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:

- T0293
- gi|12848120|dbj|BAB27835.1|_42:90 unnamed protein product [Mus musculus]
- gi|14042068|dbj|BAB55094.1|_42:90 unnamed protein product [Homo sapiens]
- gi|21362066|ref|NP_076991.2| hypothetical protein LOC79066 [Homo sapiens]
- gi|29791720|gb|AAH50603.1|_42:90 METT10D protein [Homo sapiens]
- gi|67967559|dbj|BAE00262.1|_42:90 unnamed protein product [Macaca fascicularis]
- gi|31873510|emb|CAD89999.2|_42:90 hypothetical protein [Homo sapiens]
- gi|56205950|emb|CAI24378.1|_42:90 novel protein [Mus musculus]
- gi|56205388|emb|CAI24251.1| novel protein [Mus musculus]
- gi|62656526|ref|XP_340845.2|_42:90 PREDICTED: similar to RIKEN cDNA 2810013M15 [Rattus norvegicus]
- gi|55644871|ref|XP_523533.1|_154:202 PREDICTED: similar to MGC3329 protein [Pan troglodytes]
- gi|74202960|dbj|BAE26189.1|_42:90 unnamed protein product [Mus musculus]
- gi|56205951|emb|CAI24379.1|_42:90 novel protein [Mus musculus]
- gi|56205387|emb|CAI24250.1| novel protein [Mus musculus]
- gi|74216910|dbj|BAE26574.1| unnamed protein product [Mus musculus]
- gi|74222968|dbj|BAE40630.1| unnamed protein product [Mus musculus]
- gi|12849683|dbj|BAB28440.1| unnamed protein product [Mus musculus]
- gi|32451971|gb|AAH54724.1| Hypothetical protein LOC67493 [Mus musculus]
- gi|29436824|gb|AAH49897.1| Hypothetical protein LOC67493 [Mus musculus]
- gi|21312938|ref|NP_080473.1| hypothetical protein LOC67493 [Mus musculus]
- gi|76643676|ref|XP_586212.2|_42:90 PREDICTED: similar to CG7544-PA [Bos taurus]
- gi|73967246|ref|XP_868505.1|_42:90 PREDICTED: similar to Hypothetical UPF0049 protein ZK1128.2 in chromosome III isoform 2 [Canis familiaris]
- gi|73967244|ref|XP_537774.2|_42:90 PREDICTED: similar to Hypothetical UPF0049 protein ZK1128.2 in chromosome III isoform 1 [Canis familiaris]
- gi|71896227|ref|NP_001026773.1|_42:90 hypothetical protein LOC431184 [Gallus gallus]
- gi|53136428|emb|CAG32543.1| hypothetical protein [Gallus gallus]
- gi|49257234|gb|AAH71096.1|_42:90 MGC81116 protein [Xenopus laevis]
- gi|50417838|gb|AAH78220.1|_42:90 Hypothetical protein LOC445217 [Danio rerio]
- gi|57525677|ref|NP_001003611.1| hypothetical protein LOC445217 [Danio rerio]
- gi|12654743|gb|AAH01213.1|_42:90 METT10D protein [Homo sapiens]
- gi|47212445|emb|CAG11398.1|_44:90 unnamed protein product [Tetraodon nigroviridis]
- gi|72054094|ref|XP_793611.1|_44:90 PREDICTED: similar to CG7544-PA [Strongylocentrotus purpuratus]
- gi|91095139|ref|XP_973052.1|_41:89 PREDICTED: similar to Hypothetical UPF0049 protein ZK1128.2 in chromosome III [Tribolium castaneum]
- gi|56753878|gb|AAW25136.1|_43:90 SJCHGC03211 protein [Schistosoma japonicum]
- gi|55234795|gb|EAA00148.2|_42:89 ENSANGP00000021275 [Anopheles gambiae str. PEST]
- gi|58394283|ref|XP_320636.2| ENSANGP00000021275 [Anopheles gambiae str. PEST]
- gi|66560989|ref|XP_624889.1|_43:89 PREDICTED: similar to Zgc:100981 [Apis mellifera]
- gi|19922302|ref|NP_611015.1|_47:95 CG7544-PA [Drosophila melanogaster]
- gi|16185375|gb|AAL13909.1| LD39460p [Drosophila melanogaster]
- gi|21627173|gb|AAF58169.2| CG7544-PA [Drosophila melanogaster]
- gi|54635817|gb|EAL25220.1|_45:93 GA20428-PA [Drosophila pseudoobscura]
- gi|50904849|ref|XP_463913.1|_54:101 SAM-dependent methyltransferase-like protein [Oryza sativa (japonica cultivar-group)]
- gi|51963820|ref|XP_506693.1| PREDICTED OSJNBb0088N06.22 gene product [Oryza sativa (japonica cultivar-group)]
- gi|41052744|dbj|BAD07600.1| SAM-dependent methyltransferase-like protein [Oryza sativa (japonica cultivar-group)]
- gi|41052631|dbj|BAD08140.1| SAM-dependent methyltransferase-like protein [Oryza sativa (japonica cultivar-group)]
- gi|57225872|gb|AAW42333.1|_37:82 conserved hypothetical protein [Cryptococcus neoformans var. neoformans JEC21]
- gi|58264968|ref|XP_569640.1| hypothetical protein [Cryptococcus neoformans var. neoformans JEC21]
- gi|50259505|gb|EAL22178.1|_37:82 hypothetical protein CNBC3160 [Cryptococcus neoformans var. neoformans B-3501A]
- gi|24817626|emb|CAD54175.1|_42:86 Hypothetical protein ZK1128.2b [Caenorhabditis elegans]
- gi|32564933|ref|NP_871660.1| ZK1128.2b [Caenorhabditis elegans]
- gi|68544986|ref|ZP_00584537.1|_56:104 Protein of unknown function DUF890 [Shewanella amazonensis SB2B]
- gi|68516854|gb|EAN40564.1| Protein of unknown function DUF890 [Shewanella amazonensis SB2B]
- gi|24817627|emb|CAA87421.2|_42:86 Hypothetical protein ZK1128.2a [Caenorhabditis elegans]
- gi|32564931|ref|NP_499247.2| ZK1128.2a [Caenorhabditis elegans]
- gi|29840843|sp|Q09357|YS02_CAEEL Hypothetical UPF0049 protein ZK1128.2 in chromosome III [Taxonomy]
- gi|39590668|emb|CAE65038.1|_42:86 Hypothetical protein CBG09879 [Caenorhabditis briggsae]
- gi|28829833|gb|AAO52335.1|_60:104 similar to ZK1128.2.p [Caenorhabditis elegans] [Dictyostelium discoideum]
- gi|66820304|ref|XP_643782.1|_79:124 hypothetical protein DDB0203108 [Dictyostelium discoideum]
- gi|60471928|gb|EAL69882.1| hypothetical protein DDBDRAFT_0203108 [Dictyostelium discoideum AX4]
- gi|79322590|ref|NP_001031382.1|_53:97 unknown protein [Arabidopsis thaliana]
- gi|52354261|gb|AAU44451.1|_53:97 hypothetical protein AT2G21070 [Arabidopsis thaliana]
- gi|42569208|ref|NP_179703.2|_53:97 unknown protein [Arabidopsis thaliana]
- gi|55733759|gb|AAV59276.1| At2g21070 [Arabidopsis thaliana]
- gi|53850469|gb|AAU95411.1| At2g21070 [Arabidopsis thaliana]
- gi|77814335|ref|ZP_00813595.1|_83:129 Protein of unknown function DUF890 [Shewanella putrefaciens CN-32]
- gi|77810606|gb|EAO94984.1| Protein of unknown function DUF890 [Shewanella putrefaciens CN-32]
- gi|82740238|ref|ZP_00902980.1| conserved hypothetical protein [Shewanella sp. W3-18-1]
- gi|82722352|gb|EAP57176.1| conserved hypothetical protein [Shewanella sp. W3-18-1]
- gi|67153802|ref|ZP_00415547.1|_67:112 Protein of unknown function DUF890 [Azotobacter vinelandii AvOP]
- gi|67087935|gb|EAM07401.1| Protein of unknown function DUF890 [Azotobacter vinelandii AvOP]

              10        20          30        40         
              |         |           |         |         
   1 VSLNFKDPEAVRALTCTLLREDFGLS.I.DIPLERLIPTVPLRLNYIHWVE
   2 VSLNFKDPEAVRALTCTLLREDFGLS.I.DIPLERLIPTVPLRLNYIHWVE
   3 VSLNFKDPEAVRALTCTLLREDFGLS.I.DIPLERLIPTVPLRLNYIHWVE
   4 VSLNFKDPEAVRALTCTLLREDFGLS.I.DIPLERLIPTVPLRLNYIHWVE
   5 VSLNFKDPEAVRALTCTLLREDFGLS.I.DIPLERLIPTVPLRLNYIHWVE
   6 VSLNFKDPEAVRALTCTLLREDFGLS.I.DIPLERLIPTVPLRLNYIHWVE
   7 VSLNFKDPEAVRALTCTLLREDFGLS.I.DIPLERLIPTVPLRLNYIHWVE
   8 VSLNFKDPEAVRALTCTLLREDFGLS.I.DIPLERLIPTVPLRLNYIHWVE
   9 VSLNFKDPEAVRALTCTLLREDFGLS.I.DIPLERLIPTVPLRLNYIHWVE
  10 VSLNFKDPEAVRALTCTLLREDFGLS.I.DIPLERLIPTVPLRLNYIHWVE
  11 VSLNFKDPEAVRALTCTLLREDFGLS.I.DIPLERLIPTVPLRLNYIHWVE
  12 VSLNFKDPEAVRALTCTLLREDFGLS.I.DIPLERLIPTVPLRLNYIHWVE
  13 VSLNFKDPEAVRALTCTLLKEDFGLS.I.DIPLERLIPTVPLRLNYIHWVE
  14 VSLNFKDPEAVRALTCTLLKEDFGLS.I.DIPLERLIPTVPLRLNYIHWVE
  15 VSLNFKDPEAVRALTCTLLKEDFGLT.I.DIPLERLIPTVPLRLNYIHWVE
  16 VSLNFKDPCAVRALTCTLLKEDFGLT.I.DIPLERLIPTVPLRLNYIHWVE
  17 VTLNFKDPEAVRALTCTLLKEDFGLT.I.EIPLERLIPTVPLRLNYIHWVE
  18 VSLNFKDPEAVRALTCTLLREDFGLS.I.DIPLERLIPTVPLRLNYIHWVE
  19 --VNFKEPEAVRALTCTLLKEDFGLT.I.QIPLERLIPTVPLRLNYIHWVE
  20 --LDFHDSESLRSLTCTLLKEDFGLE.V.ELPLDRLIPTLSLRLNYIHWIE
  21 VTIDFKNVGALRALTCTLLKKDFDLN.I.EIPPGKLIPTIPLRLNYILWLE
  22 -MLDFRTPSHLAALSKALLMKDFGLN.V.NFPSDRLIPTVPLRLNYILWLE
  23 -RLDYRNKRAVHLLSKCLLLRDFGLK.L.ELPPDKLVPTLPLRLNYIHWLE
  24 --IDFKNEESLRVLTEVLLKHDFNLE.V.KIPPNKLVPTLPLRINYILWIE
  25 VSVNFRNEKTLRELTKMLLKEYYDLD.V.DFAPGSLVPTLALRLNYILWLE
  26 VSVNFRNEKTLRELSKMLLKEYFELD.V.DFAPGSLVPTLALRLNYILWLE
  27 -SIDFTDFAATRELTRVLLLHDHGVN.W.WIPDGQLCPTVPNRSNYIHWIE
  28 -SINFQDPTALRELTKCLLKEDWNLD.V.DLREDRLCPTIPNRLDYIYH--
  29 -SINFQDPTALRELTKCLLKEDWNLD.V.DLREDRLCPTIPNRLDYIYH--
  30 VTFDFKKDAAVRCLTQTLLKKDFNLD.V.EIPPGHLVPRVPQKLNYC----
  31 -SIDFALPEAVKALNCALLKHHYGISrW.DIPKGFLCPPIPGRVDYLHHLE
  32 VTFDFKKDAAVRCLTQTLLKKDFNLD.V.EIPPGHLVPRVPQKLNYC----
  33 VTLDFRKDAAVRCLTQTLLKKDFSLN.V.NLPAGHLVPRVPQKLNYC----
  34 ---NWKDSNATKELTRVLLDHDFGLR.I.ELPDNYLCPTLTLRINYLYWI-
  35 --IDWKDSNATKELTRVLLDHDFGLR.I.ELPDNYLCPTLTLRINYLYWI-
  36 ---DWTDYNATRELTRVLLLHDHGVN.W.WIPDGQLCPTVPNRSNYIHWI-
  37 ---DWTDYNATRELTRVLLLHDHGVN.W.WIPDGQLCPTVPNRSNYIHWI-
  38 ---DWTDYNATRELTRVLLLHDHGVN.W.WIPDGQLCPTVPNRSNYIHWI-
  39 -SIDFADPEAVKTLNTALLKHHYGID.FwDIPKGALCPPIPGRVDYLHY--
  40 -SIDFADPEAVKALNRALLAEHYGIRqW.DIPPGYLCPPIPGRADYLH---