# 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/Homo_sapiens.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-30 107.3 0.0 9.5e-30 105.9 0.0 1.8 2 sp|Q13395|TARB1_HUMAN Probable methyltransferase TARBP1 OS= 1.5e-27 98.8 0.0 1.9e-27 98.4 0.0 1.2 1 sp|Q6IN84|MRM1_HUMAN rRNA methyltransferase 1, mitochondri 7e-21 77.1 0.0 2e-19 72.4 0.0 2.2 1 sp|Q9HC36|RMTL1_HUMAN RNA methyltransferase-like protein 1 4.2e-12 48.7 0.0 5.2e-12 48.4 0.0 1.1 1 tr|K7EJT9|K7EJT9_HUMAN Mitochondrial rRNA methyltransferase 1.3e-11 47.1 0.0 1.6e-11 46.8 0.0 1.1 1 sp|Q6IN84-2|MRM1_HUMAN Isoform 2 of rRNA methyltransferase 1 1.7e-05 27.3 0.0 2.6e-05 26.6 0.0 1.3 1 tr|I3L443|I3L443_HUMAN RNA methyltransferase-like protein 1 ------ inclusion threshold ------ 0.061 15.7 0.1 0.082 15.3 0.1 1.1 1 sp|Q9NRF9|DPOE3_HUMAN DNA polymerase epsilon subunit 3 OS=H Domain annotation for each sequence (and alignments): >> sp|Q13395|TARB1_HUMAN Probable methyltransferase TARBP1 OS=Homo sapiens GN=TARBP1 PE=1 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.2 0.0 3.3 4.1e+04 54 92 .. 981 1019 .. 971 1029 .. 0.80 2 ! 105.9 0.0 7.5e-34 9.5e-30 2 141 .. 1464 1605 .. 1463 1606 .. 0.92 Alignments for each domain: == domain 1 score: -3.2 bits; conditional E-value: 3.3 HHHHEEEESSHHHHHHHHCCCTEEEEEESTT-SEGCCSH CS SpoU_methylase 54 evlelkvvdsleealkelkeegfalvatslkgkslseid 92 + +l +++l+++++ + ++++ ++a++ kg+ + +i+ sp|Q13395|TARB1_HUMAN 981 SNTQLIFWANLKAFVQFVFDNKVLTIAAKIKGQAYFKIK 1019 556778899999999999999899999988999998774 PP == domain 2 score: 105.9 bits; conditional E-value: 7.5e-34 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEE..SSHHHHHHHHCCCTEEEEEESTT- CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvv..dsleealkelkeegfalvatslkg 85 livv i++p+NlG ++Rt+++fgas lv+ + ++ + ++++++++++a+++l+l++v ++l ++l++ k eg++++++++ + sp|Q13395|TARB1_HUMAN 1464 LIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQC--ISDKQFQHLSVSAEQWLPLVEVkpPQLIDYLQQKKTEGYTIIGVEQTA 1547 799***********************7777766666..5*****************888856799*******************77 PP SEGC..CSHHHTTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHH CS SpoU_methylase 86 ksls..eidlkekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvaill 141 ksl+ ++ ++ek +l++GnE++G++ +l++++d +v+Ip++g ++SLNv+v+ a+l+ sp|Q13395|TARB1_HUMAN 1548 KSLDltQYCFPEKSLLLLGNEREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLI 1605 66555599**********************************************9987 PP >> sp|Q6IN84|MRM1_HUMAN rRNA methyltransferase 1, mitochondrial OS=Homo sapiens GN=MRM1 PE=1 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 98.4 0.0 1.5e-31 1.9e-27 2 142 .] 146 301 .. 145 301 .. 0.85 Alignments for each domain: == domain 1 score: 98.4 bits; conditional E-value: 1.5e-31 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEEST..T-SEG CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatsl..kgksl 88 l +vl++i+dp+N+Ga++R+a +g+++++ ++++s +l+p + +++aga ev+++ d+l +l+ ++g+ + +t + ++++ sp|Q6IN84|MRM1_HUMAN 146 LWLVLDGIQDPRNFGAVLRSAHFLGVDKVITSRRNSC-PLTPVVSKSSAGAMEVMDVFSTDDLTGFLQTKAQQGWLVAGTVGcpSTEDP 233 569****************************987776.***********************************9999999887644444 PP C..CS........HHHTTEEEEEEBTTTBS-HHHHCTSSEEEE-....---TTSSS--HHHHHHHHHH CS SpoU_methylase 89 s..ei........dlkekvalvfGnEdkGlsnelleladrlvkI....pmsgeveSLNvavAvailly 142 + ei ++++++lv+GnE++Gls+e+ + ++ l++I + eSLNv+vA++ill+ sp|Q6IN84|MRM1_HUMAN 234 QssEIpimsclefLWERPTLLVLGNEGSGLSQEVQASCQLLLTIlprrQLPPGLESLNVSVAAGILLH 301 4343333333333666***********************999995443346788***********985 PP >> sp|Q9HC36|RMTL1_HUMAN RNA methyltransferase-like protein 1 OS=Homo sapiens GN=RNMTL1 PE=1 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 72.4 0.0 1.6e-23 2e-19 2 142 .] 210 400 .. 209 400 .. 0.83 Alignments for each domain: == domain 1 score: 72.4 bits; conditional E-value: 1.6e-23 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEEST....T- CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatsl....kg 85 l +++++++dpgNlG+i+R+a+ +g+s+++l+k ++d ++p+++ra++ga++ +++ ++e + + l ++++++++ + sp|Q9HC36|RMTL1_HUMAN 210 LLLICDNLRDPGNLGTILRSAAGAGCSKVLLTK-GCVDAWEPKVLRAGMGAHFRMPIINNLEWETVPNYLPPD-TRVYVADNcglyAQ 295 6799***************************88.**********************99999****99999999.99*99999766422 PP SEGC.CS................HHH............................TTEEEEEEBTTTBS-HHHHCTSS....EEEE--- CS SpoU_methylase 86 ksls.ei................dlk............................ekvalvfGnEdkGlsnellelad....rlvkIpm 124 ++s ++ + ++a+v+G E+ G+s e l+la+ + + Ip+ sp|Q9HC36|RMTL1_HUMAN 296 AEMSnKAsdhgwvcdqrvmkfhkY-EeeedvetgasqdwlphvevqsydsdwteAPAAVVIGGETYGVSLESLQLAEstggKRLLIPV 382 233333356677776666666650.15556666677777777788888899999********************99955556899*** PP -TTSSS--HHHHHHHHHH CS SpoU_methylase 125 sgeveSLNvavAvailly 142 + v+SLN a+A++ill+ sp|Q9HC36|RMTL1_HUMAN 383 VPGVDSLNSAMAASILLF 400 ***************985 PP >> tr|K7EJT9|K7EJT9_HUMAN Mitochondrial rRNA methyltransferase 1 homolog (S. cerevisiae), isoform CRA_b OS=Homo sapiens # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 48.4 0.0 4.1e-16 5.2e-12 54 142 .] 2 106 .. 1 106 [. 0.78 Alignments for each domain: == domain 1 score: 48.4 bits; conditional E-value: 4.1e-16 HHHHEEEESSHHHHHHHHCCCTEEEEEEST..T-SEGC..........CSHHHTTEEEEEEBTTTBS-HHHHCTSSEEEE-....-- CS SpoU_methylase 54 evlelkvvdsleealkelkeegfalvatsl..kgksls..........eidlkekvalvfGnEdkGlsnelleladrlvkI....pm 124 ev+++ d+l +l+ ++g+ + +t + ++++ + e+ ++++++lv+GnE++Gls+e+ + ++ l++I tr|K7EJT9|K7EJT9_HUMAN 2 EVMDVFSTDDLTGFLQTKAQQGWLVAGTVGcpSTEDPQsseipimsclEFLWERPTLLVLGNEGSGLSQEVQASCQLLLTIlprrQL 88 5678889999***********99999998876444444342323333333666***********************99999544334 PP -TTSSS--HHHHHHHHHH CS SpoU_methylase 125 sgeveSLNvavAvailly 142 + eSLNv+vA++ill+ tr|K7EJT9|K7EJT9_HUMAN 89 PPGLESLNVSVAAGILLH 106 6788***********985 PP >> sp|Q6IN84-2|MRM1_HUMAN Isoform 2 of rRNA methyltransferase 1, mitochondrial OS=Homo sapiens GN=MRM1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 46.8 0.0 1.2e-15 1.6e-11 59 142 .] 4 103 .. 1 103 [. 0.76 Alignments for each domain: == domain 1 score: 46.8 bits; conditional E-value: 1.2e-15 EEESSHHHHHHHHCCCTEEEEEEST..T-SEGC..........CSHHHTTEEEEEEBTTTBS-HHHHCTSSEEEE-....---TTSS CS SpoU_methylase 59 kvvdsleealkelkeegfalvatsl..kgksls..........eidlkekvalvfGnEdkGlsnelleladrlvkI....pmsgeve 129 d+l +l+ ++g+ + +t + ++++ + e+ ++++++lv+GnE++Gls+e+ + ++ l++I + e sp|Q6IN84-2|MRM1_HUMAN 4 FSTDDLTGFLQTKAQQGWLVAGTVGcpSTEDPQsseipimsclEFLWERPTLLVLGNEGSGLSQEVQASCQLLLTIlprrQLPPGLE 90 567889999999999999999998776444444342323333344666***********************999995443346788* PP S--HHHHHHHHHH CS SpoU_methylase 130 SLNvavAvailly 142 SLNv+vA++ill+ sp|Q6IN84-2|MRM1_HUMAN 91 SLNVSVAAGILLH 103 **********985 PP >> tr|I3L443|I3L443_HUMAN RNA methyltransferase-like protein 1 (Fragment) OS=Homo sapiens GN=RNMTL1 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 26.6 0.0 2.1e-09 2.6e-05 2 36 .. 137 171 .. 136 176 .. 0.89 Alignments for each domain: == domain 1 score: 26.6 bits; conditional E-value: 2.1e-09 EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGS CS SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkpr 36 l +++++++dpgNlG+i+R+a+ +g+s+++l+k + tr|I3L443|I3L443_HUMAN 137 LLLICDNLRDPGNLGTILRSAAGAGCSKVLLTKGK 171 6799***************************8854 PP >> sp|Q9NRF9|DPOE3_HUMAN DNA polymerase epsilon subunit 3 OS=Homo sapiens GN=POLE3 PE=1 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 15.3 0.1 6.5e-06 0.082 8 89 .. 22 102 .. 16 118 .. 0.84 Alignments for each domain: == domain 1 score: 15.3 bits; conditional E-value: 6.5e-06 S-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEESTT-SEGC CS SpoU_methylase 8 eiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatslkgksls 89 + d N+++ aR+a as vl ++ +a+ + + kr +++a +vl + + ++++++++ lke+ ++ + +++kgk+ sp|Q9NRF9|DPOE3_HUMAN 22 ALPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVLSAMEEMEFQRFVTPLKEA-LEAYRREQKGKKEA 102 55667799999****9999999*********************************************.*****999665433 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (142 nodes) Target sequences: 88473 (35070517 residues searched) Passed MSV filter: 1552 (0.0175421); expected 1769.5 (0.02) Passed bias filter: 1442 (0.0162988); expected 1769.5 (0.02) Passed Vit filter: 105 (0.0011868); expected 88.5 (0.001) Passed Fwd filter: 7 (7.91202e-05); expected 0.9 (1e-05) Initial search space (Z): 88473 [actual number of targets] Domain search space (domZ): 7 [number of targets reported over threshold] # CPU time: 0.38u 0.02s 00:00:00.40 Elapsed: 00:00:00.19 # Mc/sec: 26210.60 // [ok]