# hmmscan :: search sequence(s) against a profile 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 sequence file: AA/23726_FusoPortal_Gene_341.faa # target HMM database: Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 23726_FusoPortal_Gene_341 [L=1185] Description: # 374145 # 377699 # -1 # ID=1_341;partial=00;start_type=GTG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.320 Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-162 539.2 0.1 9.3e-161 535.1 0.1 2.6 3 RNA_pol_Rpb2_6 RNA polymerase Rpb2, domain 6 1.4e-30 105.1 0.0 2.7e-30 104.2 0.0 1.5 1 RNA_pol_Rpb2_3 RNA polymerase Rpb2, domain 3 3e-25 88.3 0.1 1e-24 86.6 0.1 2.0 2 RNA_pol_Rpb2_7 RNA polymerase Rpb2, domain 7 1.2e-23 83.7 3.1 5.7e-17 61.9 0.3 2.8 3 RNA_pol_Rpb2_2 RNA polymerase Rpb2, domain 2 3.9e-23 81.9 0.0 4.2e-22 78.6 0.0 2.1 1 RNA_pol_Rpb2_1 RNA polymerase beta subunit 1.3e-19 70.1 5.7 2.7e-19 69.1 0.5 3.0 2 RNA_pol_Rpb2_45 RNA polymerase beta subunit external 1 domai ------ inclusion threshold ------ 0.096 12.6 0.0 0.29 11.1 0.0 1.7 1 PepSY_2 Peptidase propeptide and YPEB domain 0.1 12.4 1.1 0.27 11.1 0.6 1.9 2 DUF3052 Protein of unknown function (DUF3052) Domain annotation for each model (and alignments): >> RNA_pol_Rpb2_6 RNA polymerase Rpb2, domain 6 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -2.2 0.0 0.71 1.5e+03 316 380 .. 236 302 .. 189 306 .. 0.69 2 ? 0.4 0.0 0.12 2.5e+02 2 28 .. 623 649 .. 622 657 .. 0.88 3 ! 535.1 0.1 4.5e-164 9.3e-161 2 390 .] 676 1063 .. 675 1063 .. 0.98 Alignments for each domain: == domain 1 score: -2.2 bits; conditional E-value: 0.71 ..S.HHHHHHHHHTTS-TT-EE-EEETTTS-B-.SS-EEB-EEEEEEBS--CCCS----SS--B-TT CS RNA_pol_Rpb2_6 316 ake.eeikelLeeagleasGkevlydGrtGekl.eaeifvGviYylkLkhlvedKihaRstGpysll 380 +ke ee+ + L+++ + ke + d tGe + eae f+ + kL dKi Gp s+l 23726_FusoPortal_Gene_341 236 SKEpEELLNVLKQELDGSIVKEDILDEETGEFIaEAEAFINEEVINKLIENKVDKISYWYVGPESKL 302 2335777778888777778999999999999874578999999999999999999999999998876 PP == domain 2 score: 0.4 bits; conditional E-value: 0.12 HHT-SS-TTB-HHHHHHHHHHGGGB-S CS RNA_pol_Rpb2_6 2 aklapvvehvqspriiiqaamekqalg 28 a l+p+ eh +++r ++ ++m++qa+ 23726_FusoPortal_Gene_341 623 AGLIPFLEHDDANRALMGSNMQRQAVP 649 7899*******************9965 PP == domain 3 score: 535.1 bits; conditional E-value: 4.5e-164 HHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS.........GGGS-SEEEEE CS RNA_pol_Rpb2_6 2 aklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvl.dgaatekgelalGqnal 82 +k+++ v++v+ ++iii+ +++k++ iy+l +++rsnq++ c++q+Plv gdkv+ g+++ dg+at+ g+l+lG+n+l 23726_FusoPortal_Gene_341 676 TKVSGKVTYVDGKKIIIEDKDKKEH--IYRLLNYERSNQSM---CLHQTPLVDLGDKVKTGDIIaDGPATKLGDLSLGRNIL 752 578999*************777766..**************...************************************** PP BBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS---.-S--..--SS-GGGS-TTSB--SS-EEETT-EE CS RNA_pol_Rpb2_6 83 VAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklgeeeitrdipnvseealkkLdedGivrvgaevkegdil 164 +++m++eGYn+EDai++++rl ++dvftsihi+eye++ar+tklg+eeitr+ipnvse+al++Lde+G++ +g+ev +gdil 23726_FusoPortal_Gene_341 753 MGFMPWEGYNYEDAILISDRLRKDDVFTSIHIEEYEIDARTTKLGDEEITREIPNVSENALRNLDENGVIMIGSEVGPGDIL 834 ********************************************************************************** PP E---...B-----...-----------..-B---EE--TT-EEEEEEEEE.......EE-TT--EEEEEEEEEEE---TT-B CS RNA_pol_Rpb2_6 165 vgkvt.kgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgdelkagvnklvkvyvaqkRklqvGDK 245 vgk++ kgete +eekllraifgekar+v+dtsl++++g++gvV+++ +sre+gdelkagvnk ++v va+kRk++vGDK 23726_FusoPortal_Gene_341 835 VGKTApKGETEPPAEEKLLRAIFGEKARDVRDTSLTMPHGSKGVVVDILELSRENGDELKAGVNKSIRVLVAEKRKITVGDK 916 ********************************************************************************** PP EEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHHHHHCCCS..SSS--B--TT-...SHHHHHHH CS RNA_pol_Rpb2_6 246 fasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtllgkaaal..egkkvdatvFdgakeeeikelL 325 +++rhG+KGvvs++lp eDmPfledG+ +D+vlNPlgvPSRm+igq+lE++lg+a ++ g+ ++++vFdga+ee++k++L 23726_FusoPortal_Gene_341 917 MSGRHGNKGVVSRVLPAEDMPFLEDGTHLDVVLNPLGVPSRMNIGQVLEVHLGMAMRTlnGGTCIATPVFDGATEEQVKDYL 998 *******************************************************99744689******************* PP HHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS----SS--B-TTT--B-SCGGG CS RNA_pol_Rpb2_6 326 eeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKihaRstGpyslltqQPlgGkaq 390 e++g+ ++Gk +lydGrtGek++++++vG++Y+lkL+hlvedK+haR++Gpysl+tqQPlgGkaq 23726_FusoPortal_Gene_341 999 EKQGYPRTGKVTLYDGRTGEKFDNKVTVGIMYMLKLHHLVEDKMHARAIGPYSLVTQQPLGGKAQ 1063 ***************************************************************97 PP >> RNA_pol_Rpb2_3 RNA polymerase Rpb2, domain 3 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 104.2 0.0 1.3e-33 2.7e-30 1 68 [] 471 539 .. 471 539 .. 0.99 Alignments for each domain: == domain 1 score: 104.2 bits; conditional E-value: 1.3e-33 RNA_pol_Rpb2_3 1 qvldrlnplselshlrrvssl.rgglskerkttevRklhpshwGriCpveTPEGencGlvksLaltarv 68 q++d+ npl+el+h+rr+s+l +ggls+er+++evR++h sh+GriCp+eTPEG+n+Gl+ sLa++a++ 23726_FusoPortal_Gene_341 471 QFMDQSNPLAELTHKRRISALgPGGLSRERAGFEVRDVHDSHYGRICPIETPEGPNIGLIGSLATYAKI 539 89*****************************************************************98 PP >> RNA_pol_Rpb2_7 RNA polymerase Rpb2, domain 7 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.4 0.0 6.1 1.3e+04 25 47 .. 180 202 .. 178 223 .. 0.74 2 ! 86.6 0.1 5e-28 1e-24 1 85 [. 1065 1139 .. 1065 1141 .. 0.97 Alignments for each domain: == domain 1 score: -3.4 bits; conditional E-value: 6.1 HHTTTTTEEEEEEESSSSSCCCE CS RNA_pol_Rpb2_7 25 rltikSDavevdvcgrckllaaa 47 t+k D ++v++ ++ k+la++ 23726_FusoPortal_Gene_341 180 FETDKNDFLSVKIDRKKKVLATV 202 55788899999999999988874 PP == domain 2 score: 86.6 bits; conditional E-value: 5e-28 BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEEEBTTTTCSSSEEEEEEEHHHHHHHHHHHHTTBEE CS RNA_pol_Rpb2_7 1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaaneCkivkseekiekveipeafklLlqeLqslgial 82 GG+r+GEME++al+ayGa+++L+e+lt+kSD d++gr+k+++a i+k+e+ +e+ +pe+fk+Ll+e+q+l++++ 23726_FusoPortal_Gene_341 1065 GGQRLGEMEVWALEAYGASNILQEMLTVKSD----DITGRTKTYEA-----IIKGEAMPESD-LPESFKVLLKEFQALALDI 1136 9******************************....***********.....******99988.******************9 PP EEE CS RNA_pol_Rpb2_7 83 kll 85 +l 23726_FusoPortal_Gene_341 1137 ELC 1139 986 PP >> RNA_pol_Rpb2_2 RNA polymerase Rpb2, domain 2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -2.7 0.0 1.7 3.6e+03 79 120 .. 93 134 .. 87 141 .. 0.69 2 ! 21.4 0.1 6.9e-08 0.00015 1 105 [. 147 245 .. 147 292 .. 0.78 3 ! 61.9 0.3 2.7e-20 5.7e-17 89 190 .] 305 412 .. 288 412 .. 0.89 Alignments for each domain: == domain 1 score: -2.7 bits; conditional E-value: 1.7 THHHHHHHHHHHHHHCSS-SSHHHHHHHHHCSSTTSSSCHHH CS RNA_pol_Rpb2_2 79 dsqlleelleeleekeeiqtqeealdyigkvvalrrgeearl 120 +++ +++ +l +k+ + +e l y+g+v+++ + + 23726_FusoPortal_Gene_341 93 TYSNSLKVRLRLINKKMGNEIQESLVYFGEVPKMTDRATFII 134 556666777788888888888888888888777766655555 PP == domain 2 score: 21.4 bits; conditional E-value: 6.9e-08 -SSEEEEEE-STSSSESSSCCEECCEEEEEECCCCSTSEEEEEECTTSSSEEEHHHHHHHTT--STT.HHHHHHTSSSTTHHHH CS RNA_pol_Rpb2_2 1 rsngiyvekekdknkisatvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdr.eIlericydsedsqll 83 rs+g+ + ke + + + ++ +i ++g +l++e+d+++++ + i++k+k+ + ++lkA+ + +d+ eI + ++ 23726_FusoPortal_Gene_341 147 RSPGVSFSKEVNTQTGKDLFSGKIIPYKGTWLEFETDKNDFLSVKIDRKKKVLATVFLKAVDFFKDNnEIRD-------YFLEV 223 78999999998888778999******************************************9998524444.......34555 PP HHHHHHHHHHCSS-SSHHHHHH CS RNA_pol_Rpb2_2 84 eelleeleekeeiqtqeealdy 105 +el+ ++ k++ + ee l+ 23726_FusoPortal_Gene_341 224 KELKLKALYKKYSKEPEELLNV 245 5555555555555555555555 PP == domain 3 score: 61.9 bits; conditional E-value: 2.7e-20 HHHHHCSS-SSHHHHHHHHHCSSTTSSSCHHHCHHHHHHH......HHHHHHHHTTTCSSTSTTTSSSTCHH...HHHHHHHHH CS RNA_pol_Rpb2_2 89 eleekeeiqtqeealdyigkvvalrrgeearlqsareilq......krydlgeigreklnkhlglseslenkr.lkaqdilymi 165 ++ + t++ea ++ k +lr+g+++++ sar +++ +rydl+ +gr+k+nk+l+l+ + e ++ l+ +d+l i 23726_FusoPortal_Gene_341 305 NTLMNDTTLTEDEAVVEVFK--KLRPGDQVTVDSARSLIRqmffnpQRYDLEPVGRYKMNKRLKLDVP-EEQIsLTKEDVLGTI 385 55666677899999999999..9*********************************************.55666********** PP HHHHHHHTTSS-S..--TTSGGGEEEE CS RNA_pol_Rpb2_2 166 drLlslklgrrev..DDiDhlgnkRvr 190 +++++l g+ +v DDiD l n+R+r 23726_FusoPortal_Gene_341 386 KYVIELNNGEQNVhtDDIDNLSNRRIR 412 *******99865333**********97 PP >> RNA_pol_Rpb2_1 RNA polymerase beta subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 78.6 0.0 2e-25 4.2e-22 3 202 .. 23 457 .. 21 458 .. 0.96 Alignments for each domain: == domain 1 score: 78.6 bits; conditional E-value: 2e-25 THHHHHHHHHHHHCHHHHHCCHSCCCHHHSSSHCSCCC....EEEEEEEEEECS...CCCEHTTSCEEE..HHHHHHTTSBXEE CS xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx RF RNA_pol_Rpb2_1 3 vsqqldSFnkfveqdlekiikeeaaieseeeiqssgee....lelkfvsirlgk...PvvdesdasereiyPkearlrnltYsa 79 ++ ql+S+++f+++++ +ee+ +e+++++ +++e+ + l++ + l + P de e++ r+ tYs 23726_FusoPortal_Gene_341 23 LEFQLNSYEDFLQTNMSPNKREEKGFELAFKEIFPIESsngdVRLEYIGYELHEaeaPLNDE----------LECKKRGKTYSN 96 578*************************9998877776666688888888887611144444..........7*********** PP EEEEEEEEEECCCCTTTEEEEEEEEEEEEEXBTTSTTSSSTTS.HHHHHHTTS.TT...SSEEETTEEEEEXEEEE........ CS xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF RNA_pol_Rpb2_1 80 plyvklklvvyekdnkeeikeeevyiGelPlMlrskacvlseaseeelvelkEcpldqGGyFiinGtekvivaqek........ 155 l v+l+l+ k+ ++ei+e+ vy Ge+P M++ +FiinG+e+v+v+q++ 23726_FusoPortal_Gene_341 97 SLKVRLRLIN--KKMGNEIQESLVYFGEVPKMTDR------------------------ATFIINGAERVVVSQLHrspgvsfs 154 ********99..68999******************........................8************************ PP .................................................................................... CS .................................................................................... RF RNA_pol_Rpb2_1 156 .................................................................................... 155 23726_FusoPortal_Gene_341 155 kevntqtgkdlfsgkiipykgtwlefetdkndflsvkidrkkkvlatvflkavdffkdnneirdyflevkelklkalykkyske 238 ************************************************************************************ PP .................................................................................... CS .................................................................................... RF RNA_pol_Rpb2_1 156 .................................................................................... 155 23726_FusoPortal_Gene_341 239 peellnvlkqeldgsivkedildeetgefiaeaeafineevinklienkvdkisywyvgpesklvantlmndttltedeavvev 322 ************************************************************************************ PP .................................................................................... CS .................................................................................... RF RNA_pol_Rpb2_1 156 .................................................................................... 155 23726_FusoPortal_Gene_341 323 fkklrpgdqvtvdsarslirqmffnpqrydlepvgrykmnkrlkldvpeeqisltkedvlgtikyvielnngeqnvhtddidnl 406 ************************************************************************************ PP ......XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSSSHHHHSCSHHHH CS ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF RNA_pol_Rpb2_1 156 ......laGeLlaslfrvllkklerdvkerlqksleklddlmlqllvnakpit 202 +GeLl ++ +++l+k+++ v+e++ + ++ +++++q l+n++p++ 23726_FusoPortal_Gene_341 407 snrrirGVGELLLMQIKTGLAKMNKMVREKM--TTQDIETVTPQSLLNTRPLN 457 *******************************..99*************99875 PP >> RNA_pol_Rpb2_45 RNA polymerase beta subunit external 1 domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 2.0 0.5 0.11 2.3e+02 18 43 .. 261 288 .. 260 290 .. 0.83 2 ! 69.1 0.5 1.3e-22 2.7e-19 1 65 [] 549 614 .. 549 614 .. 0.93 Alignments for each domain: == domain 1 score: 2.0 bits; conditional E-value: 0.11 HHHTTSEEE-TTS-BESS..SSBSSSSE CS RNA_pol_Rpb2_45 18 deEekyviAqAnapldee..grfveerV 43 deE + iA+A+a ++ee ++++e++V 23726_FusoPortal_Gene_341 261 DEETGEFIAEAEAFINEEviNKLIENKV 288 89*************9985556666666 PP == domain 2 score: 69.1 bits; conditional E-value: 1.3e-22 EEEEE.TEE.EEEEEEEEHHHHTTSEEE-TTS-BESSSSBSSSSEEEEETTBEEEEETTT--EEESS CS RNA_pol_Rpb2_45 1 YrkVe.gkv.tdevvYLtAdeEekyviAqAnapldeegrfveerVlaRrkgevelvepeeVdymDVS 65 Y kVe g+ d+v+YL AdeE++ iAqA+++ld+++++ V++R+++e++++epe+V+ymDVS 23726_FusoPortal_Gene_341 549 YVKVEnGVAlVDDVRYLAADEEDGLFIAQADTKLDKNNKLQ-GLVVCRYGHEIVEIEPERVNYMDVS 614 88999875557************************999876.79**********************9 PP >> PepSY_2 Peptidase propeptide and YPEB domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.1 0.0 0.00014 0.29 17 56 .. 976 1016 .. 966 1019 .. 0.83 Alignments for each domain: == domain 1 score: 11.1 bits; conditional E-value: 0.00014 PepSY_2 17 AgrrdtdspkadwlpreklvakleaqGy.kvkkievddggc 56 g ++ +p+ d ++e++++ le+qGy + k+ + dg+ 23726_FusoPortal_Gene_341 976 NGGTCIATPVFDGATEEQVKDYLEKQGYpRTGKVTLYDGRT 1016 3789999*********************9999999988865 PP >> DUF3052 Protein of unknown function (DUF3052) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.1 0.6 0.00013 0.27 9 82 .. 252 325 .. 248 338 .. 0.84 2 ? -2.7 0.0 2.3 4.9e+03 65 79 .. 810 824 .. 797 828 .. 0.73 Alignments for each domain: == domain 1 score: 11.1 bits; conditional E-value: 0.00013 DUF3052 9 gqvvqelgwDdDvdedlreaiedligeelvdedadevvDvvllWwrddDgdLv.dalvdaltsLadegviwlltp 82 g++v+e D+++ e + ++ e +i+ee++++ +++vD + W+ + Lv ++l++ +t +de+v+ ++ + 23726_FusoPortal_Gene_341 252 GSIVKEDILDEETGEFI-AEAEAFINEEVINKLIENKVDKISYWYVGPESKLVaNTLMNDTTLTEDEAVVEVFKK 325 88999999999887665.567*************************99999886999999999999999988754 PP == domain 2 score: -2.7 bits; conditional E-value: 2.3 DUF3052 65 vdaltsLadegviwl 79 +al++L+++gvi++ 23726_FusoPortal_Gene_341 810 ENALRNLDENGVIMI 824 467888999998876 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (1185 residues searched) Target model(s): 16712 (2907032 nodes) Passed MSV filter: 486 (0.0290809); expected 334.2 (0.02) Passed bias filter: 359 (0.0214816); expected 334.2 (0.02) Passed Vit filter: 35 (0.0020943); expected 16.7 (0.001) Passed Fwd filter: 8 (0.000478698); expected 0.2 (1e-05) Initial search space (Z): 16712 [actual number of targets] Domain search space (domZ): 8 [number of targets reported over threshold] # CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.33 # Mc/sec: 10438.89 // [ok]