# 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/LCM.hmm.txt # target sequence database: proteomes/Mus_musculus.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: LCM [M=188] Accession: PF04072.14 Description: Leucine carboxyl methyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-38 131.9 0.0 6.6e-38 130.9 0.0 1.5 1 tr|A0A0U1RNF2|A0A0U1RNF2_MOUSE Leucine carboxyl methyltransfera 1.2e-25 90.9 0.0 3.6e-25 89.3 0.0 1.7 1 sp|Q8BYR1|TYW4_MOUSE tRNA wybutosine-synthesizing pro Domain annotation for each sequence (and alignments): >> tr|A0A0U1RNF2|A0A0U1RNF2_MOUSE Leucine carboxyl methyltransferase 1 OS=Mus musculus OX=10090 GN=Lcmt1 PE=1 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 130.9 0.0 5.9e-42 6.6e-38 3 187 .. 25 214 .. 23 215 .. 0.95 Alignments for each domain: == domain 1 score: 130.9 bits; conditional E-value: 5.9e-42 HHHHHHHHHHHH.H.HHTSSHTCCCCCCCHHHHHHHHCHCCCHCHHCHGCHCCCCT--HHHHHHHHHHHHHHHHHHHHH CS LCM 3 gvaaaralesrr.a.adglidDplaeslvsaaglellerkadkelekekeeekkekkapelnrgiavRtrffddllkaa 79 + ++ +a ++r a + g+++Dp++e+lv++++ e+kape+nrg+++R++ + +l+ka+ tr|A0A0U1RNF2|A0A0U1RNF2_MOUSE 25 RGTCEDASLCKRfAvSIGYWHDPYIEHLVRQSK---------------------ERKAPEINRGYFARVHGVSQLIKAF 82 678999******669*****************3.....................3469********************* PP H.HCTTESEEEEET-TT--HHHHHHHTT..TEEEEEEE-HHHHHHHHHHHHHSHHHHH..................EEC CS LCM 80 l.saagirqvViLGAGlDtrayRlpwla..glkvfEvDqpevlefKretlkelgaepk..................ael 137 l ++++++q+ +LGAG+Dt++++l+++ k+fEvD+p+++++K t+k ++ + + ++ tr|A0A0U1RNF2|A0A0U1RNF2_MOUSE 83 LrKTECHCQILNLGAGMDTTFWKLKDEGllPNKYFEVDFPMIVTRKLLTIKSKPLLFRpimelhpedtlqmgnhmlDSK 161 ****************************9999**********************99999***************99777 PP SE..EE--TTS.HHHHHHHHHHTT-TTSEEEEEEESSGGGS-HHHHHHHHHHH CS LCM 138 ry..vpvDlrd.ddwpeaLaaagfdpekptawvaeGvlvYLtpeasdalleai 187 ry +++Dlrd ++++e+L++++++++ pt+++ e+vlvY+tpe+s++ll++ tr|A0A0U1RNF2|A0A0U1RNF2_MOUSE 162 RYaiIGADLRDlSELEEKLKKCNMNTQLPTLLITECVLVYMTPEQSANLLKWA 214 7777**********************************************996 PP >> sp|Q8BYR1|TYW4_MOUSE tRNA wybutosine-synthesizing protein 4 OS=Mus musculus OX=10090 GN=Lcmt2 PE=2 SV=4 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 89.3 0.0 3.2e-29 3.6e-25 19 187 .. 32 206 .. 12 207 .. 0.87 Alignments for each domain: == domain 1 score: 89.3 bits; conditional E-value: 3.2e-29 SSHTCCCCCCCHHHHHHHHCHCCCHCHHCHGCHCCCCT--HHHHHHHHHHHHHHHHHHHHHH.HCTT......ESEEEEET-TT--HHH CS LCM 19 lidDplaeslvsaaglellerkadkelekekeeekkekkapelnrgiavRtrffddllkaal.saag......irqvViLGAGlDtray 100 +++Dp+a+ lv +++p ++rg++vR+r++++ ++a+l + +q+ LG+G D++ + sp|Q8BYR1|TYW4_MOUSE 32 YVRDPFAALLVPGP----------------------VRRTPLIHRGYYVRARAVRHCVRAFLeLT-SalpsrtRAQILSLGSGSDSLYF 97 55555555555444......................45789*******************99433.247888778************** PP HHHHTT...TEEEEEEE-HHHHHHHHHHHHHSHHHHH..................EECSEEE--TTS.HHHHHHHHHHTT-TTSEEEEE CS LCM 101 Rlpwla...glkvfEvDqpevlefKretlkelgaepk..................aelryvpvDlrd.ddwpeaLaaagfdpekptawv 167 Rl+ + v EvD+p+v ++K+e+++e ++++ a+ r ++Dlr+ +++ eaL ag+d++ pt+++ sp|Q8BYR1|TYW4_MOUSE 98 RLKAAGllaRAAVWEVDFPDVSRLKAERIEETPELRAqtgpfkigdsasslcfesADYRILGADLRElQRLGEALDGAGLDATSPTLLL 186 ****99999************************99999***************9889999***************************** PP EESSGGGS-HHHHHHHHHHH CS LCM 168 aeGvlvYLtpeasdalleai 187 ae vl YL+p +++al+++ sp|Q8BYR1|TYW4_MOUSE 187 AEAVLTYLEPSSATALIAWA 206 *****************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 22289 (11757923 residues searched) Passed MSV filter: 690 (0.030957); expected 445.8 (0.02) Passed bias filter: 507 (0.0227466); expected 445.8 (0.02) Passed Vit filter: 44 (0.00197407); expected 22.3 (0.001) Passed Fwd filter: 2 (8.97304e-05); expected 0.2 (1e-05) Initial search space (Z): 22289 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.18u 0.01s 00:00:00.19 Elapsed: 00:00:00.08 # Mc/sec: 27631.12 // [ok]