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:

- T0271 1vgg, Thermus thermophilus
- gi|17545138|ref|NP_518540.1|_1:161 PROBABLE TRANSMEMBRANE PROTEIN [Ralstonia solanacearum GMI1000]
- gi|17427429|emb|CAD13947.1| PROBABLE TRANSMEMBRANE PROTEIN [Ralstonia solanacearum]
- gi|27380465|ref|NP_771994.1|_1:161 bll5354 [Bradyrhizobium japonicum USDA 110]
- gi|27353629|dbj|BAC50619.1| bll5354 [Bradyrhizobium japonicum USDA 110]
- gi|46132840|ref|ZP_00171564.2|_1:161 COG1839: Uncharacterized conserved protein [Ralstonia eutropha JMP134]
- gi|48770129|ref|ZP_00274473.1|_1:161 COG1839: Uncharacterized conserved protein [Ralstonia metallidurans CH34]
- gi|39996287|ref|NP_952238.1|_3:161 conserved hypothetical protein [Geobacter sulfurreducens PCA]
- gi|39983167|gb|AAR34561.1| conserved hypothetical protein [Geobacter sulfurreducens PCA]
- gi|46199034|ref|YP_004701.1|_1:161 hypothetical conserved protein [Thermus thermophilus HB27]
- gi|46196658|gb|AAS81074.1| hypothetical conserved protein [Thermus thermophilus HB27]
- gi|16082614|ref|NP_394809.1|_1:159 Uncharacterized conserved protein [Thermoplasma acidophilum DSM 1728]
- gi|48845902|ref|ZP_00300172.1|_3:161 COG1839: Uncharacterized conserved protein [Geobacter metallireducens GS-15]
- gi|15897561|ref|NP_342166.1|_5:162 Conserved hypothetical protein [Sulfolobus solfataricus P2]
- gi|25305025|pir||E90212 conserved hypothetical protein [imported] - Sulfolobus solfataricus [Taxonomy]
- gi|6015824|emb|CAB57651.1| hypothetical protein [Sulfolobus solfataricus]
- gi|13813818|gb|AAK40956.1| Conserved hypothetical protein [Sulfolobus solfataricus P2]
- gi|46315607|ref|ZP_00216189.1|_3:161 COG1839: Uncharacterized conserved protein [Burkholderia cepacia R18194]
- gi|23474187|ref|ZP_00129481.1|_1:160 COG1839: Uncharacterized conserved protein [Desulfovibrio desulfuricans G20]
- gi|23476029|ref|ZP_00131266.1| COG1839: Uncharacterized conserved protein [Desulfovibrio desulfuricans G20]
- gi|15678726|ref|NP_275842.1|_9:168 unknown [Methanothermobacter thermautotrophicus]
- gi|7429768|pir||B69193 hypothetical protein MTH699 - Methanobacterium thermoautotrophicum (strain Delta H) [Taxonomy]
- gi|2621785|gb|AAB85204.1| unknown [Methanothermobacter thermautotrophicus str. Delta H]
- gi|37521614|ref|NP_924991.1|_1:160 hypothetical protein glr2045 [Gloeobacter violaceus PCC 7421]
- gi|35212612|dbj|BAC89986.1| glr2045 [Gloeobacter violaceus PCC 7421]
- gi|15610871|ref|NP_218252.1|_5:162 hypothetical protein Rv3735 [Mycobacterium tuberculosis H37Rv]
- gi|31794907|ref|NP_857400.1| CONSERVED HYPOTHETICAL PROTEIN [Mycobacterium bovis AF2122/97]
- gi|7429769|pir||H70797 hypothetical protein Rv3735 - Mycobacterium tuberculosis (strain H37RV) [Taxonomy]
- gi|2960159|emb|CAA18057.1| CONSERVED HYPOTHETICAL PROTEIN [Mycobacterium tuberculosis H37Rv]
- gi|31620505|emb|CAD95948.1| CONSERVED HYPOTHETICAL PROTEIN [Mycobacterium bovis AF2122/97]
- gi|15843356|ref|NP_338393.1|_7:165 conserved hypothetical protein [Mycobacterium tuberculosis CDC1551]
- gi|13883720|gb|AAK48207.1| conserved hypothetical protein [Mycobacterium tuberculosis CDC1551]
- gi|13541328|ref|NP_111016.1|_1:159 Uncharacterized conserved protein [Thermoplasma volcanium GSS1]
- gi|14324712|dbj|BAB59639.1| hypothetical protein [Thermoplasma volcanium GSS1]
- gi|48425362|pdb|1RLH|A_22:172 Chain A, Structure Of A Conserved Protein From Thermoplasma Acidophilum [Taxonomy]
- gi|15921805|ref|NP_377474.1|_4:161 162aa long conserved hypothetical protein [Sulfolobus tokodaii str. 7]
- gi|15622592|dbj|BAB66583.1| 162aa long conserved hypothetical protein [Sulfolobus tokodaii str. 7]
- gi|10640696|emb|CAC12474.1|_3:152 conserved hypothetical protein [Thermoplasma acidophilum]
- gi|14601971|ref|NP_148516.1|_33:190 hypothetical protein APE2289 [Aeropyrum pernix K1]
- gi|7517069|pir||E72455 hypothetical protein APE2289 - Aeropyrum pernix (strain K1) [Taxonomy]
- gi|5105990|dbj|BAA81301.1| 191aa long hypothetical protein [Aeropyrum pernix K1]
- gi|48478083|ref|YP_023789.1|_5:158 hypothetical protein PTO1011 [Picrophilus torridus DSM 9790]
- gi|48430731|gb|AAT43596.1| hypothetical protein PTO1011 [Picrophilus torridus DSM 9790]
- gi|15642969|ref|NP_228011.1|_3:151 conserved hypothetical protein [Thermotoga maritima MSB8]
- gi|7445299|pir||D72407 conserved hypothetical protein - Thermotoga maritima (strain MSB8) [Taxonomy]
- gi|4980692|gb|AAD35288.1| conserved hypothetical protein [Thermotoga maritima MSB8]
- gi|48851801|ref|ZP_00305997.1|_1:159 COG1839: Uncharacterized conserved protein [Ferroplasma acidarmanus]
- gi|18976620|ref|NP_577977.1|_3:161 hypothetical protein PF0248 [Pyrococcus furiosus DSM 3638]
- gi|18892187|gb|AAL80372.1| hypothetical protein [Pyrococcus furiosus DSM 3638]
- gi|14591660|ref|NP_143747.1|_3:161 hypothetical protein PH1918 [Pyrococcus horikoshii OT3]
- gi|7429766|pir||D71206 hypothetical protein PH1918 - Pyrococcus horikoshii [Taxonomy]
- gi|14521892|ref|NP_127369.1|_3:161 hypothetical protein PAB1234 [Pyrococcus abyssi GE5]
- gi|7445298|pir||H75019 hypothetical protein PAB1234 - Pyrococcus abyssi (strain Orsay) [Taxonomy]
- gi|5459112|emb|CAB50598.1| Hypothetical protein [Pyrococcus abyssi]
- gi|18313250|ref|NP_559917.1|_4:158 conserved hypothetical protein [Pyrobaculum aerophilum str. IM2]
- gi|18160770|gb|AAL64099.1| conserved hypothetical protein [Pyrobaculum aerophilum str. IM2]
- gi|11499998|ref|NP_071244.1|_1:161 hypothetical protein [Archaeoglobus fulgidus DSM 4304]
- gi|7429767|pir||G69552 hypothetical protein AF2422 - Archaeoglobus fulgidus [Taxonomy]
- gi|2650677|gb|AAB91249.1| A. fulgidus predicted coding region AF2422 [Archaeoglobus fulgidus DSM 4304]

              10         20         30        40        50        60   
              |          |          |         |         |         |   
   1 MELKLIPIEKPE.NLNVILGQAHF.IKTVEDLHEALVTAVPGIRFGLAFSEASGKRLVRRSGTDE
   2 MELTVVPIVKPE.ATNFILGQSHF.IKTVEDLHEALVGAVPGIRFGLAFCEASGKRLVRWSGNDD
   3 MELTVVPIVKPD.ATNFIFGQSHF.IKTVEDLHEALVGAVPGIRFGLAFCEASGKRLVRWSGNDE
   4 MELLSVPVTKPE.ATNFIFGQSHF.IKTVEDLHEVLVGTVPGIRFGLAFCEASGKRLVRWSGTDE
   5 MELSAVPVSKPA.DTNFIFGQSHF.IKTVEDLHEALVGTVPGIRFGIAFCEASGKRLVRWSGTDE
   6 LEIHTIKVDIPQ.DCNVILGQTHF.IKTAEDLYEVVATTVPQARFGIAFTEASGPCLIRTEGNDE
   7 MELKLIPIEKPE.NLNVILGQAHF.IKTVEDLHEALVTAVPGIRFGLAFSEASGKRLVRRSGTDP
   8 MSIETVDMVIPA.EANIIVGYSHF.IKTVEDLNEIIRTHVPGSKYGIGFSEASGDRLIRYDGNDD
   9 LEINAIAIDIPD.DCNLILGQTHF.IKTAEDLYEIIATTVSLARFGIAFTEASGPCLIRTEGNDD
  10 -KIDVVRIDIPE.GTNVIIGQSHF.IKTVEDLYETLSSSSPNLKFGIAFNEASSKRLIRYDGNDQ
  11 -QLHTVAVDKPE.TMNFILGQSHF.IKSVEDIHEALVGTVPGIRFGLAFCEASGKRLVRHSGTDA
  12 MQLHTVSVKNPE.SLNMILGQSHF.IKTVEDVHEAIVCTVPGAKFGIAFCEASADCLIRWSGTDQ
  13 MELKKVKIESWE.DINLILGQSHF.IKTVEDIYEAIVNTVPQAKFGIAFAEASGDCLVRRAGNDE
  14 MEFKAVTMVIPE.DCNLILGQAHF.IKTVEDLHEIFVGISAQVKFGIAFCEASGPCLIRLSGNDA
  15 --WDVVSVDKPD.DVNVVIGQAHF.IKAVEDLHEAMVGVSPSLRFGLAFCEASGPRLVRHTGNDG
  16 -AWDVVSVDKPD.DVNVVIGQAHF.IKAVEDLHEAMVGVSPSLRFGLAFCEASGPRLVRHTGNDG
  17 MDIEAVDMIVPN.DSNIIVGYSHF.IKTVEDLNEIVHTSMPKCRYAIAFSEASGDRLIRYEGNDD
  18 --------VIPA.EANIIVGYSHF.IKTVEDLNEIIRTHVPGSKYGIGFSEASGDRLIRYDGNDD
  19 -KIDVIRVEIPE.GTNVIIGQSHF.IKTVEDLYETLASSSPHLKFGIAFCEASGKRLIRWDGNDE
  20 ---------IPA.EANIIVGYSHF.IKTVEDLNEIIRTHVPGSKYGIGFSEASGDRLIRYDGNDD
  21 -KLEVVDIEIPE.GANVIIGRSHF.IKTVEDLYEALVTSCPSLKFGIAFCEASGKRLVRHDGNDE
  22 -----IVIERPD.DSNVILGYSHF.IKTIEDLKEIVVTSVPKCRFGIAFSEASGERLIRFDGNDR
  23 -------VSIPE.NANIILGHSHF.IKTVEDLYEVMVTTNPNLKFGIAFNEASGPCLIRYEGNDE
  24 MEIVAVEINKPE.DVNIILGYSHF.IKTVEDMNEIIKTTIPGCEYAIVFSEASGDKLIRYEGNNK
  25 -RIEVVDIEKPE.GVEVIIGQGNFsIFTVDDLARALLTTVPGIKFGIAMNEAK-PQLTRYTGNDP
  26 -RIEVIDIEKPE.GVEVIIGQGNFsIFTVDDLARALLTAVPGIKFGIAMNEAK-PQLTRYTGNDP
  27 -RIEVVEIEKPE.GVEVIIGQGNFsIFTVDDLARALLTAVPGIKFGIAMNEAK-PQLTRYTGNDP
  28 -KFELIDVPIPQ.GTNVIIGQAHF.IKTVEDLYEALVTSVPGVKFGIAFCEASGKRLVRHEANDE
  29 MKLEKVEILNPDlKYQIVVGQANFsVFTVDDLFRALLTAVPGIKVAVAMNEAA-PKLVRVTGNDE


           70        80        90       100       110       120        
           |         |         |         |         |         |        
   1 ALVELAVKNLLNLACGHVFLIVLGEGFYPINVLHAVKACPEVVRIYAATANPLKVVVAE.EGEQR
   2 AALKLARDNALAIGAGHVFLIFLGDGFFPVNVLAAVRAVPEVCRIYCATANPTQVIVAQ.TEQGR
   3 AAIALARDNAMAIGAGHTFLIFLGDGFFPVNVLAAVRAAPEVCRIYCATANPTQVIVAQ.TEQGC
   4 SLIDLACENARAVGAGHSFFIFLGDGFFPVNVLGAVRAVPEVCRIYCATANPAEIIVAQ.TDSGR
   5 AMIDLACQNATAIAAGHTFLIFLGGGFFPVNVLGAVRAVPEVCRIYCATANPTEVIVAQ.TDLGR
   6 ELIRVCVRNLQAIGAGHVFCVLLKEA-YPINILNQIKNCPEVCRIFCATANPLQVIVAS.TSQGW
   7 ELVELAVKNLLNLACGHAFLIVLGEGFYPINVLHAVKACPEVVRIYAATANPLKVVVAE.EGEQR
   8 DLVKACIENIRRISAGHTFVILIRNA-YPINILNAVKMCQEVGSIFAATANPLQIIVYK.GERGN
   9 ELTQACVRNLQAIGAGHVFCILLRDA-YPINILNQIKNCPEVCSIYCATANPLQVIVAS.TAQGS
  10 ELIKLAIENAKKIGAGHVFVIYLKNG-YPINVLNRIKNVEEVVRIFVATANPLQVIVAE.TDQGR
  11 TLVELACRNASAIGAGHAFIVFLGDGFYPVNVLNAIKAVPEVCRIYCATANPTEVIVAE.TAQGR
  12 SLIDLAVTNAQALGCGHTFIIFMRDM-FPINILNTIQQVPEVVRIFCATANPVQGIVAE.TDQGR
  13 ELEELAAETMLEIAAGHSFIVFLKDA-FPINVLQRIKDVPEVVNIYCATANPVEVIIAE.TDQGR
  14 PLQEVATANAQALGAGHCFVILLKEA-YPINFLNAIKQCAEVCTIYCATANPTQVIVAV.TEQGN
  15 DLVELATRTALAIAAGHSFVIFLREG-FPINILNPVQAVPEVCTIYCATANPVDVVVAV.TPHGR
  16 DLVELATRTALAIAAGHSFVIFLREG-FPINILNPVQAVPEVCTIYCATANPVDVVVAV.TPHGR
  17 ELVNAAIENIKRISAGHTFVILLRDA-YPINILNAVKSCQEVGGIFAATANSLKIIIYK.GENGN
  18 DLVKACIENIRRISAGHTFVILIRNA-YPINILNAVKMCQEVGSIFAATANPLQIIVYK.GERGN
  19 ELIKLAQQTALKIGAGHTFVIYIKNG-FPINVLNRIKNVEEVVRIFAATANPLQVLVAE.TDQGR
  20 DLVKACIENIRRISAGHTFVILIRNA-YPINILNAVKMCQEVGSIFAATANPLQIIVYK.GERGN
  21 DLRKKAIEACMKIGAGHVFVVYIRNG-WPINVLNAIKSVQEVVSIDAATANPVKVVVAD.LGEQR
  22 ELTDIAVKNLLNVKSGHTFIIIIRDA-YPINMLNAIKMCQEVGTIFAATANPLSVIVYE.GSNGN
  23 ELVNQAIETAKKIGAGHTFVIYIRGG-YPINILNQIKNVQEVCRIYTATANPLQVIVGI.TSQGR
  24 ELIDCGIENIKKISAGHTFMILLRNA-FPINILPQLKMTQELGAIFAATANPIKVILAK.TENTN
  25 ELEKLAAKNALKIGAGHVFVILMKNA-YPINVLNTIKNHPAVAMVYGASENPFQVIVAE.TELGR
  26 ELEALAAKNAVKIGAGHVFVILMKNA-YPINVLNTIKNHPAVAMIYGASENPFQVIVAE.TELGR
  27 ELEKLAAKNAVKIGAGHVFVILMKNA-YPINVLNTIKNHPAVAMVYGASENPFQVIVAE.TDLGR
  28 ELRNLAIDLCKKIAAGHVFVIYIRNA-WPINVLNAIKNVPEVVRIFAATANPLKVIVAEvEPERR
  29 ELKKIAAENALRIAASHVFVVVTSNA-FPINILNTIKLHPAVCNVFVASANPIEIIVAE.TELGR


      130       140       150       160 
       |         |         |         | 
   1 AILGVMDGFTPLGVEDEAEVAWRKDLLRRLGYKL
   2 GVLGVVDGASPLGIETDADIAWRKDLLRQIGYKL
   3 GVLGVVDGASPLGVETDEDIAWRKDLLRKIGYKL
   4 AVLGVVDGASPLGIETDADISERRELLRKFGYKL
   5 AVLGVVDGEPPLGIETTADIADRKQLLRQIGYKL
   6 GVLGVIDGHPPKGVETDDDRQHRRDFLRAIGYK-
   7 AILGVMDGFTPLGVEDEAEVAWRKDLLRRLGYKL
   8 GVLGVIDGYSPVGVESDADIEKRRQFLRRIGYK-
   9 GVLGVIDGFPPKGVESDDDRQKRRDFLRAIGYK-
  10 GVIGVVDGYAPLGVESEADIQERKEFLRKIGYK-
  11 GIVGVVDGFGPLGVENDDDIRWRKDLLRTIGYK-
  12 GLMGVVDGFAPKGVETEEHIAKRKGFLRTIGYKL
  13 GILGVIDGNSPGEIEGDEDIAARKKFLRVIGYKF
  14 GILGVVDGFAPRGVESPADVQQRQAFLRRVGYKL
  15 GIVGVVDGQTPLGVETDRDIAQRRDLLRAIGYKL
  16 GIVGVVDGQTPLGVETDRDIAQRRDLLRAIGYKL
  17 GVLGVIDGMSPVGVESDDDKKKRRDLLRKIGYK-
  18 GVLGVIDGYSPVGVESDADIEKRRQFLRRIGYK-
  19 GVIGVVDGYTPLGIETEADIKERKELLRKFGYK-
  20 GVLGVIDGYSPVGVESDADIEKRRQFLRRIGYK-
  21 ALLGVADGFKPLGVEGEDDIRERKEFLRKIGYK-
  22 GILGVIDGYSPLGIEDEAAKEKRKKLLRDIGYK-
  23 AVLGVVDGYSPKGVEGEEDKRKRHAFLREI----
  24 AVIGVADGYSPVGVETDKDKEKRRKFLRDIGYK-
  25 AVIGVVDGKAATKIETEEQKKERRELVEKIGYKI
  26 AVIGVVDGKAANKIETDEQKKERRELVEKIGYKI
  27 SVIGVVDGKAANKIETEEQKKERRELVEKIGYKI
  28 GVVGVVDGHSPLGVETEKDREERKKFLRE-----
  29 AVLGAVDGAAVTRIENEEEKRQRRELCEKLGYRL