFWDLA.K.SINEEEGFHWKIWTENQETKEAGGIYVF
   5 ...MA.YV.LQVDFPFEGPF.G.EEMEKAFLDLA.K.SINEEEGFHWKIWTENEETNEAGGIYVF
   6 ...MA.TL.LQLHFAFNGPF.G.DAMAEQLKPLA.E.SINQEPGFLWKVWTESEKNHEAGGIYLF
   7 ...MSkTL.LQIHFNFSGPF.G.EEMTQQLVGLA.E.SINEEPGFIWKIWTESEKNQQAGGIYLF
   8 ...MA.TL.LQLHFAFNGPF.G.DAMAEQLKPLA.E.SINQEPGFLWKVWTESEKNHEAGGIYLF
   9 ...MA.TL.LQLHFAFNGPF.G.DAMAEQLKPLA.E.SINQEPGFLWKVWTESEKNHEAGGIYLF
  10 ...MA.KL.LQVDFEFHGPF.G.EEMSNTLVDLA.K.SINQEPGMIWKVWTESEKDKLGGGIYLF
  11 dttMA.KL.LQVDFEFNGPF.G.EDMAKAFVELA.E.SINREPGMIWKIWTESAKDKLGGGIYLF
  12 ...MG.YV.LQVDFKMNGPF.G.DEMAEQFSGLA.K.SINEEEGFMWKIWTESPERNEAGGIYVF
  13 ...MS.YI.LQVDFPYTGPW.G.NEMTKAMEGLA.R.SIAEEPGLIWKIWTVNETTNEAGGIYLF
  14 ...MP.SL.LQIHFNFPAELmG.PALTAAAIPLA.E.SITKEPGFISKIWTENPRTCEAGGIYLF
  15 ...MT.TL.LVFEFPSTGPF.G.ADAETAYADLA.H.DIAGEAGLIWKVWTEDPQREVAGGVYLF
  16 m..IT.TV.VQ--FHMATPI.SlEEAKKRFESSA.P.KYQKLPGLIRKYYIRSEDGTTAGGIYLW
  17 pstSS.RI.LQINFKYNNST.S.D-FRKQMKDVA.P.RIAKAPGLRWKIWSIDEGNKEASGFYLF
  18 ...MS.NLiLQINVTYDCSQ.A.E-LENVFSHAV.G.AIAAFPGLTWKIWIINDGTKEAGGLYCF
  19 m..IS.TM.--TTFTLRKPI.TrEEARAIFLSTA.P.KYQAVPGLIRKTYILSEDGTVAGGLYLW
  20 msqPN.RVyLYAEFQNSAPF.-.---TKAIWGDAnP.AMQTVPGLRSKTWLSGLNTQSVGGFYEF
  21 m..IT.AI.VRYRLPADIDR.A.-ACRDHFESIA.P.GFQSVKGLLSKHFIWSERG-VAGGVYQW
  22 m..IT.AI.VQFSLPRALTR.A.E-VKDLFAQVA.G.QFRGVPGLVRKYFLLSEDGTTGGGVYLW
  23 mp.VS.KVfLYAEYQVSIPF.S.----QIDWKSA.NvEMKKFPGLKSKTWLSALNTNTVGGFYEF
  24 m..IT.EI.VFFKLQPDVDL.-.PTLRERYEATA.A.KWAVNPDLLHKWYFYDAATHEGGGVYVW


        60          70            80        90       100     
        |           |             |         |         |     
   1 TDEKSALA.YLE.KHTA.RL.K.N.LGVEEVVAKVFDVNEPLSQINQAKL....A
   2 EEKQDAEK.YAE.MHKS.RL.E.A.AGVKDIRVKIFNINEKLTELNRGYIk...-
   3 EEKQDAEK.YAE.MHKN.RL.E.A.AGVKDIRVKIFNINEKLTELNRGYTk...-
   4 EEKQDAEK.YAE.MHKN.RL.E.A.AGVKDIRVRIFNINEKLTELNRGYTk...-
   5 EEKQDAEK.YAE.MHKN.RL.Q.T.FGVKDIRVRIFAINEKLTKLNRGYSk...-
   6 TDEKSALA.YLE.KHTA.RL.K.N.LGVEEVVAKVFDVNEPLSQINQAKL....A
   7 ESEETAQA.YIK.KHTA.RL.K.N.LGVDEVTFTLFGVNDALTKINHGNLcr..-
   8 TDEKSALA.YLE.KHTA.QL.K.K.LGVEEVVAKVFDVNEPLSQINQAKL....A
   9 SDEKSALT.YLE.KHTA.RL.K.N.LGVEEVVAKVFDVNVSLSQFNQAKL....A
  10 EDEATAQA.YLE.MHAA.RL.R.K.MGVVEVRGQIFDINVPLTTINQGPIgg..-
  11 EDEASAQA.YLQ.MHTA.RL.Q.Q.MGIGEVRGHIFDINQPLTAINNSPInqr.-
  12 ETKETAEK.YLD.MHSK.RL.A.G.FGVTGVNAKIFAINSKLSEITNGPVkq..-
  13 SDISAAKA.YLA.MHTA.RL.K.S.FGIPHVNGKIFLVNEALSQLDRAPI....-
  14 EDEASALA.YAT.MHEQ.RV.L.A.MGASAVQFKLFDVNEPLSRLTR---....-
  15 ADEASTQA.YVE.KHTA.RL.A.G.FGITDITATSYEVNEVLSRIDHAVLgr..-
  16 ESREAAESvYGG.EWRA.RV.A.AlYGAEPV-MSWFDSPVIVDNADGGTItts.A
  17 EDEKSLNN.YVE.NIFNvGM.R.NnSAISNIVVKKFNILEDPTIVTRGPIsqlk-
  18 DSETALTA.YVNsPIIT.AL.KaN.PLLPTVQIKAFEAITALTTQTRGPVpal.A
  19 NSRAEAEAlYTP.EWRA.FVtE.K.YGTEPV-VAYFESPVVVDNLTQQILsd..A
  20 DSVENARA.YAE.GMLA.GF.A.K.AAGASLTVKLFD-GDVVAEASRGMSspy.Y
  21 ASQADAEAfYSG.PWRD.GIvR.R.YGMEP-EIEFFTVFAKTDN-EAGTVtvve-
  22 ESRQAAERfYAG.GLLR.QIaE.Q.YGSEP-SVFYFESPVIVDNTVAEPVavg.-
  23 DSVENAQN.YID.GILI.PF.A.K.QVNGNLTVKLFD-GDITKEASTGMSspf.Y
  24 RTREAAAR.WHGdDYKA.MV.E.RvYGFPPV-IRVLDTVAHVD-ATQGRYeivg-