# 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/TruB_N.hmm.txt # target sequence database: proteomes/Mus_musculus.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TruB_N [M=149] Accession: PF01509.17 Description: TruB family pseudouridylate synthase (N terminal domain) 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-51 173.4 0.1 7.4e-51 172.7 0.1 1.3 1 sp|Q8C0D0|TRUB1_MOUSE Probable tRNA pseudouridine synthase 1 2.6e-26 93.1 0.0 3.9e-26 92.5 0.0 1.2 1 sp|Q91WG3|TRUB2_MOUSE Mitochondrial mRNA pseudouridine synth 1.7e-20 74.2 4.2 1.8e-18 67.6 0.1 3.5 2 sp|Q9ESX5|DKC1_MOUSE H/ACA ribonucleoprotein complex subuni Domain annotation for each sequence (and alignments): >> sp|Q8C0D0|TRUB1_MOUSE Probable tRNA pseudouridine synthase 1 OS=Mus musculus OX=10090 GN=Trub1 PE=1 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 172.7 0.1 9.9e-55 7.4e-51 2 149 .] 95 243 .. 94 243 .. 0.96 Alignments for each domain: == domain 1 score: 172.7 bits; conditional E-value: 9.9e-55 HHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHHHHHHHC-EEE- CS TruB_N 2 rllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgaetdteDaegeileeekveklteekleevlkkftGeie 89 r ++ kvGh+GtLD +a+GvLvv++g++Tk+l+++l+ +K+Y++ +lg++tdt D++g+++ee+ ++k+t+e++e +l+kftG+i+ sp|Q8C0D0|TRUB1_MOUSE 95 RQKQTLKVGHGGTLDSAAQGVLVVGIGRGTKMLTSMLSGSKRYITIGELGKATDTLDSTGKVTEEKPYDKITREDIEGILQKFTGNIM 182 556778***********************************************************99********************* PP ---------------------------.-----EEEEEEEEEEEEEEEEEEEEEESTTTTH CS TruB_N 90 qvppmySAvkvnGkrlyelaregeeve.rkkrkvtiyelelleveepevelevecskGtYi 149 qvpp ySA+k++G+rl +l+++g+ ve r++r+vt+++++ll++++p ++l+vec G+Yi sp|Q8C0D0|TRUB1_MOUSE 183 QVPPLYSALKKDGQRLSTLMKKGKVVEaRPARPVTVHSISLLKFQPPFFTLDVECGGGFYI 243 **************************94566*****************************8 PP >> sp|Q91WG3|TRUB2_MOUSE Mitochondrial mRNA pseudouridine synthase Trub2 OS=Mus musculus OX=10090 GN=Trub2 PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 92.5 0.0 5.3e-30 3.9e-26 6 147 .. 88 231 .. 84 233 .. 0.96 Alignments for each domain: == domain 1 score: 92.5 bits; conditional E-value: 5.3e-30 -S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-..EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHHHHHHHC-EEE--- CS TruB_N 6 akkvGhtGtLDplatGvLvvavgeaTklleyllead..KeYeatirlgaetdteDaegeileeekveklteekleevlkkftGeieqv 91 k+G ++ LD +a+GvLv+avg++ ll+ + +a+ K Y++ lg++td+ ++g+ +e+++++++t+e+l+++l+ ++G+ ++ sp|Q91WG3|TRUB2_MOUSE 88 NLKIGVGHRLDVQASGVLVLAVGHGRSLLTDMYDAHltKDYTVRGLLGKATDNFCEDGRLIEKTTYDHVTRERLDRILAVIQGSHQKA 175 569***************************99977666*************************99*********************** PP ------------------------------EEEEEEEEEEEEEEEEEEEEEESTTT CS TruB_N 92 ppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGt 147 myS+++ +++++ye+a +g+ ++k ++ i+ +++l++ +pe+ lev+c + t sp|Q91WG3|TRUB2_MOUSE 176 LVMYSNLDLKSQEAYEMAVQGVIRPMNKSPMLISGIRCLHFAPPEFLLEVQCMHET 231 ****************************************************9987 PP >> sp|Q9ESX5|DKC1_MOUSE H/ACA ribonucleoprotein complex subunit DKC1 OS=Mus musculus OX=10090 GN=Dkc1 PE=1 SV=4 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 67.6 0.1 2.5e-22 1.8e-18 1 149 [] 110 226 .. 110 226 .. 0.92 2 ? -3.3 0.7 1.8 1.3e+04 39 67 .. 470 498 .. 460 507 .. 0.60 Alignments for each domain: == domain 1 score: 67.6 bits; conditional E-value: 2.5e-22 HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHHHHHHHC-EEE- CS TruB_N 1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgaetdteDaegeileeekveklteekleevlkkftGeie 89 +r+l+++k Gh+GtLDp++tG+L+v++++aT+l+++ ++a KeY+ +rl+ + + +l+++l+++tG++ sp|Q9ESX5|DKC1_MOUSE 110 RRILRVEKTGHSGTLDPKVTGCLIVCIERATRLVKSQQSAGKEYVGIVRLHNAIEGGT-----------------QLSRALETLTGALF 181 89************************************************99876653.................5899********** PP --------------------------------EEEEEEEEEEEEEE..EEEEEEEESTTTTH CS TruB_N 90 qvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveep..evelevecskGtYi 149 q+pp ++Avk r+ r tiye +++e++++ + v+c++GtYi sp|Q9ESX5|DKC1_MOUSE 182 QRPPLIAAVK-----------------RQLRVRTIYESKMIEYDPErrLGIFWVSCEAGTYI 226 **********.................89999999999999998876567799999999998 PP == domain 2 score: -3.3 bits; conditional E-value: 1.8 TS-EEEEEEEEETEEETTSBTTS-EEE-. CS TruB_N 39 eadKeYeatirlgaetdteDaegeileee 67 ++dK+ +++++ g et + D++ + +++ sp|Q9ESX5|DKC1_MOUSE 470 KKDKKPKTVLESGGETGDGDNDTTKKKKK 498 56666677777777777777665555442 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (149 nodes) Target sequences: 22289 (11757923 residues searched) Passed MSV filter: 636 (0.0285343); expected 445.8 (0.02) Passed bias filter: 453 (0.0203239); expected 445.8 (0.02) Passed Vit filter: 29 (0.00130109); expected 22.3 (0.001) Passed Fwd filter: 3 (0.000134596); expected 0.2 (1e-05) Initial search space (Z): 22289 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.18u 0.01s 00:00:00.19 Elapsed: 00:00:00.09 # Mc/sec: 19465.89 // [ok]