# 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/Pan_troglodytes.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-49 168.8 0.0 2.3e-49 168.1 0.0 1.3 1 tr|K7DSE5|K7DSE5_PANTR THUMP domain containing 3 OS=Pan 2.4e-26 93.0 0.0 7.7e-26 91.3 0.0 1.8 1 tr|H2QHS9|H2QHS9_PANTR THUMP domain containing 2 OS=Pan 1.1e-11 45.2 0.0 2.3e-11 44.1 0.0 1.5 1 tr|H2R4E3|H2R4E3_PANTR TRMT11 isoform 3 OS=Pan troglody 1e-07 32.2 0.2 6.5e-07 29.6 0.2 2.0 1 tr|A0A2I3SPD6|A0A2I3SPD6_PANTR Methyltransferase like 5 OS=Pan 1.9e-05 24.8 0.0 7e-05 22.9 0.0 1.8 1 tr|H2QW66|H2QW66_PANTR Trimethylguanosine synthase 1 OS 9.6e-05 22.5 0.0 0.0002 21.5 0.0 1.5 1 tr|K7BSP4|K7BSP4_PANTR HEMK1 isoform 1 OS=Pan troglodyt ------ inclusion threshold ------ 0.16 12.0 2.7 0.39 10.7 0.2 2.2 2 tr|A0A2I3RNX0|A0A2I3RNX0_PANTR MICOS complex subunit OS=Pan tro 0.16 12.0 0.4 3.1 7.8 0.4 2.2 1 tr|H2QL94|H2QL94_PANTR TRM2 tRNA methyltransferase 2 ho Domain annotation for each sequence (and alignments): >> tr|K7DSE5|K7DSE5_PANTR THUMP domain containing 3 OS=Pan troglodytes OX=9598 GN=THUMPD3 PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 168.1 0.0 7.9e-53 2.3e-49 2 195 .. 294 476 .. 292 478 .. 0.95 Alignments for each domain: == domain 1 score: 168.1 bits; conditional E-value: 7.9e-53 SSS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHH CS UPF0020 2 gyRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrv 88 ++++f gp++L++tLA++++rl++ p + ++DPmCG+G+i+IE+a+ ++++ +++ ++++ + ++++++++++ tr|K7DSE5|K7DSE5_PANTR 294 NITHF-GPTTLRSTLAYGMLRLCDPLPYDIIVDPMCGTGAIPIEGATEWSDCFHIAG-------------DNNPLAVNRAANNIASL 366 55555.5**********************************************7665.............8999999********** PP HHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHHHHHHHHHHHHHHHH-TT...-EEEEEESSHHHHH CS UPF0020 89 vqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkalekLYseflrelkrvlrgg.grlvlltsenkalek 174 +++++ + k +g i++ q+d+++L+l++g+vd+ivt++P+G+r+gskk++++LY+++lre++rv+ gr+vllt+++k+++k tr|K7DSE5|K7DSE5_PANTR 367 LTKSQIKEGKPSWGLPIDAIQWDICNLPLRTGSVDIIVTDLPFGKRMGSKKRNWNLYPACLREMSRVCTPTtGRAVLLTQDTKCFTK 453 ********************************************************************9988*************** PP CC---..ESEEEEEEETTEEEEE CS UPF0020 175 aleer..alrkvkeknvklglll 195 al+ + +rkv ++v++g+l+ tr|K7DSE5|K7DSE5_PANTR 454 ALSGMrhVWRKVDTVWVNVGGLR 476 ***99899************987 PP >> tr|H2QHS9|H2QHS9_PANTR THUMP domain containing 2 OS=Pan troglodytes OX=9598 GN=THUMPD2 PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 91.3 0.0 2.7e-29 7.7e-26 4 170 .. 274 412 .. 272 433 .. 0.92 Alignments for each domain: == domain 1 score: 91.3 bits; conditional E-value: 2.7e-29 S-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHH CS UPF0020 4 RefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvq 90 R + + a L++t+A a+ la++k+g lDPmCG Gtil+Eaa + +++ +g+D + + tr|H2QHS9|H2QHS9_PANTR 274 RAYIKTAGLRSTIAWAMASLADIKAGAFVLDPMCGLGTILLEAAKEWPDVY------------------------YVGADVSDSQLL 336 788899*********************************************........................79********** PP HHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHHHHHHHHHHHHHHHH-TT..-EEEEEESSH CS UPF0020 91 gareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkalekLYseflrelkrvlrgggrlvlltsenk 170 g+ +N+++ag++d+ie+ + + +L+l++++vd+i+++ P+G++ + k+++ ++l+e++rvl+ gg +vll+se+ tr|H2QHS9|H2QHS9_PANTR 337 GTWDNLKAAGLEDKIELLKISVIELPLPSESVDIIISDIPFGKKFKLGKDIK----SILQEMERVLHVGGTIVLLLSEDH 412 **********************************************999986....5799999999999*****999864 PP >> tr|H2R4E3|H2R4E3_PANTR TRMT11 isoform 3 OS=Pan troglodytes OX=9598 GN=TRMT11 PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 44.1 0.0 8.1e-15 2.3e-11 3 140 .. 190 320 .. 189 326 .. 0.85 Alignments for each domain: == domain 1 score: 44.1 bits; conditional E-value: 8.1e-15 SS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHH CS UPF0020 3 yRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvv 89 +R+f g++++ + L+ + + ++k+++ +DP+ G+G++lI a ga+++ + ++ + + +++r+++k +g D + tr|H2R4E3|H2R4E3_PANTR 190 KRHFIGNTSMDAGLSFIMANHGKVKENDIVFDPFVGTGGLLIACAHFGAYVY---GTDIDYNTVHGLGKATRKNQKWRGPDENI--- 270 79**************************************************...56678888888999999999******876... PP HHHHHHHHHTT-GGG.EEEEE--GGG--.STTS---EEEE----------HHH CS UPF0020 90 qgareNaekagvgdl.iefsqadaakLr.lkegevdvivtnpPYGerlgskka 140 r N++++g+++ ++ + da k +k +d+i+t+pPYG+r ++ ++ tr|H2R4E3|H2R4E3_PANTR 271 ---RANLRQYGLEKYyLDVLVSDASKPSwRKGTYFDAIITDPPYGIRESTRRT 320 ...5799999999852455666666655435559*************888765 PP >> tr|A0A2I3SPD6|A0A2I3SPD6_PANTR Methyltransferase like 5 OS=Pan troglodytes OX=9598 GN=METTL5 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 29.6 0.2 2.3e-10 6.5e-07 45 142 .. 68 140 .. 25 171 .. 0.74 Alignments for each domain: == domain 1 score: 29.6 bits; conditional E-value: 2.3e-10 HHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--.STTS-- CS UPF0020 45 EaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLr.lkegev 122 a+lga +g+D+d+ +++ ++Nae+ ++++ i+++q d++ L ++++++ tr|A0A2I3SPD6|A0A2I3SPD6_PANTR 68 GTAMLGAGLC-------------------------VGFDIDEDALEIFNRNAEEFELTN-IDMVQCDVCLLSnRMSKSF 120 5555555554.........................8********************986.788888*****998999** PP -EEEE----------HHHHH CS UPF0020 123 dvivtnpPYGerlgskkale 142 d+++ npP+G + ++ ++ tr|A0A2I3SPD6|A0A2I3SPD6_PANTR 121 DTVIMNPPFGTKNNKGTDMA 140 **********9877666554 PP >> tr|H2QW66|H2QW66_PANTR Trimethylguanosine synthase 1 OS=Pan troglodytes OX=9598 GN=TGS1 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 22.9 0.0 2.4e-08 7e-05 49 132 .. 713 769 .. 682 777 .. 0.83 Alignments for each domain: == domain 1 score: 22.9 bits; conditional E-value: 2.4e-08 HHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----- CS UPF0020 49 lganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYG 132 g + ++++D+d+ ++ ar+Nae +g++d+ief + d+ L + + dv+ pP+G tr|H2QW66|H2QW66_PANTR 713 TGMR--------------------------VIAIDIDPVKIALARNNAEVYGIADKIEFICGDFLLLA-SCLKADVVFLSPPWG 769 4444..........................569********************************999.77899*********9 PP >> tr|K7BSP4|K7BSP4_PANTR HEMK1 isoform 1 OS=Pan troglodytes OX=9598 GN=HEMK1 PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 21.5 0.0 6.9e-08 0.0002 77 131 .. 184 242 .. 173 252 .. 0.90 Alignments for each domain: == domain 1 score: 21.5 bits; conditional E-value: 6.9e-08 --EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--....STTS---EEEE---- CS UPF0020 77 lklygsDldrrvvqgareNaekagvgdliefsqadaakLr....lkegevdvivtnpPY 131 +++++D+ ++++ + eNa++ +++d+i + +d+++ r l+ g vd+iv+npPY tr|K7BSP4|K7BSP4_PANTR 184 SRVIAVDKGEAAISLTHENAQRLRLQDRIWIIHLDMTSERswthLPWGPVDLIVSNPPY 242 4599********************************998877778899*********** PP >> tr|A0A2I3RNX0|A0A2I3RNX0_PANTR MICOS complex subunit OS=Pan troglodytes OX=9598 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 1.6 0.4 0.086 2.5e+02 133 179 .. 83 129 .. 82 148 .. 0.67 2 ? 10.7 0.2 0.00014 0.39 64 99 .. 148 187 .. 123 207 .. 0.74 Alignments for each domain: == domain 1 score: 1.6 bits; conditional E-value: 0.086 -----HHHHHHHHHHHHHHHHHH-TT..-EEEEEESSHHHHHCC--- CS UPF0020 133 erlgskkalekLYseflrelkrvlrgggrlvlltsenkalekaleer 179 +rl+++ a+e+L++++lre + ++++++ l+ + ++ ++l+++ tr|A0A2I3RNX0|A0A2I3RNX0_PANTR 83 KRLKQAAANEQLTRAILRERISSEEERAKAKHLARQLEEKDRVLKKQ 129 68999999999999999886665555555555555555555555555 PP == domain 2 score: 10.7 bits; conditional E-value: 0.00014 S...HHHHHHHHHH.HH--EEEEES-HHHHHHHHHHHHHT CS UPF0020 64 e...lkaeaeeear.aelklygsDldrrvvqgareNaeka 99 + + +e+e++++ +e + +++Dl+++++q++reN ++ tr|A0A2I3RNX0|A0A2I3RNX0_PANTR 148 QyqkAAEEVEAKFKrYESHPVCADLQAKILQCCRENTCQT 187 13336677777777667779****************8665 PP >> tr|H2QL94|H2QL94_PANTR TRM2 tRNA methyltransferase 2 homolog A OS=Pan troglodytes OX=9598 GN=TRMT2A PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 7.8 0.4 0.0011 3.1 14 101 .. 418 479 .. 409 512 .. 0.66 Alignments for each domain: == domain 1 score: 7.8 bits; conditional E-value: 0.0011 HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT CS UPF0020 14 etLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekag 100 e L ++ a++++g++ lD CG+Gti + a +++++ g++l +++v+ ar Na+ + tr|H2QL94|H2QL94_PANTR 418 EVLYTVIQDWAQLDAGSTVLDVCCGTGTIGLALARKVKRVI--------------------------GVELCPEAVEDARVNAQDNE 478 55556667778888999999999999999776655555555..........................55555555555555555555 PP - CS UPF0020 101 v 101 + tr|H2QL94|H2QL94_PANTR 479 L 479 4 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (197 nodes) Target sequences: 23008 (11942255 residues searched) Passed MSV filter: 597 (0.0259475); expected 460.2 (0.02) Passed bias filter: 464 (0.0201669); expected 460.2 (0.02) Passed Vit filter: 47 (0.00204277); expected 23.0 (0.001) Passed Fwd filter: 8 (0.000347705); expected 0.2 (1e-05) Initial search space (Z): 23008 [actual number of targets] Domain search space (domZ): 8 [number of targets reported over threshold] # CPU time: 0.21u 0.01s 00:00:00.22 Elapsed: 00:00:00.09 # Mc/sec: 26140.27 // [ok]