# 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/Strongylocentrotus_purpuratus.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-42 146.6 1.2 6.7e-30 105.1 0.0 2.1 2 tr|W4XNX2|W4XNX2_STRPU Uncharacterized protein OS=Strongyloc 2.2e-23 83.9 0.2 1.5e-20 74.7 0.2 3.4 1 tr|W4XFN0|W4XFN0_STRPU Uncharacterized protein OS=Strongyloc 3.5e-09 37.9 0.1 5.5e-09 37.2 0.1 1.2 1 tr|W4XLI0|W4XLI0_STRPU Uncharacterized protein OS=Strongyloc 0.00013 23.0 0.0 0.0046 18.0 0.0 2.2 1 tr|W4ZGE0|W4ZGE0_STRPU Uncharacterized protein OS=Strongyloc ------ inclusion threshold ------ 0.39 11.7 3.9 1.4 9.9 1.3 2.7 2 tr|W4ZF97|W4ZF97_STRPU Uncharacterized protein OS=Strongyloc Domain annotation for each sequence (and alignments): >> tr|W4XNX2|W4XNX2_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 105.1 0.0 1.2e-33 6.7e-30 3 106 .. 73 177 .. 71 180 .. 0.93 2 ! 41.6 0.5 4.3e-14 2.5e-10 2 42 .. 175 215 .. 174 219 .. 0.91 Alignments for each domain: == domain 1 score: 105.1 bits; conditional E-value: 1.2e-33 HTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHHHHHHHC-EEE- CS TruB_N 3 llkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgaetdteDaegeileeekveklteekleevlkkftGeie 89 +k k+Gh+GtLD +atGvLv+++g++Tkll+++l+ K Y+a+ rlg +tdt Da+g+ +e+++ +++te+ le++l++f G+i tr|W4XNX2|W4XNX2_STRPU 73 RIKLPKMGHGGTLDMNATGVLVIGCGRGTKLLSSYLQGGKVYRAQGRLGRATDTMDASGKEVETAQFDHVTESGLERCLESFVGDIL 159 56788***********************************************************99********************* PP ----------.------- CS TruB_N 90 qvppmySAvk.vnGkrly 106 qvpp+ S + v+G+r tr|W4XNX2|W4XNX2_STRPU 160 QVPPVCSDKQrVDGQRWI 177 *******87537888865 PP == domain 2 score: 41.6 bits; conditional E-value: 4.3e-14 HHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-E CS TruB_N 2 rllkakkvGhtGtLDplatGvLvvavgeaTklleylleadK 42 r +k k+Gh+GtLD +atGvLv+++g++Tkll+++l+ K tr|W4XNX2|W4XNX2_STRPU 175 RWIKLPKMGHGGTLDMNATGVLVIGCGRGTKLLSSYLQGGK 215 567888****************************9999887 PP >> tr|W4XFN0|W4XFN0_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 74.7 0.2 2.7e-24 1.5e-20 1 149 [] 103 219 .. 103 219 .. 0.93 Alignments for each domain: == domain 1 score: 74.7 bits; conditional E-value: 2.7e-24 HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHHHHHHHC-EE CS TruB_N 1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgaetdteDaegeileeekveklteekleevlkkftGe 87 k++l+++k Gh+GtLDp++tG+L+v++++aT+l+++ ++a KeY++ +rl+ + +++ kl ++++++tG+ tr|W4XFN0|W4XFN0_STRPU 103 KKILRVEKTGHSGTLDPKVTGCLIVCIERATRLVKSQQSAGKEYVCIVRLHDAIENQS-----------------KLAKAIETLTGA 172 899***********************************************98876655.................68999******* PP E---------------------------------EEEEEEEEEEEEEE..EEEEEEEESTTTTH CS TruB_N 88 ieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveep..evelevecskGtYi 149 + q+pp +SAvk r+ r tiye +l+e++++ + v+c++GtYi tr|W4XFN0|W4XFN0_STRPU 173 LFQRPPLISAVK-----------------RQLRVRTIYESKLIEYDPQrhLGIFWVSCEAGTYI 219 ************.................89999***********9886566799********8 PP >> tr|W4XLI0|W4XLI0_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 37.2 0.1 9.7e-13 5.5e-09 15 104 .. 105 195 .. 101 200 .. 0.89 Alignments for each domain: == domain 1 score: 37.2 bits; conditional E-value: 9.7e-13 --TT-EEEEEEEEGGGGGGHHHCTTS-..EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHHHHHHHC-EEE----------- CS TruB_N 15 LDplatGvLvvavgeaTklleyllead..KeYeatirlgaetdteDaegeileeekveklteekleevlkkftGeieqvppmySAvk 99 LD ++ Gv+v+av ++ kl++++++a+ ++Y++ r+g++tdt+D++g++ +++++e + ++ ++l+k+ +i q + SA+ tr|W4XLI0|W4XLI0_STRPU 105 LDTKSCGVMVLAVRDGKKLVSQYQTARlpRQYTIRGRFGVATDTHDSQGKVWQKTTYELTSYADTAQYLRKVIHDIGQEL-KSSAIA 190 9********************99977666***********************998899999999********99999985.568877 PP ----- CS TruB_N 100 vnGkr 104 + +r tr|W4XLI0|W4XLI0_STRPU 191 TQVRR 195 77666 PP >> tr|W4ZGE0|W4ZGE0_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 18.0 0.0 8e-07 0.0046 77 149 .] 2 59 .. 1 59 [. 0.89 Alignments for each domain: == domain 1 score: 18.0 bits; conditional E-value: 8e-07 HHHHHHHC-EEE---------------------------------EEEEEEEEEEEEEE..EEEEEEEESTTTTH CS TruB_N 77 leevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveep..evelevecskGtYi 149 l ++++++tG++ q+pp +SAvk r+ r tiye +l+e++++ + v+c++GtYi tr|W4ZGE0|W4ZGE0_STRPU 2 LANAIETLTGALFQRPPLISAVK-----------------RQLRVRTIYESKLIEYDPQrhLGIFWVSCEAGTYI 59 56789999999999999999999.................999*************9886566799********8 PP >> tr|W4ZF97|W4ZF97_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 9.9 1.3 0.00024 1.4 57 131 .. 126 199 .. 111 208 .. 0.79 2 ? 0.6 0.1 0.18 1e+03 105 131 .. 400 426 .. 396 435 .. 0.87 Alignments for each domain: == domain 1 score: 9.9 bits; conditional E-value: 0.00024 SBTTS-EEE-.--TT--HHHHHHHHHHC-EEE---------------------------------EEEEEEEEEE CS TruB_N 57 eDaegeileeekveklteekleevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelle 131 e++ e l+e++ +k++ e+ ++++++ +e eq + S +G ++ l+re +e+e++ r+ + ++l+ ++ tr|W4ZF97|W4ZF97_STRPU 126 ENTARELLDEHERTKMELEETMNAMSQVASEKEQL-SHASESYLEGIKALALVREQKELELQRRESEMHQLSSVN 199 44445556666688889999999999999998887.567888889*************************98775 PP == domain 2 score: 0.6 bits; conditional E-value: 0.18 -----------------EEEEEEEEEE CS TruB_N 105 lyelaregeeverkkrkvtiyelelle 131 + l+re +e+e++ r+ + ++l+ ++ tr|W4ZF97|W4ZF97_STRPU 400 ALALVREQKELELQRRESEMHQLSSVN 426 56799*****************98765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (149 nodes) Target sequences: 28594 (14266044 residues searched) Passed MSV filter: 863 (0.0301812); expected 571.9 (0.02) Passed bias filter: 556 (0.0194446); expected 571.9 (0.02) Passed Vit filter: 34 (0.00118906); expected 28.6 (0.001) Passed Fwd filter: 5 (0.000174862); expected 0.3 (1e-05) Initial search space (Z): 28594 [actual number of targets] Domain search space (domZ): 5 [number of targets reported over threshold] # CPU time: 0.20u 0.01s 00:00:00.21 Elapsed: 00:00:00.10 # Mc/sec: 21256.41 // [ok]