a2m2html output for file 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, 1999.
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:

- T0115-134-250 Homoserine kinase, Methanococcus jannaschii
- gi|2497515|sp|Q58504|KHSE_METJA_135:250 HOMOSERINE KINASE (HK) (Methanococcus jannaschii)
- gi|2127974|pir||G64437 homoserine kinase (EC 2.7.1.39) - Methanococcus jannaschii (Methanococcus jannaschii)
- gi|1591748|gb|AAB99107.1| (U67553) homoserine kinase (thrB) [Methanococcus jannaschii] (Methanococcus jannaschii)
- gi|266419|sp|P00547|KHSE_ECOLI_135:248 HOMOSERINE KINASE (HK) (Escherichia coli)
- gi|1361027|pir||S56630 homoserine kinase (EC 2.7.1.39) thrB - Escherichia coli (Escherichia coli)
- gi|7428038|pir||KIECM homoserine kinase (EC 2.7.1.39) - Escherichia coli (Escherichia coli)
- gi|529240|gb|AAA20618.1| (L13601) homoserine kinase [Escherichia coli] (Escherichia coli)
- gi|537246|gb|AAA97302.1| (U14003) homoserine kinase [Escherichia coli] (Escherichia coli)
- gi|1786184|gb|AAC73114.1| (AE000111) homoserine kinase [Escherichia coli] (Escherichia coli)
- gi|125395|sp|P27722|KHSE_SERMA_135:248 HOMOSERINE KINASE (HK) (Serratia marcescens)
- gi|421255|pir||C47057 homoserine kinase (EC 2.7.1.39) - Serratia marcescens (Serratia marcescens)
- gi|47274|emb|CAA43213.1| (X60821) homoserine kinase [Serratia marcescens] (Serratia marcescens)
- gi|216967|dbj|BAA38482.1| (D10387) homoserine kinase [Serratia marcescens] (Serratia marcescens)
- gi|9656932|gb|AAF95506.1|_141:252 (AE004306) homoserine kinase [Vibrio cholerae] (Vibrio cholerae)
- gi|1170650|sp|P44504|KHSE_HAEIN_140:254 HOMOSERINE KINASE (HK) (Haemophilus influenzae)
- gi|1074209|pir||I64047 homoserine kinase (EC 2.7.1.39) - Haemophilus influenzae (strain Rd KW20) (Haemophilus influenzae)
- gi|1573039|gb|AAC21766.1| (U32694) homoserine kinase (thrB) [Haemophilus influenzae Rd] (Haemophilus influenzae Rd)
- gi|6225592|sp|O67332|KHSE_AQUAE_122:232 HOMOSERINE KINASE (HK) (Aquifex aeolicus)
- gi|7450507|pir||A70413 homoserine kinase - Aquifex aeolicus (Aquifex aeolicus)
- gi|2983721|gb|AAC07283.1| (AE000733) homoserine kinase [Aquifex aeolicus] (Aquifex aeolicus)
- gi|125393|sp|P04947|KHSE_FREDI_130:243 HOMOSERINE KINASE (HK) (Fremyella diplosiphon)
- gi|79795|pir||S03743 homoserine kinase (EC 2.7.1.39) - Calothrix sp (Calothrix sp.)
- gi|43396|emb|CAA68576.1| (Y00522) homoserine kinase (AA 1-307) [Calothrix PCC7601] (Calothrix PCC7601)
- gi|2497514|sp|P73646|KHSE_SYNY3_129:242 HOMOSERINE KINASE (HK) (Synechocystis PCC6803)
- gi|7450506|pir||S77133 homoserine kinase (EC 2.7.1.39) - Synechocystis sp. (strain PCC 6803) (Synechocystis sp.)
- gi|1652772|dbj|BAA17691.1| (D90908) homoserine kinase [Synechocystis sp.] (Synechocystis sp.)
- gi|7450509|pir||B64651_121:234 homoserine kinase - Helicobacter pylori (strain 26695) (Helicobacter pylori)
- gi|2314197|gb|AAD08095.1| (AE000612) homoserine kinase (thrB) [Helicobacter pylori 26695] (Helicobacter pylori 26695)
- gi|7450510|pir||C71940_121:234 homoserine kinase - Helicobacter pylori (strain J99) (Helicobacter pylori)
- gi|4154901|gb|AAD05950.1| (AE001472) HOMOSERINE KINASE [Helicobacter pylori J99] (Helicobacter pylori J99)
- gi|6967628|emb|CAB72618.1|_122:235 (AL139074) homoserine kinase [Campylobacter jejuni] (Campylobacter jejuni)
- gi|7450512|pir||D71103_104:214 probable homoserine kinase - Pyrococcus horikoshii (Pyrococcus horikoshii)
- gi|3257503|dbj|BAA30186.1| (AP000004) 271aa long hypothetical homoserine kinase [Pyrococcus horikoshii] (Pyrococcus horikoshii)
- gi|7434441|pir||H75080_126:236 homoserine kinase (EC 2.7.1.39) (hk). PAB1676 - Pyrococcus abyssi (strain Orsay) (Pyrococcus abyssi)
- gi|5458461|emb|CAB49949.1| (AJ248286) HOMOSERINE KINASE (EC 2.7.1.39) (HK). [Pyrococcus abyssi] (Pyrococcus abyssi)
- gi|7532410|gb|AAF63224.1|_189:302 (AC002329) 3-hydroxy-3-methylglutaryl-coenzyme A reductase 2 [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|147980|gb|AAA83915.1|_135:247 (J01706) homoserine kinase [Escherichia coli] (Escherichia coli)
- gi|216436|dbj|BAA01287.1| (D10483) homoserine kinase [Escherichia coli] (Escherichia coli)
- gi|4927412|gb|AAD33097.1|AF082525_1_189:302 (AF082525) homoserine kinase [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|7472024|pir||G75280_130:240 homoserine kinase - Deinococcus radiodurans (strain R1) (Deinococcus radiodurans)
- gi|6460205|gb|AAF11935.1|AE002069_9 (AE002069) homoserine kinase [Deinococcus radiodurans] (Deinococcus radiodurans)
- gi|2497513|sp|P72535|KHSE_STRPN_118:232 HOMOSERINE KINASE (HK) (Streptococcus pneumoniae)
- gi|1498295|gb|AAC44297.1| (U41735) homoserine kinase homolog [Streptococcus pneumoniae] (Streptococcus pneumoniae)
- gi|1730045|sp|P52991|KHSE_LACLA_122:234 HOMOSERINE KINASE (HK) (Lactococcus lactis subsp. lactis)
- gi|2126613|pir||JC6050 homoserine kinase (EC 2.7.1.39) - Lactococcus lactis (Lactococcus lactis)
- gi|1255940|emb|CAA65714.1| (X96988) thrB [Lactococcus lactis] (Lactococcus lactis)
- gi|80285|pir||B25364_129:240 homoserine kinase (EC 2.7.1.39) - Bacillus subtilis (Bacillus subtilis)
- gi|40212|emb|CAA28271.1| (X04603) homoserine kinase [Bacillus subtilis] (Bacillus subtilis)
- gi|6648061|sp|P04948|KHSE_BACSU_130:241 HOMOSERINE KINASE (HK) (Bacillus subtilis)
- gi|7450505|pir||H69722 homoserine kinase (EC 2.7.1.39) - Bacillus subtilis (Bacillus subtilis)
- gi|2635721|emb|CAB15214.1| (Z99120) homoserine kinase [Bacillus subtilis] (Bacillus subtilis)
- gi|4614|emb|CAA37083.1|_141:289 (X52901) homoserine kinase (AA 1-356) [Saccharomyces cerevisiae] (Saccharomyces cerevisiae)
- gi|6321814|ref|NP_011890.1|_142:290 homoserine kinase; Thr1p (Saccharomyces cerevisiae)
- gi|125396|sp|P17423|KHSE_YEAST HOMOSERINE KINASE (HK) (Saccharomyces cerevisiae)
- gi|630045|pir||S46772 homoserine kinase (EC 2.7.1.39) - yeast (Saccharomyces cerevisiae) (Saccharomyces cerevisiae)
- gi|172978|gb|AAA35154.1| (M37692) homoserine kinase [Saccharomyces cerevisiae] (Saccharomyces cerevisiae)
- gi|500690|gb|AAB68871.1| (U10399) Thr1p: Homoserine kinase [Saccharomyces cerevisiae] (Saccharomyces cerevisiae)
- gi|7521143|pir||E72511_167:282 probable homoserine kinase APE2067 - Aeropyrum pernix (strain K1) (Aeropyrum pernix)
- gi|5105765|dbj|BAA81077.1| (AP000063) 343aa long hypothetical homoserine kinase [Aeropyrum pernix] (Aeropyrum pernix)
- gi|125390|sp|P07128|KHSE_BRELA_133:248 HOMOSERINE KINASE (HK) (Brevibacterium lactofermentum)
- gi|39588|emb|CAA68332.1| (Y00140) homoserine kinase (AA 1-309) [Corynebacterium glutamicum] (Corynebacterium glutamicum)
- gi|125391|sp|P08210|KHSE_CORGL_133:248 HOMOSERINE KINASE (HK) (Corynebacterium glutamicum)
- gi|66855|pir||KIFKMG homoserine kinase (EC 2.7.1.39) - Corynebacterium glutamicum (Corynebacterium glutamicum)
- gi|40504|emb|CAA68615.1| (Y00546) homoserine kinase (HK) (AA 1-309) [Corynebacterium glutamicum] (Corynebacterium glutamicum)
- gi|7490646|pir||T40495_131:271 homoserine kinase - fission yeast (Schizosaccharomyces pombe) (Schizosaccharomyces pombe)
- gi|2832883|emb|CAA16824.1| (AL021730) homoserine kinase [Schizosaccharomyces pombe] (Schizosaccharomyces pombe)
- gi|7450508|pir||F72364_121:221 hypothetical protein TM0545 - Thermotoga maritima (strain MSB8) (Thermotoga maritima)
- gi|4981059|gb|AAD35630.1|AE001729_10 (AE001729) homoserine kinase, putative [Thermotoga maritima] (Thermotoga maritima)
- gi|1170651|sp|P45836|KHSE_MYCLE_137:243 HOMOSERINE KINASE (HK) (Mycobacterium leprae)
- gi|7434440|pir||T09990 homoserine kinase (EC 2.7.1.39) - Mycobacterium leprae (Mycobacterium leprae)
- gi|699339|gb|AAA63100.1| (U15186) homoserine kinase [Mycobacterium leprae] (Mycobacterium leprae)
- gi|7387824|sp|O66132|KHSE_BUCAI_2:95 HOMOSERINE KINASE (HK) (Buchnera aphidicola (Acyrthosiphon pisum))
- gi|3036933|dbj|BAA25384.1| (AB004856) homoserine kinase [Buchnera aphidicola] (Buchnera aphidicola)
- gi|1730046|sp|Q10603|KHSE_MYCTU_139:244 HOMOSERINE KINASE (HK) (Mycobacterium tuberculosis)
- gi|7434439|pir||D70773 probable thrB protein - Mycobacterium tuberculosis (strain H37RV) (Mycobacterium tuberculosis)
- gi|1322420|emb|CAA97729.1| (Z73419) thrB [Mycobacterium tuberculosis] (Mycobacterium tuberculosis)
- gi|9107373|gb|AAF85023.1|AE004035_2_151:260 (AE004035) homoserine kinase [Xylella fastidiosa] (Xylella fastidiosa)

              10        20                  30        40           50  
              |         |                   |         |            |  
   1 SGAKHADNVAPAIFGGFTMVT.....NYEPLE.....VLHIPIDFKLDILIAIPNISIN...TKE
   2 -GAKHADNVAPAIFGGFTMVT.....NYEPLE.....VLHIPIDFKLDILIAIPNISIN...TKE
   3 SGSIHYDNVAPCFLGGMQLMI.....EENDII.....SQQVPGFDEWLWVLAYPGIKVS...TAE
   4 SGSVHYDNVAPCYLGGLQLML.....EEEGII.....SQEVPCFDDWLWVMAYPGIKVS...TAE
   5 SGSIHYDNVAPCYLGGVQLML.....EELGII.....SQSVPSFDDWYWVMAYPGIKVS...TAE
   6 SGSIHYDNVAPCYLGGVQFMV.....QSLGNI.....CQKLPFFDNWYWVLAYPGIEVS...TAE
   7 EFEKHPDNIIPAFVGGFTVCAt....SESGVI.....FKKLPFPEDIKIVFVIPDFEVS...TSE
   8 AMEGHPDNVVPALLGGCRLAAt....SAEGWE.....ICDVPWDENVVPVVAIPDFELS...TQE
   9 AMEGHPDNVAPALLGGCQLAVk....NGDHWQ.....LVALDWPSKFVPVLAIPNFELS...TEA
  10 IYENHPDNITPAVFGGYNAAFv....EKKKVI.....SLKTKIPSFLKAVMVIPNRAIS...TKQ
  11 IYENHPDNITPAVFGGYNAAFv....EKKKVI.....SLKTKIPSFLKAVMVIPNRVIS...TKQ
  12 IYENHPDNIAPATLGGFVCSLv....EKNKVY.....SIKKEIDKDLAAVVVIPNLAMS...TEQ
  13 SGEPHPDNVVPSYYGGFTVIE.....SKSPLR.....VHFV--DAKLRGVVVLPEVEIP...TAK
  14 SGSPHGDNVIPSYYGGFNILE.....SLNPLR.....VHRV--DVELNVVVVLPEVEVP...TKE
  15 --GYHADNIAPAIMGGFVLIR.....NYEPLDlk...PLRFPSDKDLFFVLVSPDFEAP...TKK
  16 SGSIHYDNVAPCFLGGMQLMI.....EENDII.....SQQVQGLMSGCGCSRIRGLK-S...RRQ
  17 --GYHADNIAPAIMGGFVLIR.....NYEPLDlk...PLKFPSDKDLFFVLVSPEFEAP...TKK
  18 -EEGHPDNVAPALFGGIVVATl....DKLGTH.....YVRLDPPAHLGVTVLVPDFELS...TSK
  19 -IEGHPDNVAPAIYGNLVIAS.....SVEGQV.....SAIVADFPECDFLAYIPNYELR...TRD
  20 EIEGHPDNVAPALLGNLVIAS.....TVAGKT.....SHIVADFPSCALLAFVPDYELK...TVE
  21 -EEGHPDNAGASLVGGLVIGL.....HEDDET.....QMIRVPNADIDVVVVIPFYEVL...TRD
  22 -EEGHPDNAGASLVGGLVIGL.....HEDDET.....QMIRVPNADIDVVVVIPFYEVL...TRD
  23 MIERHPDNITAAMMGGFCGSFlr...DLTPQ-e35grHVKYQWNPAIKCIAIIPQFELS...TAD
  24 MIERHPDNITAAMMGGFCGSFlr...DLTPQ-e35grHVKYQWNPAIKCIAIIPQFELS...TAD
  25 -GQPHFDNAAASILGGLAVVA.....SDAAGK.....LRVFRVPFKAWFAVVTPMNPVPqgkTGV
  26 AFEGHPDNAAASVLGGAVVSWtn8gkSQPQYA.....AVPLEVQDNIRATALVPNFHAS...TEA
  27 AFEGHPDNAAASVLGGAVVSWtn8gkSQPQYA.....AVPLEVQDNIRATALVPNFHAS...TEA
  28 MIERHPDNVMASMMGGFVGSFlrel.----SEe28gtFARLPWASELKAIVVIPEFHLA...TSK
  29 ELEGHPDNVVPAFTGGLVVCYq....NGSHLD.....FEKFEIDLSLTFLV--PNFPVC...TNE
  30 EFEGHPDNAAAAVLGGAVVSWvdrsyDQPDYC.....AVPLRLHPDIHLFAAIPEERSS...TAE
  31 -------------LGGLQLIL.....EDSKII.....SQTIPNFKNWFWIVAWPGTKVP...TAE
  32 EFEGHPDNAAAAVLGGAVVSWtdhsgDRPNYS.....AVSLRLHPDIRLFTAIPEQRSS...TAE
  33 SGSRHGDNLGPLFLGGLVLCT.....LER---.....LVPVTVPAAWHSLLVHPDTLLE...TRR


            60        70        80        90        100       110      
            |         |         |         |          |         |      
   1 AREILPKAVGLKDLVNNVGKACGMVYALYNKDKSLFGRY.MMSDKVIEPVRGKLIPNYFKIKEEV
   2 AREILPKAVGLKDLVNNVGKACGMVYALYNKDKSLFGRY.MMSDKVIEPVRGKLIPNYFKIKEEV
   3 ARAILPAQYRRQDCIAHGRHLAGFIHACYSRQPELAAK-.LMKDVIAEPYRERLLPGFRQARQA-
   4 ARAILPAQYRRQDCISHGRYLAGFIHACHTRQPQLAAK-.LMQDVIAEPYRTRLLPGFAEARKA-
   5 ARAILPAQYRRQDIVAHGRYLAGFIHACHTQQPELAAK-.MIKDVIAEPYREKLLPGFAKAR---
   6 ARAILPKSYTRQNVIAHGRHLGGFVHACHTHQENLAAI-.MMKDVIAEPYRESLLPNFAEVKQAT
   7 ARRVLPKKVELKEAVFNVQRSALFVSALLTKDYKLL-RE.AVRDKLHQPYREKLVPGLSE-----
   8 ARRVLPTEFSRADAIFNTAHLGLLLRGLATGKGEWL-KT.ALQDKLHQPYRKALIPGYDAVNQ--
   9 ARAVLPHQYDRSAAIFNASHLALLVQAFSQGRGDWLAL-.ALQDQIHQPYRQSLIPAYDQLHQ--
  10 SRHLLPKRYSVQESVFNLSHASLMTMAIVQGKWDLL-RC.CSKDRMHQYKRMQTYPVLFAIQK--
  11 SRHLLPKRYSVQESVFNLSHASLMTMAIVQGKWDLL-RC.CSKDRMHQYKRMQTYPVLFAIQK--
  12 SRQALAKNLSFNDAVFNLSHASFLTACFLEKKYEFL-KF.ASQDKLHEINRMKNLPELFEVQK--
  13 ARKILPSMVPLKDAVKNIAMASSLILALKEGDLETIGR-.LLDDNLALPYRKKLMPWFDEIRR--
  14 ARRIVPEKVPLKDAIKNLAMASSLVLALKEGDIETVGR-.LLDDNLALPYRKKLMPWFDEVRK--
  15 MRAALPTEIPMVHHVWNSSQAAALVAAVLEGDAVMLGKA.LSSDKIVEPTRAPLIPGMEAVKK--
  16 KQGYLPAQYRRQDCIAHGRHLAGFIHACYSRQPELAAK-.LMKDVIAEPYRERLLPGFRQARQA-
  17 MRAALPTEIPMVHHVWNSSQAAALVAAVLEGDAVMLGKA.LSSDKIVEPTRAPLIPGMEAVKK--
  18 ARAVLPREYSRADTVHALSHAALLAAALAQGRLDLL-RH.AMQDYVHQVWRAPLVPGLSDI----
  19 SRSVLPKKLSYKEAVAASSIANVAVAALLAGDMVTAGQA.IEGDLFHERYRQDLVREFAMIKQVT
  20 SRKVLPNELTYKEAVAASSIANVLTASLLTNNLEVAGQM.MEADRFHESYRASLIPELQLLR---
  21 ARDVLPKEFPYADAVKASAVSNILIAAIMSKDWPLVGKI.MKKDMFHQPYRAMLVPELSKVE---
  22 ARDVLPKEFPYADAVKASAVSNILIAAIMSKDWPLVGKI.MKKDMFHQPYRAMLVPELSKVE---
  23 SRGVLPKAYPTQDLVFNLQRLAVLTTALTMDPPNADLIYpAMQDRVHQPYRKTLIPGLTEI----
  24 SRGVLPKAYPTQDLVFNLQRLAVLTTALTMDPPNADLIYpAMQDRVHQPYRKTLIPGLTEI----
  25 MRKVLPENVSFRDAVRNFSRAAGIVAAAVNGDLKSMGAL.MMSDEIVEPRRRSYVPCYTQVRK--
  26 VRRVLPTEVTHIDARFNVSRVAVMIVALQQRPD--LLWE.GTRDRLHQPYRAEVLPVTS------
  27 VRRVLPTEVTHIDARFNVSRVAVMIVALQQRPD--LLWE.GTRDRLHQPYRAEVLPITS------
  28 ARSVLPTSYGRTDVVYNLQRLALLTTALGQTPINPHLVYeVMKDKVHQPYRASLIPGLQNI----
  29 MRKILPEKVPFEDAVFNIKNSCQFLAKIAAGKIKEALK-.YVGDRLHQNYRI-------------
  30 SRVLLPARVSHDDARFNVSRAALLVVALTERPD--LLMA.ATEDVLHQPHRAS------------
  31 ARDILPKKYKKETCIKNSRYLAGFIHASYSQQPHLAAR-.LMQDFIAEPYRIKLLPN--------
  32 TRVLLPAQVSHDDARFNVSRAALLVVALTERPD--LLMA.ATEDLLHQPQRA-------------
  33 AREVLKDPYLLPDIVTQSANLALVLAGCYHGDAELV-RA.GLRDVLIEPRRAPLIAGFTAAQQ--


       
      
   1 K
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