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|50904849|ref|XP_463913.1|_53:101 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|73967244|ref|XP_537774.2|_42:90 PREDICTED: similar to Hypothetical UPF0049 protein ZK1128.2 in chromosome III isoform 1 [Canis familiaris]
- gi|73967246|ref|XP_868505.1|_42:90 PREDICTED: similar to Hypothetical UPF0049 protein ZK1128.2 in chromosome III isoform 2 [Canis familiaris]
- gi|50417838|gb|AAH78220.1|_42:90 Hypothetical protein LOC445217 [Danio rerio]
- gi|57525677|ref|NP_001003611.1| hypothetical protein LOC445217 [Danio rerio]
- gi|71896227|ref|NP_001026773.1|_42:90 hypothetical protein LOC431184 [Gallus gallus]
- gi|53136428|emb|CAG32543.1| hypothetical protein [Gallus gallus]
- gi|55644871|ref|XP_523533.1|_154:202 PREDICTED: similar to MGC3329 protein [Pan troglodytes]
- gi|12848120|dbj|BAB27835.1|_42:90 unnamed protein product [Mus musculus]
- gi|74202960|dbj|BAE26189.1|_42:90 unnamed protein product [Mus musculus]
- gi|62656526|ref|XP_340845.2|_42:90 PREDICTED: similar to RIKEN cDNA 2810013M15 [Rattus norvegicus]
- 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|67967559|dbj|BAE00262.1|_42:90 unnamed protein product [Macaca fascicularis]
- gi|56205950|emb|CAI24378.1|_42:90 novel protein [Mus musculus]
- gi|56205388|emb|CAI24251.1| novel protein [Mus musculus]
- gi|29791720|gb|AAH50603.1|_42:90 METT10D protein [Homo sapiens]
- gi|76643676|ref|XP_586212.2|_42:90 PREDICTED: similar to CG7544-PA [Bos taurus]
- gi|31873510|emb|CAD89999.2|_42:90 hypothetical protein [Homo sapiens]
- gi|12654743|gb|AAH01213.1|_42:90 METT10D protein [Homo sapiens]
- gi|14042068|dbj|BAB55094.1|_42:90 unnamed protein product [Homo sapiens]
- gi|21362066|ref|NP_076991.2| hypothetical protein LOC79066 [Homo sapiens]
- gi|49257234|gb|AAH71096.1|_42:90 MGC81116 protein [Xenopus laevis]
- gi|91095139|ref|XP_973052.1|_41:89 PREDICTED: similar to Hypothetical UPF0049 protein ZK1128.2 in chromosome III [Tribolium castaneum]
- gi|47212445|emb|CAG11398.1|_42:90 unnamed protein product [Tetraodon nigroviridis]
- gi|42569208|ref|NP_179703.2|_50:98 unknown protein [Arabidopsis thaliana]
- gi|55733759|gb|AAV59276.1| At2g21070 [Arabidopsis thaliana]
- gi|53850469|gb|AAU95411.1| At2g21070 [Arabidopsis thaliana]
- gi|79322590|ref|NP_001031382.1|_50:98 unknown protein [Arabidopsis thaliana]
- gi|52354261|gb|AAU44451.1|_50:98 hypothetical protein AT2G21070 [Arabidopsis thaliana]
- gi|83943756|ref|ZP_00956214.1|_41:90 putative S-adenosyl-L-methionine-dependent methyltransferase [Sulfitobacter sp. EE-36]
- gi|83845436|gb|EAP83315.1| putative S-adenosyl-L-methionine-dependent methyltransferase [Sulfitobacter sp. EE-36]
- gi|83955232|ref|ZP_00963887.1|_41:90 putative S-adenosyl-L-methionine-dependent methyltransferase [Sulfitobacter sp. NAS-14.1]
- gi|83840225|gb|EAP79399.1| putative S-adenosyl-L-methionine-dependent methyltransferase [Sulfitobacter sp. NAS-14.1]
- gi|86140167|ref|ZP_01058729.1|_41:90 putative S-adenosyl-L-methionine-dependent methyltransferase [Roseobacter sp. MED193]
- gi|85823104|gb|EAQ43317.1| putative S-adenosyl-L-methionine-dependent methyltransferase [Roseobacter sp. MED193]
- gi|24817627|emb|CAA87421.2|_42:90 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|24817626|emb|CAD54175.1|_42:90 Hypothetical protein ZK1128.2b [Caenorhabditis elegans]
- gi|32564933|ref|NP_871660.1| ZK1128.2b [Caenorhabditis elegans]
- gi|66560989|ref|XP_624889.1|_41:89 PREDICTED: similar to Zgc:100981 [Apis mellifera]
- gi|72054094|ref|XP_793611.1|_42:90 PREDICTED: similar to CG7544-PA [Strongylocentrotus purpuratus]
- gi|39590668|emb|CAE65038.1|_42:90 Hypothetical protein CBG09879 [Caenorhabditis briggsae]
- gi|50259505|gb|EAL22178.1|_36:84 hypothetical protein CNBC3160 [Cryptococcus neoformans var. neoformans B-3501A]
- gi|57225872|gb|AAW42333.1|_36:84 conserved hypothetical protein [Cryptococcus neoformans var. neoformans JEC21]
- gi|58264968|ref|XP_569640.1| hypothetical protein [Cryptococcus neoformans var. neoformans JEC21]
- gi|28829833|gb|AAO52335.1|_57:105 similar to ZK1128.2.p [Caenorhabditis elegans] [Dictyostelium discoideum]
- gi|66820304|ref|XP_643782.1|_77:125 hypothetical protein DDB0203108 [Dictyostelium discoideum]
- gi|60471928|gb|EAL69882.1| hypothetical protein DDBDRAFT_0203108 [Dictyostelium discoideum AX4]
- gi|56753878|gb|AAW25136.1|_42:90 SJCHGC03211 protein [Schistosoma japonicum]
- gi|55234795|gb|EAA00148.2|_41:89 ENSANGP00000021275 [Anopheles gambiae str. PEST]
- gi|58394283|ref|XP_320636.2| ENSANGP00000021275 [Anopheles gambiae str. PEST]
- 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]

                      10        20         30        40               
                      |         |          |         |               
   1 ...VS...L..NFKDPEAVRALTCTLLREDFGLS.IDIPLERLIPTVPLRLNYIHWV...E...
   2 ggrAS...I..DFTDFAATRELTRVLLLHDHGVN.WWIPDGQLCPTVPNRSNYIHWI...Edll
   3 sgrVS...L..NFKDPEAVRALTCTLLKEDFGLS.IDIPLERLIPTVPLRLNYIHWV...Edli
   4 sgrVS...L..NFKDPEAVRALTCTLLKEDFGLS.IDIPLERLIPTVPLRLNYIHWV...Edli
   5 tgrVT...L..NFKDPEAVRALTCTLLKEDFGLT.IEIPLERLIPTVPLRLNYIHWV...Edli
   6 agrVS...L..NFKDPEAVRALTCTLLKEDFGLT.IDIPLERLIPTVPLRLNYIHWV...Edli
   7 ngrVS...L..NFKDPEAVRALTCTLLREDFGLS.IDIPLERLIPTVPLRLNYIHWV...Edli
   8 ngrVS...L..NFKDPEAVRALTCTLLREDFGLS.IDIPLERLIPTVPLRLNYIHWV...Edli
   9 ngrVS...L..NFKDPEAVRALTCTLLREDFGLS.IDIPLERLIPTVPLRLNYIHWV...Edli
  10 ngrVS...L..NFKDPEAVRALTCTLLREDFGLS.IDIPLERLIPTVPLRLNYIHWV...Edli
  11 ngrVS...L..NFKDPEAVRALTCTLLREDFGLS.IDIPLERLIPTVPLRLNYIHWV...Edli
  12 ngrVS...L..NFKDPEAVRALTCTLLREDFGLS.IDIPLERLIPTVPLRLNYIHWV...Edli
  13 ngrVS...L..NFKDPEAVRALTCTLLREDFGLS.IDIPLERLIPTVPLRLNYIHWV...Edli
  14 ngrVS...L..NFKDPEAVRALTCTLLREDFGLS.IDIPLERLIPTVPLRLNYIHWV...Edli
  15 ngrVS...L..NFKDPEAVRALTCTLLREDFGLS.IDIPLERLIPTVPLRLNYIHWV...Edli
  16 ngrVS...L..NFKDPEAVRALTCTLLREDFGLS.IDIPLERLIPTVPLRLNYIHWV...Edli
  17 ngrVS...L..NFKDPEAVRALTCTLLREDFGLS.IDIPLERLIPTVPLRLNYIHWV...Edli
  18 dgrVS...L..NFKDPEAVRALTCTLLREDFGLS.IDIPLERLIPTVPLRLNYIHWV...Edli
  19 agrVS...L..NFKDPCAVRALTCTLLKEDFGLT.IDIPLERLIPTVPLRLNYIHWV...Edli
  20 sgkVT...I..DFKNVGALRALTCTLLKKDFDLN.IEIPPGKLIPTIPLRLNYILWL...Edll
  21 ...TGrlvV..NFKEPEAVRALTCTLLKEDFGLT.IQIPLERLIPTVPLRLNYIHWV...Edli
  22 gsrAR...I..DWTDYNATRELTRVLLLHDHGVN.WWIPDGQLCPTVPNRSNYIHWI...Ndll
  23 gsrAR...I..DWTDYNATRELTRVLLLHDHGVN.WWIPDGQLCPTVPNRSNYIHWI...Ndll
  24 gsrAR...I..DWTDYNATRELTRVLLLHDHGVN.WWIPDGQLCPTVPNRSNYIHWI...Ndll
  25 agqTT...I..DFRDVAAVRMLNRALLKADYGIDfWDIPPNYLCPPIPGRVDYIHHL...Adll
  26 agqTT...I..DFRDVAAVRMLNRALLKADYGIDfWDIPPNYLCPPIPGRVDYIHHL...Adll
  27 agrST...I..DFQDVNAVRMLNRALLKAHYDIDfWDIPDGYLCPAIPGRVDYIHYL...Adll
  28 ngkVT...F..DFKKDAAVRCLTQTLLKKDFNLD.VEIPPGHLVPRVPQKLNYCLLI...Ddll
  29 ngkVT...F..DFKKDAAVRCLTQTLLKKDFNLD.VEIPPGHLVPRVPQKLNYCLLI...Ddll
  30 tgkIK...I..DFKNEESLRVLTEVLLKHDFNLE.VKIPPNKLVPTLPLRINYILWI...Edlm
  31 agkAT...L..DFHDSESLRSLTCTLLKEDFGLE.VELPLDRLIPTLSLRLNYIHWI...Edll
  32 ngkVT...L..DFRKDAAVRCLTQTLLKKDFSLN.VNLPAGHLVPRVPQKLNYCLLI...Ddil
  33 dgyTS...I..NFQDPTALRELTKCLLKEDWNLD.VDLREDRLCPTIPNRLDYIYHVldlE...
  34 dgyTS...I..NFQDPTALRELTKCLLKEDWNLD.VDLREDRLCPTIPNRLDYIYHVldlE...
  35 n..FK...LlaNWKDSNATKELTRVLLDHDFGLR.IELPDNYLCPTLTLRINYLYWI...Sdql
  36 ekiYN...I..DWKDSNATKELTRVLLDHDFGLR.IELPDNYLCPTLTLRINYLYWI...Sdql
  37 cgrVM...L..DFRTPSHLAALSKALLMKDFGLN.VNFPSDRLIPTVPLRLNYILWL...Edli
  38 agkVR...L..DYRNKRAVHLLSKCLLLRDFGLK.LELPPDKLVPTLPLRLNYIHWL...Edig
  39 ngkVS...V..NFRNEKTLRELTKMLLKEYYDLD.VDFAPGSLVPTLALRLNYILWL...Edlm
  40 tgkVS...V..NFRNEKTLRELSKMLLKEYFELD.VDFAPGSLVPTLALRLNYILWL...Edml