# hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: pfam_list/DNA_methylase.hmm.txt # target sequence database: proteomes/Thermococcus_kodakarensis.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: DNA_methylase [M=335] Accession: PF00145.17 Description: C-5 cytosine-specific DNA methylase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.0022 14.5 0.0 0.0035 13.8 0.0 1.2 1 tr|Q5JD70|Q5JD70_THEKO Met-10+ like protein OS=Thermococcus 0.0027 14.2 0.0 0.0038 13.7 0.0 1.2 1 tr|Q5JEI4|Q5JEI4_THEKO tRNA(Phe) (4-demethylwyosine(37)-C(7) 0.0088 12.5 0.1 0.018 11.5 0.0 1.5 2 tr|Q5JJ78|Q5JJ78_THEKO Probable tRNA/rRNA methyltransferase ------ inclusion threshold ------ 0.01 12.3 0.0 0.015 11.7 0.0 1.1 1 tr|Q5JDP7|Q5JDP7_THEKO Predicted DNA methylase OS=Thermococc Domain annotation for each sequence (and alignments): >> tr|Q5JD70|Q5JD70_THEKO Met-10+ like protein OS=Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) OX # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 13.8 0.0 6e-06 0.0035 3 54 .. 185 242 .. 184 258 .. 0.84 Alignments for each domain: == domain 1 score: 13.8 bits; conditional E-value: 6e-06 EEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-........-SEEEES-TTT CS DNA_methylase 3 fidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk.......kvsigDitkid 54 ++d+faG+G ++ l+++ + v+a +i+++a+ +e n+k +++gD++k++ tr|Q5JD70|Q5JD70_THEKO 185 VFDMFAGVGPYSILLAKKA-KLVFACDINPWAVRYLEENKKlnktpnvIPILGDVRKVA 242 58***********999887.********************9987776666778888776 PP >> tr|Q5JEI4|Q5JEI4_THEKO tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase OS=Thermococcus kodakare # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 13.7 0.0 6.6e-06 0.0038 3 43 .. 129 169 .. 128 200 .. 0.73 Alignments for each domain: == domain 1 score: 13.7 bits; conditional E-value: 6.6e-06 EEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-. CS DNA_methylase 3 fidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk 43 ++d+faGiG ++l + ++ v+a+e+d++ + ++ n+ tr|Q5JEI4|Q5JEI4_THEKO 129 VVDMFAGIGHLSLPMTVHKGARVIAIEKDPYTFRFLVENIW 169 69*****************************9999988765 PP >> tr|Q5JJ78|Q5JJ78_THEKO Probable tRNA/rRNA methyltransferase OS=Thermococcus kodakarensis (strain ATCC BAA-918 / JCM # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -2.7 0.0 0.63 3.6e+02 232 232 .. 111 111 .. 57 179 .. 0.53 2 ! 11.5 0.0 3.1e-05 0.018 1 48 [. 219 267 .. 219 292 .. 0.87 Alignments for each domain: == domain 1 score: -2.7 bits; conditional E-value: 0.63 H CS DNA_methylase 232 e 232 tr|Q5JJ78|Q5JJ78_THEKO 111 G 111 0 PP == domain 2 score: 11.5 bits; conditional E-value: 3.1e-05 -EEEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-..-SEEE CS DNA_methylase 1 lkfidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk.kvsig 48 ++++d f + GGf++ + ag + v+a+++ ++a+++ + n k + ++ tr|Q5JJ78|Q5JJ78_THEKO 219 MRVLDVFTYTGGFAIHAAVAGADEVVAVDKSPWAINMVKENAKlNGVED 267 799************************************9997655444 PP >> tr|Q5JDP7|Q5JDP7_THEKO Predicted DNA methylase OS=Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.7 0.0 2.6e-05 0.015 3 70 .. 51 121 .. 50 121 .. 0.79 Alignments for each domain: == domain 1 score: 11.7 bits; conditional E-value: 2.6e-05 EEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-.-SEEEE.S-TTTS-..GS--.-SEEEE--- CS DNA_methylase 3 fidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfkkvsigD.itkidkk..klpediDlLvgGfP 70 + dL aG G + +g g e v+a+e dk+a ++ + n ++ +D i+ ++ + +++ ++D ++ +P tr|Q5JDP7|Q5JDP7_THEKO 51 IADLGAGTGVLGIGAVLLGAENVYAVERDKEALEIARENARSLGVEDkIEFVNADvsEFSVNVDTVIMNPP 121 579*************************************9554444145444446677767887776665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (335 nodes) Target sequences: 2301 (637680 residues searched) Passed MSV filter: 106 (0.0460669); expected 46.0 (0.02) Passed bias filter: 88 (0.0382442); expected 46.0 (0.02) Passed Vit filter: 10 (0.00434594); expected 2.3 (0.001) Passed Fwd filter: 4 (0.00173837); expected 0.0 (1e-05) Initial search space (Z): 2301 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 21362.28 // [ok]