# 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/SpoU_methylase.hmm.txt # target sequence database: proteomes/Macaca_mulatta.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: SpoU_methylase [M=142] Accession: PF00588.18 Description: SpoU rRNA Methylase family 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-31 108.4 0.0 1.1e-30 107.0 0.0 1.8 2 tr|F7EZY1|F7EZY1_MACMU TAR (HIV-1) RNA binding protein 1 OS= 1.1e-28 100.4 0.0 1.5e-28 100.0 0.0 1.2 1 tr|F6Y1D2|F6Y1D2_MACMU Mitochondrial rRNA methyltransferase ------ inclusion threshold ------ 0.015 15.7 0.1 0.02 15.3 0.1 1.1 1 tr|F7EVY7|F7EVY7_MACMU DNA polymerase epsilon 3, accessory s Domain annotation for each sequence (and alignments): >> tr|F7EZY1|F7EZY1_MACMU TAR (HIV-1) RNA binding protein 1 OS=Macaca mulatta OX=9544 GN=TARBP1 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.3 0.0 1.5 1.1e+04 54 92 .. 969 1007 .. 958 1016 .. 0.80 2 ! 107.0 0.0 1.5e-34 1.1e-30 2 141 .. 1452 1593 .. 1451 1594 .. 0.93 Alignments for each domain: == domain 1 score: -3.3 bits; conditional E-value: 1.5 HHHHEEEESSHHHHHHHHCCCTEEEEEESTT-SEGCCSH CS SpoU_methylase 54 evlelkvvdsleealkelkeegfalvatslkgkslseid 92 + +l +++l+++++ + ++++ ++a++ kg+ + +i+ tr|F7EZY1|F7EZY1_MACMU 969 SNTQLIFWPNLKAFVQFVFDNKVLTIAAKIKGQAYFKIK 1007 556778899999999999999899999988999998774 PP == domain 2 score: 107.0 bits; conditional E-value: 1.5e-34 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEE..SSHHHHHHHHCCCTEEEEEESTT CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvv..dsleealkelkeegfalvatslk 84 livv i++p+NlG ++Rt+++fgas+lv+ + ++ ++++++++++a+++l+l++v ++l ++l++ k eg++++++++ tr|F7EZY1|F7EZY1_MACMU 1452 LIVVASLIDKPTNLGGLCRTCEVFGASALVVGSLQCI--SDKQFQHLSVSAEQWLPLVEVkpPHLIDYLQQKKTEGYTIIGVEQT 1534 799****************************998885..9****************888856799*******************7 PP -SEGC..CSHHHTTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHH CS SpoU_methylase 85 gksls..eidlkekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvaill 141 +ksl+ ++ ++ek +l++GnE++G++ +l++++d +v+Ip++g ++SLNv+v+ a+l+ tr|F7EZY1|F7EZY1_MACMU 1535 AKSLDltQYCFPEKSLLLLGNEREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLI 1593 766555599**********************************************9987 PP >> tr|F6Y1D2|F6Y1D2_MACMU Mitochondrial rRNA methyltransferase 1 OS=Macaca mulatta OX=9544 GN=MRM1 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 100.0 0.0 2.1e-32 1.5e-28 2 142 .] 146 301 .. 145 301 .. 0.86 Alignments for each domain: == domain 1 score: 100.0 bits; conditional E-value: 2.1e-32 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEEST..T-S CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatsl..kgk 86 l +vl++i+dp+N+Ga++R+a +g+++++ ++++s +l+p + +a+aga ev+++ d+l +l+ ++g+ + +t + +++ tr|F6Y1D2|F6Y1D2_MACMU 146 LWLVLEGIQDPRNFGAVLRSAHFLGVDKVITSRRNSC-PLTPVVSKASAGAMEVMDVFSTDDLTGFLQTKAQQGWLVAGTVGcpRAE 231 569****************************987776.*************************************999998888666 PP EGC..CS........HHHTTEEEEEEBTTTBS-HHHHCTSSEEEE-....---TTSSS--HHHHHHHHHH CS SpoU_methylase 87 sls..ei........dlkekvalvfGnEdkGlsnelleladrlvkI....pmsgeveSLNvavAvailly 142 + + ei ++++++lv+GnE++Gls+e+ + ++ l++I + eSLNv+vA++ill+ tr|F6Y1D2|F6Y1D2_MACMU 232 DPQssEIpitsclefPWDRPTLLVLGNEGSGLSQEVQASCQVLLTIlprrQLPPGLESLNVSVAAGILLH 301 666453333444433666************************99995443346788***********985 PP >> tr|F7EVY7|F7EVY7_MACMU DNA polymerase epsilon 3, accessory subunit OS=Macaca mulatta OX=9544 GN=POLE3 PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 15.3 0.1 2.8e-06 0.02 8 89 .. 22 102 .. 16 118 .. 0.84 Alignments for each domain: == domain 1 score: 15.3 bits; conditional E-value: 2.8e-06 S-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEESTT-SEGC CS SpoU_methylase 8 eiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatslkgksls 89 + d N+++ aR+a as vl ++ +a+ + + kr +++a +vl + + ++++++++ lke+ ++ + +++kgk+ tr|F7EVY7|F7EVY7_MACMU 22 ALPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVLSAMEEMEFQRFVTPLKEA-LEAYRREQKGKKEA 102 55667799999****9999999*********************************************.*****999665433 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (142 nodes) Target sequences: 21211 (10888574 residues searched) Passed MSV filter: 375 (0.0176795); expected 424.2 (0.02) Passed bias filter: 348 (0.0164066); expected 424.2 (0.02) Passed Vit filter: 27 (0.00127292); expected 21.2 (0.001) Passed Fwd filter: 3 (0.000141436); expected 0.2 (1e-05) Initial search space (Z): 21211 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.14u 0.01s 00:00:00.15 Elapsed: 00:00:00.08 # Mc/sec: 19327.22 // [ok]