# 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/Homo_sapiens.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-49 170.4 0.1 2.3e-49 169.9 0.1 1.3 1 sp|Q8WWH5|TRUB1_HUMAN Probable tRNA pseudouridine synthase 3.7e-27 97.8 0.0 5e-27 97.4 0.0 1.1 1 tr|B7Z7G5|B7Z7G5_HUMAN Probable tRNA pseudouridine synthase 5.8e-27 97.1 0.0 7.9e-27 96.7 0.0 1.2 1 sp|O95900|TRUB2_HUMAN Probable tRNA pseudouridine synthase 3.2e-21 78.5 0.2 5.2e-18 68.1 0.2 3.1 1 sp|O60832-2|DKC1_HUMAN Isoform 3 of H/ACA ribonucleoprotein 4.1e-21 78.2 0.1 7.4e-18 67.6 0.1 3.5 1 sp|O60832|DKC1_HUMAN H/ACA ribonucleoprotein complex subun 1.3e-20 76.5 0.1 7.1e-16 61.2 0.0 3.0 2 tr|H7C0M1|H7C0M1_HUMAN H/ACA ribonucleoprotein complex subun 1.5e-19 73.1 0.1 3.8e-17 65.3 0.1 2.3 1 tr|C9IYT0|C9IYT0_HUMAN H/ACA ribonucleoprotein complex subun 4.2e-12 48.9 0.0 6.2e-12 48.4 0.0 1.2 1 tr|H7C2Q9|H7C2Q9_HUMAN H/ACA ribonucleoprotein complex subun ------ inclusion threshold ------ 0.15 14.6 0.0 0.27 13.9 0.0 1.4 1 tr|H7BZF2|H7BZF2_HUMAN H/ACA ribonucleoprotein complex subun Domain annotation for each sequence (and alignments): >> sp|Q8WWH5|TRUB1_HUMAN Probable tRNA pseudouridine synthase 1 OS=Homo sapiens GN=TRUB1 PE=1 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 169.9 0.1 2.3e-53 2.3e-49 1 149 [] 106 255 .. 106 255 .. 0.98 Alignments for each domain: == domain 1 score: 169.9 bits; conditional E-value: 2.3e-53 HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHHHHHHHC-EEE CS TruB_N 1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgaetdteDaegeileeekveklteekleevlkkftGei 88 kr+ ++ k+Gh+GtLD +a GvLvv++g++Tk+l+++l+ +K+Y+a +lg++tdt D++g+++ee+ ++k+t+e++e +l+kftG+i sp|Q8WWH5|TRUB1_HUMAN 106 KRKKQTLKIGHGGTLDSAARGVLVVGIGSGTKMLTSMLSGSKRYTAIGELGKATDTLDSTGRVTEEKPYDKITQEDIEGILQKFTGNI 193 5677888***********************************************************99******************** PP -------------------------------.--EEEEEEEEEEEEEEEEEEEEEESTTTTH CS TruB_N 89 eqvppmySAvkvnGkrlyelaregeeverkk.rkvtiyelelleveepevelevecskGtYi 149 +qvpp ySA+k++G+rl +l+++ge ve k+ r+vt+y+++l ++++p ++l+vec G+Yi sp|Q8WWH5|TRUB1_HUMAN 194 MQVPPLYSALKKDGQRLSTLMKRGEVVEAKPaRPVTVYSISLQKFQPPFFTLDVECGGGFYI 255 ****************************8877*****************************8 PP >> tr|B7Z7G5|B7Z7G5_HUMAN Probable tRNA pseudouridine synthase 2 OS=Homo sapiens GN=TRUB2 PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 97.4 0.0 5.1e-31 5e-27 7 148 .. 33 176 .. 28 177 .. 0.96 Alignments for each domain: == domain 1 score: 97.4 bits; conditional E-value: 5.1e-31 S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-..EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHHHHHHHC-EEE--- CS TruB_N 7 kkvGhtGtLDplatGvLvvavgeaTklleyllead..KeYeatirlgaetdteDaegeileeekveklteekleevlkkftGeieqv 91 kvG ++ LD +a+GvLv++vg++++ll+ + +a+ K Y++ lg++td+ ++g+ +e+++++++t+ekl+++l+ ++G+ ++ tr|B7Z7G5|B7Z7G5_HUMAN 33 LKVGVGHRLDAQASGVLVLGVGHGCRLLTDMYNAHltKDYTVRGLLGKATDDFREDGRLVEKTTYDHVTREKLDRILAVIQGSHQKA 119 59***************************99977666*************************99*********************** PP ------------------------------EEEEEEEEEEEEEEEEEEEEEESTTTT CS TruB_N 92 ppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtY 148 myS+++ + +++ye+a +g ++k ++ i+ +++l + +pe+ lev+c + t+ tr|B7Z7G5|B7Z7G5_HUMAN 120 LVMYSNLDLKTQEAYEMAVRGLIRPMNKSPMLITGIRCLYFAPPEFLLEVQCMHETQ 176 ****************************************************99885 PP >> sp|O95900|TRUB2_HUMAN Probable tRNA pseudouridine synthase 2 OS=Homo sapiens GN=TRUB2 PE=1 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 96.7 0.0 8.1e-31 7.9e-27 7 148 .. 89 232 .. 84 233 .. 0.96 Alignments for each domain: == domain 1 score: 96.7 bits; conditional E-value: 8.1e-31 S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-..EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHHHHHHHC-EEE---- CS TruB_N 7 kkvGhtGtLDplatGvLvvavgeaTklleyllead..KeYeatirlgaetdteDaegeileeekveklteekleevlkkftGeieqvp 92 kvG ++ LD +a+GvLv++vg++++ll+ + +a+ K Y++ lg++td+ ++g+ +e+++++++t+ekl+++l+ ++G+ ++ sp|O95900|TRUB2_HUMAN 89 LKVGVGHRLDAQASGVLVLGVGHGCRLLTDMYNAHltKDYTVRGLLGKATDDFREDGRLVEKTTYDHVTREKLDRILAVIQGSHQKAL 176 59***************************99977666*************************99************************ PP -----------------------------EEEEEEEEEEEEEEEEEEEEEESTTTT CS TruB_N 93 pmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtY 148 myS+++ + +++ye+a +g ++k ++ i+ +++l + +pe+ lev+c + t+ sp|O95900|TRUB2_HUMAN 177 VMYSNLDLKTQEAYEMAVRGLIRPMNKSPMLITGIRCLYFAPPEFLLEVQCMHETQ 232 ***************************************************99885 PP >> sp|O60832-2|DKC1_HUMAN Isoform 3 of H/ACA ribonucleoprotein complex subunit 4 OS=Homo sapiens GN=DKC1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 68.1 0.2 5.3e-22 5.2e-18 1 149 [] 110 226 .. 110 226 .. 0.92 Alignments for each domain: == domain 1 score: 68.1 bits; conditional E-value: 5.3e-22 HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHHHHHHHC-EE CS TruB_N 1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgaetdteDaegeileeekveklteekleevlkkftGe 87 +r+l+++k Gh+GtLDp++tG+L+v++++aT+l+++ ++a KeY+ +rl+ + + +l+++l+++tG+ sp|O60832-2|DKC1_HUMAN 110 RRILRVEKTGHSGTLDPKVTGCLIVCIERATRLVKSQQSAGKEYVGIVRLHNAIEGGT-----------------QLSRALETLTGA 179 89************************************************99876653.................5899******** PP E---------------------------------EEEEEEEEEEEEEE..EEEEEEEESTTTTH CS TruB_N 88 ieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveep..evelevecskGtYi 149 + q+pp ++Avk r+ r tiye +++e++++ + v+c++GtYi sp|O60832-2|DKC1_HUMAN 180 LFQRPPLIAAVK-----------------RQLRVRTIYESKMIEYDPErrLGIFWVSCEAGTYI 226 ************.................89999999999999998876567799999999998 PP >> sp|O60832|DKC1_HUMAN H/ACA ribonucleoprotein complex subunit 4 OS=Homo sapiens GN=DKC1 PE=1 SV=3 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 67.6 0.1 7.5e-22 7.4e-18 1 149 [] 110 226 .. 110 226 .. 0.92 Alignments for each domain: == domain 1 score: 67.6 bits; conditional E-value: 7.5e-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|O60832|DKC1_HUMAN 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|O60832|DKC1_HUMAN 182 QRPPLIAAVK-----------------RQLRVRTIYESKMIEYDPErrLGIFWVSCEAGTYI 226 **********.................89999999999999998876567799999999998 PP >> tr|H7C0M1|H7C0M1_HUMAN H/ACA ribonucleoprotein complex subunit 4 (Fragment) OS=Homo sapiens GN=DKC1 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 61.2 0.0 7.2e-20 7.1e-16 1 53 [. 96 148 .. 96 153 .. 0.96 2 ! 11.3 0.0 0.00016 1.6 76 102 .. 154 180 .. 148 223 .. 0.68 Alignments for each domain: == domain 1 score: 61.2 bits; conditional E-value: 7.2e-20 HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEE CS TruB_N 1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgae 53 +r+l+++k Gh+GtLDp++tG+L+v++++aT+l+++ ++a KeY+ +rl+ + tr|H7C0M1|H7C0M1_HUMAN 96 RRILRVEKTGHSGTLDPKVTGCLIVCIERATRLVKSQQSAGKEYVGIVRLHNA 148 89***********************************************9976 PP == domain 2 score: 11.3 bits; conditional E-value: 0.00016 HHHHHHHHC-EEE-------------- CS TruB_N 76 kleevlkkftGeieqvppmySAvkvnG 102 +l+++l+++tG++ q+pp ++Avk + tr|H7C0M1|H7C0M1_HUMAN 154 QLSRALETLTGALFQRPPLIAAVKRQL 180 78999******************9653 PP >> tr|C9IYT0|C9IYT0_HUMAN H/ACA ribonucleoprotein complex subunit 4 (Fragment) OS=Homo sapiens GN=DKC1 PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 65.3 0.1 3.9e-21 3.8e-17 1 101 [. 110 193 .. 110 216 .. 0.89 Alignments for each domain: == domain 1 score: 65.3 bits; conditional E-value: 3.9e-21 HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHHHHHHHC-EE CS TruB_N 1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgaetdteDaegeileeekveklteekleevlkkftGe 87 +r+l+++k Gh+GtLDp++tG+L+v++++aT+l+++ ++a KeY+ +rl+ + + +l+++l+++tG+ tr|C9IYT0|C9IYT0_HUMAN 110 RRILRVEKTGHSGTLDPKVTGCLIVCIERATRLVKSQQSAGKEYVGIVRLHNAIEGGT-----------------QLSRALETLTGA 179 89************************************************99876554.................578899999999 PP E------------- CS TruB_N 88 ieqvppmySAvkvn 101 + q+pp ++Avk + tr|C9IYT0|C9IYT0_HUMAN 180 LFQRPPLIAAVKRQ 193 99999999999965 PP >> tr|H7C2Q9|H7C2Q9_HUMAN H/ACA ribonucleoprotein complex subunit 4 (Fragment) OS=Homo sapiens GN=DKC1 PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 48.4 0.0 6.3e-16 6.2e-12 1 39 [. 96 134 .. 96 139 .. 0.94 Alignments for each domain: == domain 1 score: 48.4 bits; conditional E-value: 6.3e-16 HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTT CS TruB_N 1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylle 39 +r+l+++k Gh+GtLDp++tG+L+v++++aT+l+++ ++ tr|H7C2Q9|H7C2Q9_HUMAN 96 RRILRVEKTGHSGTLDPKVTGCLIVCIERATRLVKSQQS 134 89********************************98876 PP >> tr|H7BZF2|H7BZF2_HUMAN H/ACA ribonucleoprotein complex subunit 4 (Fragment) OS=Homo sapiens GN=DKC1 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 13.9 0.0 2.7e-05 0.27 75 102 .. 12 39 .. 5 64 .. 0.81 Alignments for each domain: == domain 1 score: 13.9 bits; conditional E-value: 2.7e-05 HHHHHHHHHC-EEE-------------- CS TruB_N 75 ekleevlkkftGeieqvppmySAvkvnG 102 ++l+++l+++tG++ q+pp ++Avk + tr|H7BZF2|H7BZF2_HUMAN 12 TQLSRALETLTGALFQRPPLIAAVKRQL 39 57999********************764 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (149 nodes) Target sequences: 88473 (35070517 residues searched) Passed MSV filter: 2527 (0.0285624); expected 1769.5 (0.02) Passed bias filter: 1818 (0.0205486); expected 1769.5 (0.02) Passed Vit filter: 128 (0.00144677); expected 88.5 (0.001) Passed Fwd filter: 9 (0.000101726); expected 0.9 (1e-05) Initial search space (Z): 88473 [actual number of targets] Domain search space (domZ): 9 [number of targets reported over threshold] # CPU time: 0.49u 0.03s 00:00:00.52 Elapsed: 00:00:00.24 # Mc/sec: 21772.95 // [ok]