# 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/UPF0020.hmm.txt # target sequence database: proteomes/Dictyostelium_discoideum.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: UPF0020 [M=197] Accession: PF01170.17 Description: Putative RNA methylase family UPF0020 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-11 42.8 0.1 6.8e-09 35.2 0.1 3.5 2 sp|Q54BW1|Y3380_DICDI Putative uncharacterized protein DDB_ 2.3e-07 30.2 0.2 0.016 14.5 0.0 2.6 3 sp|Q54QA6|TRM11_DICDI tRNA (guanine(10)-N2)-methyltransfera 9.2e-05 21.7 0.1 0.0037 16.5 0.1 2.2 1 tr|Q54VE3|Q54VE3_DICDI Uncharacterized protein OS=Dictyostel ------ inclusion threshold ------ 0.011 15.0 0.1 0.031 13.5 0.1 1.8 1 sp|Q54WD6|TRM5_DICDI tRNA (guanine(37)-N1)-methyltransfera 0.014 14.6 0.1 0.056 12.6 0.0 2.0 2 tr|Q54NF6|Q54NF6_DICDI Uncharacterized protein OS=Dictyostel 0.015 14.5 0.0 0.058 12.6 0.0 2.0 2 tr|Q553T0|Q553T0_DICDI Uncharacterized protein OS=Dictyostel Domain annotation for each sequence (and alignments): >> sp|Q54BW1|Y3380_DICDI Putative uncharacterized protein DDB_G0293380 OS=Dictyostelium discoideum OX=44689 GN=DDB_G029 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 35.2 0.1 3.2e-12 6.8e-09 10 138 .. 258 437 .. 249 457 .. 0.71 2 ? 1.4 0.0 0.075 1.6e+02 139 185 .. 491 537 .. 487 545 .. 0.87 Alignments for each domain: == domain 1 score: 35.2 bits; conditional E-value: 3.2e-12 -SS-HHHHHHHHHH.........TT--TT.......S-EEETT-TTSHHHHHHHHHHTT--TTTT----SS................H CS UPF0020 10 apLketLAaalvrl.........agwkpg.......epllDPmCGsGtilIEaallganiapgllrefvle................l 65 ap++etLA+a+++ +g ++g + + DP+ GsGt+ Ea + ++ p + + sp|Q54BW1|Y3380_DICDI 258 APIRETLASAIIMAiisstrrvgSGTTEGsyldlnkTNIWDPFVGSGTLIQEAISMLLKAKPSSCTNYKRSfqferfknhsterylkY 345 6666666666665333322333344444411111115799**************999999886553333224557******9998777 PP HHHHHHHHHHH--...EEEEES-HHHHHHHHHHHHHTT-GG.GEEEEE--GGG--...............STTS---EEEE------- CS UPF0020 66 kaeaeeearaelk...lygsDldrrvvqgareNaekagvgd.liefsqadaakLr...............lkegevdvivtnpPYGer 134 ++ +++ + + +k l+gsD+d+++++ + N++k g ++ i+f + d++++ +++++ +i+tn+PYG r sp|Q54BW1|Y3380_DICDI 346 LESINKPISPLIKntiLIGSDIDQKAIDSSIFNLSKQGYQHeNIKFFKGDFKSIYldqinidnsldddgdNNNNKPFTIITNLPYGTR 433 7777777775555667*********************9976269****9*9998766776667666665533444459*********9 PP ---H CS UPF0020 135 lgsk 138 + + sp|Q54BW1|Y3380_DICDI 434 VLNR 437 8655 PP == domain 2 score: 1.4 bits; conditional E-value: 0.075 HHHHHHHHHHHHHHHHH-TT..-EEEEEESSHHHHHCC---ESEEEE CS UPF0020 139 kalekLYseflrelkrvlrgggrlvlltsenkalekaleeralrkvk 185 k+l++L++ f++ +++ ++ r v+++++n+ ++++ ++ ++++ sp|Q54BW1|Y3380_DICDI 491 KDLRDLFKRFGDMIHESNESVLRDVFVLNGNSHFQSISTNNGKNNFE 537 67899***********999999*************999888776665 PP >> sp|Q54QA6|TRM11_DICDI tRNA (guanine(10)-N2)-methyltransferase homolog OS=Dictyostelium discoideum OX=44689 GN=trmt11 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.8 0.0 2.8 6e+03 143 167 .. 84 108 .. 81 131 .. 0.64 2 ! 13.0 0.0 2.1e-05 0.045 4 54 .. 206 256 .. 204 283 .. 0.87 3 ! 14.5 0.0 7.3e-06 0.016 119 139 .. 302 322 .. 292 328 .. 0.87 Alignments for each domain: == domain 1 score: -3.8 bits; conditional E-value: 2.8 HHHHHHHHHHHHH-TT..-EEEEEE CS UPF0020 143 kLYseflrelkrvlrgggrlvllts 167 +L +e+l+el++ ++++ + ++++ sp|Q54QA6|TRM11_DICDI 84 QLLDEILNELHSKFDKQFLSNYMIN 108 6777888888888877544444444 PP == domain 2 score: 13.0 bits; conditional E-value: 2.1e-05 S-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT-- CS UPF0020 4 RefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallgania 54 R++ g +++ ++L+ + ++ +k+g+ lDP+ G+G++ + a ga+ + sp|Q54QA6|TRM11_DICDI 206 RKYLGTTSMDPELSLVSANMGLVKKGHFVLDPFVGTGSFILVASHFGAQTV 256 889999*********************************998887777665 PP == domain 3 score: 14.5 bits; conditional E-value: 7.3e-06 TS---EEEE----------HH CS UPF0020 119 egevdvivtnpPYGerlgskk 139 ++ +d+i+t+pPYG+r g+ k sp|Q54QA6|TRM11_DICDI 302 NSMFDSIITDPPYGIRAGARK 322 5679************99865 PP >> tr|Q54VE3|Q54VE3_DICDI Uncharacterized protein OS=Dictyostelium discoideum OX=44689 GN=DDB0205190 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 16.5 0.1 1.7e-06 0.0037 77 114 .. 70 107 .. 30 116 .. 0.77 Alignments for each domain: == domain 1 score: 16.5 bits; conditional E-value: 1.7e-06 --EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG CS UPF0020 77 lklygsDldrrvvqgareNaekagvgdliefsqadaak 114 ++ +g+D+++++++ a+eNa+k gv++l+ f++ d+a+ tr|Q54VE3|Q54VE3_DICDI 70 IRGIGLDINPELIKSANENAKKEGVDHLVLFKVQDFAN 107 3458*****************************99874 PP >> sp|Q54WD6|TRM5_DICDI tRNA (guanine(37)-N1)-methyltransferase OS=Dictyostelium discoideum OX=44689 GN=trmt5 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 13.5 0.1 1.5e-05 0.031 75 130 .. 235 294 .. 207 296 .. 0.85 Alignments for each domain: == domain 1 score: 13.5 bits; conditional E-value: 1.5e-05 HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--....STTS---EEEE--- CS UPF0020 75 aelklygsDldrrvvqgareNaekagvgdliefsqadaakLr....lkegevdvivtnpP 130 ++ k+y+ Dl+++ v+ +eNa+ +++ ++e+s++da+++ +k+ + +v n+P sp|Q54WD6|TRM5_DICDI 235 KKCKVYANDLNPSSVKYMKENAKTNRLESKVEISNLDARDFVkslvEKSIPFTHVVMNLP 294 66789**********************************998665444556777777777 PP >> tr|Q54NF6|Q54NF6_DICDI Uncharacterized protein OS=Dictyostelium discoideum OX=44689 GN=DDB0186431 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.2 0.0 1.9 4.1e+03 77 108 .. 247 280 .. 224 291 .. 0.69 2 ? 12.6 0.0 2.6e-05 0.056 29 119 .. 324 408 .. 313 417 .. 0.75 Alignments for each domain: == domain 1 score: -3.2 bits; conditional E-value: 1.9 --EEEEES-HHHHHHHHHHHHH..TT-GGGEEEE CS UPF0020 77 lklygsDldrrvvqgareNaek..agvgdliefs 108 +++ g ++ + +a +N ++ a+ ++ i fs tr|Q54NF6|Q54NF6_DICDI 247 AEISGCKVIWHKIMTAHSNISNnkATFTHMICFS 280 4577777788888888888654115555555555 PP == domain 2 score: 12.6 bits; conditional E-value: 2.6e-05 TS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEE.S-HHHHHHHHHHHHHTT-GGGEEEEE--GGG CS UPF0020 29 gepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsD.ldrrvvqgareNaekagvgdliefsqadaak 114 ++++DP+CG G++l a + g + + l + +++++ +l + ++ +d+rv q++++N ++ ++d ++++ d + tr|Q54NF6|Q54NF6_DICDI 324 STTIIDPFCGKGSVLAVANVYGLDSVGVDL------SSGKTKNSFNLQLDVETVNkFDPRVWQQSNNNKSNLLIKDNDNIEDNDESD 404 579************999999999993222......334445555555555555526899999999999999999999999999999 PP --STT CS UPF0020 115 Lrlke 119 ++ ++ tr|Q54NF6|Q54NF6_DICDI 405 IT-NN 408 88.33 PP >> tr|Q553T0|Q553T0_DICDI Uncharacterized protein OS=Dictyostelium discoideum OX=44689 GN=DDB0202574 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.6 0.0 0.62 1.3e+03 139 173 .. 134 167 .. 127 190 .. 0.63 2 ? 12.6 0.0 2.7e-05 0.058 77 125 .. 263 311 .. 233 362 .. 0.84 Alignments for each domain: == domain 1 score: -1.6 bits; conditional E-value: 0.62 HHHHHHHHHHHHHHHHH-TT..-EEEEEESSHHHH CS UPF0020 139 kalekLYseflrelkrvlrgggrlvlltsenkale 173 +++ + +++fl+++k+ +++ g +v +++++ ++ tr|Q553T0|Q553T0_DICDI 134 REMTHTWNAFLESIKKTVET-GSIVKIAPQEDVVK 167 55556678899999998888.66666666555544 PP == domain 2 score: 12.6 bits; conditional E-value: 2.7e-05 --EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EE CS UPF0020 77 lklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvi 125 k++g++++++ v a + a+ gv+d+ +f da k++ +++ +dv+ tr|Q553T0|Q553T0_DICDI 263 CKIRGLNINKKQVGIATQRAKDLGVSDRASFDHGDAMKMPYPDNTFDVV 311 5799************************************999999987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (197 nodes) Target sequences: 12739 (6856946 residues searched) Passed MSV filter: 441 (0.0346181); expected 254.8 (0.02) Passed bias filter: 270 (0.0211948); expected 254.8 (0.02) Passed Vit filter: 26 (0.00204098); expected 12.7 (0.001) Passed Fwd filter: 6 (0.000470995); expected 0.1 (1e-05) Initial search space (Z): 12739 [actual number of targets] Domain search space (domZ): 6 [number of targets reported over threshold] # CPU time: 0.12u 0.01s 00:00:00.13 Elapsed: 00:00:00.05 # Mc/sec: 27016.37 // [ok]