# 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/Danio_rerio.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-48 165.8 0.0 1.9e-48 165.1 0.0 1.3 1 tr|B3DHG0|B3DHG0_DANRE TruB pseudouridine (psi) synthase fam 7.8e-25 88.5 0.0 1.5e-24 87.6 0.0 1.4 1 tr|F6P6I4|F6P6I4_DANRE TruB pseudouridine (psi) synthase fam 8.9e-20 72.1 8.5 1.1e-18 68.6 0.1 4.0 2 tr|F1Q749|F1Q749_DANRE Dyskeratosis congenita 1, dyskerin OS Domain annotation for each sequence (and alignments): >> tr|B3DHG0|B3DHG0_DANRE TruB pseudouridine (psi) synthase family member 1 OS=Danio rerio OX=7955 GN=trub1 PE=1 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 165.1 0.0 2.2e-52 1.9e-48 5 149 .] 59 204 .. 55 204 .. 0.97 Alignments for each domain: == domain 1 score: 165.1 bits; conditional E-value: 2.2e-52 T-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHHHHHHHC-EEE--- CS TruB_N 5 kakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgaetdteDaegeileeekveklteekleevlkkftGeieqv 91 + k+Gh+GtLD +a+GvLvv++ge+Tk+l+ +l +K+Y+a +lg++tdt D +g+++ee++++++t+e++ee +k+ftGei+qv tr|B3DHG0|B3DHG0_DANRE 59 QPFKIGHGGTLDSNASGVLVVGIGEGTKMLTTMLAGSKKYTAFGELGKATDTLDVTGNVVEEKSYDHITKEAFEEKMKQFTGEIMQV 145 455***********************************************************99*********************** PP ----------------------------.--EEEEEEEEEEEEEEEEEEEEEESTTTTH CS TruB_N 92 ppmySAvkvnGkrlyelaregeeverkk.rkvtiyelelleveepevelevecskGtYi 149 pp ySA+k++Gkr+ l ++g+eve k+ r+vt+y+l+l ++++p ++++vec G+Y+ tr|B3DHG0|B3DHG0_DANRE 146 PPLYSALKKDGKRMSVLLKQGQEVEAKPaRPVTVYNLSLEDFSPPLFTIDVECGGGFYV 204 *************************8877*****************************7 PP >> tr|F6P6I4|F6P6I4_DANRE TruB pseudouridine (psi) synthase family member 2 OS=Danio rerio OX=7955 GN=trub2 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 87.6 0.0 1.7e-28 1.5e-24 6 147 .. 92 235 .. 88 237 .. 0.96 Alignments for each domain: == domain 1 score: 87.6 bits; conditional E-value: 1.7e-28 -S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-..EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHHHHHHHC-EEE-- CS TruB_N 6 akkvGhtGtLDplatGvLvvavgeaTklleyllead..KeYeatirlgaetdteDaegeileeekveklteekleevlkkftGeieq 90 vG ++ LD +++GvLv++vg++ +le+l +++ + Y+++ ++g++td+ ++g+++e+++++++t++kle+vl++++G+ ++ tr|F6P6I4|F6P6I4_DANRE 92 KVHVGVGHRLDAFSSGVLVLGVGKGNSVLENLCKSHvtRDYTIEGEFGKATDNFSHTGRVIEKTTYDHITHDKLERVLAMLQGSNQK 178 5579****************************977556*************************99********************** PP -------------------------------EEEEEEEEEEEEEEEEEEEEEESTTT CS TruB_N 91 vppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGt 147 yS v+ + +++yela +g k + ++ l+++++++p+++lev+c + t tr|F6P6I4|F6P6I4_DANRE 179 ALITYSQVELQTQEAYELAARGLLYPDGKSPPILTGLRCIKFNPPHFTLEVRCVNET 235 *****************************************************9988 PP >> tr|F1Q749|F1Q749_DANRE Dyskeratosis congenita 1, dyskerin OS=Danio rerio OX=7955 GN=dkc1 PE=1 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 68.6 0.1 1.2e-22 1.1e-18 1 149 [] 105 221 .. 105 221 .. 0.93 2 ? -4.0 4.4 2.9 2.5e+04 56 99 .. 449 491 .. 425 503 .. 0.45 Alignments for each domain: == domain 1 score: 68.6 bits; conditional E-value: 1.2e-22 HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHHHHHHHC-EE CS TruB_N 1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgaetdteDaegeileeekveklteekleevlkkftGe 87 kr+l+++k Gh+GtLDp++tG+L+v+v++aT+l+++ ++a KeY+ +rl+ + ++e ++l ++l+ +tG+ tr|F1Q749|F1Q749_DANRE 105 KRILRVEKTGHSGTLDPKVTGCLIVCVERATRLVKSQQSAGKEYVGIVRLHNALENE-----------------HQLARALECLTGA 174 89************************************************9887655.................468999******* PP E---------------------------------EEEEEEEEEEEEEE..EEEEEEEESTTTTH CS TruB_N 88 ieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveep..evelevecskGtYi 149 + q+pp ++Avk r+ r tiye +l+e++++ + v+c++GtYi tr|F1Q749|F1Q749_DANRE 175 LFQRPPLIAAVK-----------------RQLRVRTIYESKLIEYDPErrLGIFWVSCEAGTYI 221 ************.................899999999*999999988656789999*999998 PP == domain 2 score: -4.0 bits; conditional E-value: 2.9 TSBTTS-EEE-.--TT--HHHHHHHHHHC-EEE----------- CS TruB_N 56 teDaegeileeekveklteekleevlkkftGeieqvppmySAvk 99 + ++e + +++k ++ +++ ee++++ e e + SA k tr|F1Q749|F1Q749_DANRE 449 KTEEESKKEKKKKKKEKKQKLAEEAAAEAPAEEE-TEVTESAKK 491 2222222222222333333333333333333333.233334444 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (149 nodes) Target sequences: 25687 (13798380 residues searched) Passed MSV filter: 913 (0.0355433); expected 513.7 (0.02) Passed bias filter: 639 (0.0248764); expected 513.7 (0.02) Passed Vit filter: 38 (0.00147935); expected 25.7 (0.001) Passed Fwd filter: 3 (0.000116791); expected 0.3 (1e-05) Initial search space (Z): 25687 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.19u 0.01s 00:00:00.20 Elapsed: 00:00:00.09 # Mc/sec: 22843.98 // [ok]