# 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/RrnaAD.hmm.txt # target sequence database: proteomes/Thermococcus_kodakarensis.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: RrnaAD [M=265] Accession: PF00398.19 Description: Ribosomal RNA adenine dimethylase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-54 181.3 0.0 2.6e-54 181.1 0.0 1.1 1 sp|Q5JI54|RSMA_THEKO Probable ribosomal RNA small subunit 4.7e-07 26.2 0.0 6.8e-07 25.7 0.0 1.2 1 tr|Q5JGS7|Q5JGS7_THEKO tRNA (1-methyladenosine) methyltransf 1.3e-06 24.7 0.0 1.7e-06 24.4 0.0 1.1 1 tr|Q5JEE1|Q5JEE1_THEKO Protein-L-isoaspartate O-methyltransf 0.00018 17.7 0.0 0.00028 17.1 0.0 1.3 1 tr|Q5JGN8|Q5JGN8_THEKO SAM-dependent methyltransferase, UbiE 0.00025 17.3 0.0 0.00036 16.7 0.0 1.2 1 tr|Q5JJ79|Q5JJ79_THEKO Predicted SAM-dependent methyltransfe 0.0027 13.9 0.0 0.0037 13.4 0.0 1.1 1 tr|Q5JDP7|Q5JDP7_THEKO Predicted DNA methylase OS=Thermococc 0.01 12.0 0.0 0.014 11.6 0.0 1.2 1 tr|Q5JDR0|Q5JDR0_THEKO SAM-dependent methyltransferase, UPF0 ------ inclusion threshold ------ 0.016 11.4 0.0 0.02 11.0 0.0 1.1 1 tr|Q5JEU8|Q5JEU8_THEKO Predicted SAM-dependent methyltransfe 0.022 10.9 0.0 0.031 10.4 0.0 1.2 1 tr|Q5JFS6|Q5JFS6_THEKO Predicted SAM-dependent methyltransfe 0.025 10.7 0.0 0.034 10.3 0.0 1.2 1 tr|Q5JH62|Q5JH62_THEKO Uncharacterized protein OS=Thermococc Domain annotation for each sequence (and alignments): >> sp|Q5JI54|RSMA_THEKO Probable ribosomal RNA small subunit methyltransferase A OS=Thermococcus kodakarensis (strain A # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 181.1 0.0 1.1e-56 2.6e-54 5 231 .. 17 226 .. 13 268 .. 0.91 Alignments for each domain: == domain 1 score: 181.1 bits; conditional E-value: 1.1e-56 XXGCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHHHH CS RrnaAD 5 rksygqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqDflkfetpee 93 ++++gqnfl+ + +i++ ++ +++ ek+tvleigpG G+lT +L kra +v ++E+d r++++l+ + + +++++++ D+lk e pe+ sp|Q5JI54|RSMA_THEKO 17 NRDLGQNFLIVPDIIERNIERAEVGEKDTVLEIGPGLGVLTDPLSKRAGKVYAIEKDCRIVEILRREYN-WPNVEIIEGDALKVEWPEF 104 899***************************************************************777.9*****************5 PP HCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SHHHHHHHHHEEEEEEEEC-GGCECS-- CS RrnaAD 94 vtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsrlsvlreaftdvklvakveksifsPpp 182 ++v+nlPy+is++ ++ll+ f ++++l++q efa+r++a+pg+k++srls+++ a + ++lv+ ++k +f+P p sp|Q5JI54|RSMA_THEKO 105 N----------KMVSNLPYQISSPVTFKLLS-REF--ERAVLIFQLEFAERMVAKPGDKNYSRLSLMVRAKARAELVERIGKGAFWPRP 180 5..........89*****************6.555..9*************************************************** PP SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHCCCTSTC CS RrnaAD 183 kvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstslksllpg 231 kvdsa+v le+k+++ + ++ e +v++l+ +r t+s++lk+ ++ sp|Q5JI54|RSMA_THEKO 181 KVDSAVVVLEPKPPE---ERIDLNENLVKALFQHRRSTVSAALKKSAHM 226 *************98...6899999******************987665 PP >> tr|Q5JGS7|Q5JGS7_THEKO tRNA (1-methyladenosine) methyltransferase OS=Thermococcus kodakarensis (strain ATCC BAA-918 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 25.7 0.0 2.9e-09 6.8e-07 22 74 .. 85 140 .. 76 156 .. 0.89 Alignments for each domain: == domain 1 score: 25.7 bits; conditional E-value: 2.9e-09 HHHHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTTT CS RrnaAD 22 IldklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkklsk 74 I+ + +++ +tv+e g+G G+lT La+ + +v ++E +++++++ +k++++ tr|Q5JGS7|Q5JGS7_THEKO 85 IIAYAGISPGDTVIEAGAGSGALTIFLANAVgptGKVISYEVRKDFYEIAKKNVEL 140 7888999************************9999*****************9983 PP >> tr|Q5JEE1|Q5JEE1_THEKO Protein-L-isoaspartate O-methyltransferase OS=Thermococcus kodakarensis (strain ATCC BAA-918 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 24.4 0.0 7.2e-09 1.7e-06 22 92 .. 69 142 .. 59 166 .. 0.85 Alignments for each domain: == domain 1 score: 24.4 bits; conditional E-value: 7.2e-09 HHHHH-GGTTSEEEEES-TTTCCHHHHHCC-.SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCGHHHHH CS RrnaAD 22 IldklnleekltvleigpGkGilTeeLakra.kqvvvlElderLakllqkkls..kdeklkvvhqDflkfetpe 92 l+ ++l++ ++vleig+G G + + + + v +E ++L+++ + +l+ +++ v+ D+ k p+ tr|Q5JEE1|Q5JEE1_THEKO 69 MLELADLKPGMNVLEIGTGSGWNAALISELVkTDVYTIERIPELVEFARRNLEraGVKNVHVILGDGTKGFPPK 142 577899*************************778999****************98899********99876666 PP >> tr|Q5JGN8|Q5JGN8_THEKO SAM-dependent methyltransferase, UbiE/COQ5 family OS=Thermococcus kodakarensis (strain ATCC B # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 17.1 0.0 1.2e-06 0.00028 20 94 .. 31 106 .. 26 135 .. 0.88 Alignments for each domain: == domain 1 score: 17.1 bits; conditional E-value: 1.2e-06 HHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT.TCCCEEEE-S-CCGHHHHHHH CS RrnaAD 20 neIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls.kdeklkvvhqDflkfetpeev 94 +eI+++ +e + vl+++ G+Gi T eLa+r +v l l e+++ + + k + + ++k + ++l+ ++ ee tr|Q5JGN8|Q5JGN8_THEKO 31 EEIFREDAKREVKRVLDLACGTGIPTLELAERGYEVLGLDLHEEMLRVARRKAEaRGLNVKFIRGNALDISFEEEF 106 6777777778999**************************************9999999**************9965 PP >> tr|Q5JJ79|Q5JJ79_THEKO Predicted SAM-dependent methyltransferase, DUF890 family OS=Thermococcus kodakarensis (strain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 16.7 0.0 1.6e-06 0.00036 28 82 .. 79 136 .. 69 140 .. 0.87 Alignments for each domain: == domain 1 score: 16.7 bits; conditional E-value: 1.6e-06 GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT.TCCCEEEE- CS RrnaAD 28 leekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls.kdeklkvvh 82 l+ +vleig+G ++ + +a+r+ v++ Elde++++ + +++ ++ ++k ++ tr|Q5JJ79|Q5JJ79_THEKO 79 LRGGEKVLEIGTGHTAMMALMAERLfnCDVTATELDEEFFEYAKRNIEkNGANVKPIK 136 566789*******************9999***************99996677777666 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 ! 13.4 0.0 1.6e-05 0.0037 30 105 .. 47 134 .. 32 141 .. 0.79 Alignments for each domain: == domain 1 score: 13.4 bits; conditional E-value: 1.6e-05 TTSEEEEES-TTTCCHHHH.HCC-SEEEEE-S-HHHHHHHHCHTT...TCCCEEEE-S-CCGHHHHHHHCT.........TTCCCCE CS RrnaAD 30 ekltvleigpGkGilTeeL.akrakqvvvlElderLakllqkkls...kdeklkvvhqDflkfetpeevte.........kdsihqe 103 e + + ++g+G+G+l + a++v ++E d++ +++ +++ + + k++ v++D+ +f++ + + + ++ tr|Q5JDP7|Q5JDP7_THEKO 47 EGKVIADLGAGTGVLGIGAvLLGAENVYAVERDKEALEIARENARslgVEDKIEFVNADVSEFSVNVDT-VimnppfgsqVKHADRP 132 677899*********976526667******************9889999**************998744.23556666655555555 PP EE CS RrnaAD 104 fl 105 fl tr|Q5JDP7|Q5JDP7_THEKO 133 FL 134 65 PP >> tr|Q5JDR0|Q5JDR0_THEKO SAM-dependent methyltransferase, UPF0020 family OS=Thermococcus kodakarensis (strain ATCC BAA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 11.6 0.0 6.1e-05 0.014 24 87 .. 121 189 .. 111 227 .. 0.83 Alignments for each domain: == domain 1 score: 11.6 bits; conditional E-value: 6.1e-05 HHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT.....TCCCEEEE-S-CCG CS RrnaAD 24 dklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls.....kdeklkvvhqDflk 87 +++ ++e tvl+ G G + e kr v +E+d++ +++ + ++ ++k++v++ D+ + tr|Q5JDR0|Q5JDR0_THEKO 121 NTVMPREGETVLDTCMGLGYTAIEASKRGAYVITIEKDPNVIEIARINPWsrelfTGGKIQVIQGDAFE 189 5666789**********************************998876544455559**********865 PP >> tr|Q5JEU8|Q5JEU8_THEKO Predicted SAM-dependent methyltransferase OS=Thermococcus kodakarensis (strain ATCC BAA-918 / # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.0 0.0 8.8e-05 0.02 32 88 .. 43 104 .. 34 167 .. 0.81 Alignments for each domain: == domain 1 score: 11.0 bits; conditional E-value: 8.8e-05 SEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT...TCCCEEEE-S-CCGH CS RrnaAD 32 ltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls...kdeklkvvhqDflkf 88 vl+i +G+G+ + Lak k ++vl +++ ++l ++ l+ ++ l++v+ D+ + tr|Q5JEU8|Q5JEU8_THEKO 43 GRVLDICAGTGVAGVALAKATgaKLLTVLDARKDDLELAKEWLKiadINPELNLVQGDAREV 104 57*****************9999*******99887777777777766899999999998765 PP >> tr|Q5JFS6|Q5JFS6_THEKO Predicted SAM-dependent methyltransferase OS=Thermococcus kodakarensis (strain ATCC BAA-918 / # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 10.4 0.0 0.00013 0.031 31 90 .. 58 120 .. 40 139 .. 0.77 Alignments for each domain: == domain 1 score: 10.4 bits; conditional E-value: 0.00013 TSEEEEES-TTTCCHHHH.HCC-.SEEEEE-S-HHHHHHHHCHTT.TCCCEEEE-S-CCGHHH CS RrnaAD 31 kltvleigpGkGilTeeL.akra.kqvvvlElderLakllqkkls.kdeklkvvhqDflkfet 90 k +vl++g G+G+lT ++ +k + vv + e+ +++ + ++ k v+ +fl++ + tr|Q5JFS6|Q5JFS6_THEKO 58 KGKVLDVGCGTGVLTFKMaLKNGvEMVVGVDRKEEVIEFCNRLGDrVTKNAKFVQGNFLEMGL 120 669************998644434899988888876666666333567899999999987765 PP >> tr|Q5JH62|Q5JH62_THEKO Uncharacterized protein 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 ? 10.3 0.0 0.00015 0.034 23 91 .. 40 113 .. 36 143 .. 0.75 Alignments for each domain: == domain 1 score: 10.3 bits; conditional E-value: 0.00015 HHHH-GGTTSEEEEES-TT.TCCHHHHHCC-...SEEEEE-S.-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHH CS RrnaAD 23 ldklnleekltvleigpGk.GilTeeLakra...kqvvvlEl.derLakllqkklskdeklkvvhqDflkfetp 91 l+ + l+e ++vleig G +i+T++La + vv++ + + +++++ + +++++ ++ D+ + +p tr|Q5JH62|Q5JH62_THEKO 40 LRFAPLREGMNVLEIGCGAhAITTVPLAYLVdetGRVVAVDKaRWHFFEEITSVAGLKHRIIPMKLDARELPFP 113 5667799***********73678888877776666677776536788888888555777777777777666655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (265 nodes) Target sequences: 2301 (637680 residues searched) Passed MSV filter: 77 (0.0334637); expected 46.0 (0.02) Passed bias filter: 60 (0.0260756); expected 46.0 (0.02) Passed Vit filter: 16 (0.0069535); expected 2.3 (0.001) Passed Fwd filter: 10 (0.00434594); expected 0.0 (1e-05) Initial search space (Z): 2301 [actual number of targets] Domain search space (domZ): 10 [number of targets reported over threshold] # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 8449.26 // [ok]