# 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_1306.faa # target HMM database: Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 23726_FusoPortal_Gene_1306 [L=754] Description: # 1419795 # 1422056 # -1 # ID=1_1306;partial=00;start_type=TTG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.256 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-125 418.4 5.2 4.9e-125 417.7 5.2 1.3 1 Topoisom_bac DNA topoisomerase 4.5e-31 107.0 0.4 4.5e-31 107.0 0.4 2.3 2 Toprim Toprim domain 8.1e-11 41.4 11.2 1.3e-09 37.5 5.0 3.4 3 zf-C4_Topoisom Topoisomerase DNA binding C4 zinc finger 5.2e-07 29.5 0.2 0.058 13.3 0.0 3.6 3 Toprim_C_rpt Topoisomerase C-terminal repeat 0.0015 18.9 0.3 0.014 15.8 0.1 2.8 2 Toprim_4 Toprim domain ------ inclusion threshold ------ 0.034 13.8 1.4 1.8 8.1 0.0 3.0 3 O-FucT GDP-fucose protein O-fucosyltransferase 0.12 12.8 0.0 0.41 11.0 0.0 1.9 1 Toprim_2 Toprim-like 0.92 9.6 10.0 0.037 14.0 2.0 2.8 2 Trans_coact Phage late-transcription coactivator Domain annotation for each model (and alignments): >> Topoisom_bac DNA topoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 417.7 5.2 2.4e-128 4.9e-125 2 412 .. 133 545 .. 132 546 .. 0.93 Alignments for each domain: == domain 1 score: 417.7 bits; conditional E-value: 2.4e-128 Topoisom_bac 2 inenlvdaaeaRrelDwliGinlsrlltkklkgkkvlsaGRVqtptLaliveRereienFvpeeyweveatl.kkekkekekk 83 in + v++++aRr+lD+l+G+++s++l+k ++ + saGRVq+++L++i+e e++i++Fvpe+yw+v++ + +k + + k 23726_FusoPortal_Gene_1306 133 INIARVNSQQARRILDRLVGYEISPFLWKLIS--PNTSAGRVQSVALKIICELEDKIKAFVPEKYWDVKGIFdTKYSLNLYKI 213 78899***********************9666..99***********************************954444444499 PP Topoisom_bac 84 kkkkkerikdkeeaeaileklkkkeakvesvekkekkkppplpfdtttLqkeasrklglsakktlsiaqkLYe.......kag 159 +kk +++kd++ +++ ++lkkk ++v s + ++k+k+pplp++t+tLq+ as++lg+sa+kt+++aqkLYe ++g 23726_FusoPortal_Gene_1306 214 DNKKIDKLKDEKLLDRVKKDLKKK-YEVISSKVSKKTKNPPLPLKTSTLQQLASSYLGFSASKTMMVAQKLYEgisikgeHKG 295 99999****************876.*******************************************************56* PP Topoisom_bac 160 litYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPteelp.kl....kelsddek 237 litY+RTdstr+seea + ++++++k++gkeyl++a+ + kk+ + kn + +aHe IrPt +++ + + l++d+ 23726_FusoPortal_Gene_1306 296 LITYMRTDSTRISEEA-KEMARNYITKNFGKEYLGSATPKAKKE-S----KNVQ-DAHEGIRPT-DINyTPenimEFLDKDQF 370 ***************9.59****************888877643.2....4788.*********.77754324555666**** PP Topoisom_bac 238 klYelIvrrflaslmkdakyeettvkleveeeefkasgktilekGfkkvykeekkeeeeeelpelkegeevkvkeveleekkT 320 klY+lI++rfl s+++++kye+ ++ le ++ e++ + ++i+++G++kv+ke+++ + ++pe+keg+++++++++++e T 23726_FusoPortal_Gene_1306 371 KLYNLIWQRFLISQLAAMKYEQFEYILEKDKIEYRGTINKIIFDGYYKVFKEDEDLPI-GDFPEIKEGDKFTLDKLDIKEDYT 452 **************************************************98888776.49********************** PP Topoisom_bac 321 kppkryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalvellekf.kdlvspelTaeleekLdeIa 402 kpp+r+te+sL+k++e +giG+p+T+a+ii++l++r+Yve ++ks+vpte G ++ l+kf +++++ ++Ta+le++Lde+ 23726_FusoPortal_Gene_1306 453 KPPARLTESSLVKTLEAEGIGRPSTYASIIDTLKKREYVELQNKSFVPTEIGYEVKTQLDKFfPNIMNIKFTAKLEDELDEVD 535 *****************************************99****************7777******************** PP Topoisom_bac 403 egkadakevl 412 +g +++ ++l 23726_FusoPortal_Gene_1306 536 SGDKNWIDLL 545 ******9876 PP >> Toprim Toprim domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 107.0 0.4 2.2e-34 4.5e-31 2 103 .] 10 118 .. 9 118 .. 0.96 2 ? -3.2 0.1 4.4 9.2e+03 53 53 .. 227 227 .. 189 251 .. 0.49 Alignments for each domain: == domain 1 score: 107.0 bits; conditional E-value: 2.2e-34 EEEESSHHHHHHHHTTCCSTCEEEEEESSSSEEECS.........TTEEEEEEETTTHHHHHHHHHHHHHHSEEEEES-SSHH CS Toprim 2 lvivEgpsdaktiakalgsgfqavtaslGhildlet.........efkpvyeeiedkkkvlkalkelakradeiilatDpDre 75 lvivE+p++akti+k+lg + ++v++s Ghi+dl++ +fkp y+ i++k +v+k lke +k+ad+i+la DpDre 23726_FusoPortal_Gene_1306 10 LVIVESPAKAKTIEKILG-SSYKVISSYGHIIDLPKtkigvdvnnDFKPSYNTIKGKGEVIKQLKEASKKADKIYLASDPDRE 91 9*****************.**************************************************************** PP HHHHHHHHHHHHTCHHTTCEEECCCSSS CS Toprim 76 Geaiawellevlkellenkigrvefsei 103 Ge iaw++++ lk l+ n+ r+ef+ei 23726_FusoPortal_Gene_1306 92 GESIAWHIANTLK-LDHNEKNRIEFHEI 118 **********999.555566******98 PP == domain 2 score: -3.2 bits; conditional E-value: 4.4 H CS Toprim 53 l 53 l 23726_FusoPortal_Gene_1306 227 L 227 1 PP >> zf-C4_Topoisom Topoisomerase DNA binding C4 zinc finger # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 1.8 0.1 0.095 2e+02 8 23 .. 580 595 .. 579 595 .. 0.90 2 ? 3.8 0.0 0.023 48 8 22 .. 647 661 .. 646 669 .. 0.87 3 ! 37.5 5.0 6.4e-13 1.3e-09 2 39 .] 716 753 .. 715 753 .. 0.96 Alignments for each domain: == domain 1 score: 1.8 bits; conditional E-value: 0.095 --EEEEEE-SSSEEEE CS zf-C4_Topoisom 8 ggdLvlkrgkkGkFvG 23 g++++ k g++G++++ 23726_FusoPortal_Gene_1306 580 GKPMIMKIGRFGRYLA 595 689**********986 PP == domain 2 score: 3.8 bits; conditional E-value: 0.023 --EEEEEE-SSSEEE CS zf-C4_Topoisom 8 ggdLvlkrgkkGkFv 22 g+ L+lk+g++G ++ 23726_FusoPortal_Gene_1306 647 GSRLLLKYGRFGAYL 661 689*********997 PP == domain 3 score: 37.5 bits; conditional E-value: 6.4e-13 EE-SSS--EEEEEE-SSSEEEEESST.T----EEB-GG CS zf-C4_Topoisom 2 ekCPkCggdLvlkrgkkGkFvGCsnYPeCkftkklkkn 39 +kC+kCg + + +g+ GkF++C+ YPeCk++kk++k+ 23726_FusoPortal_Gene_1306 716 GKCEKCGRPFKISNGRWGKFLACTGYPECKNIKKIEKK 753 79********************************9985 PP >> Toprim_C_rpt Topoisomerase C-terminal repeat # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 13.3 0.0 2.8e-05 0.058 4 31 .. 579 610 .. 578 618 .. 0.80 2 ! 7.6 0.0 0.0017 3.6 5 31 .. 647 678 .. 645 694 .. 0.68 3 ? 4.1 0.0 0.02 42 5 23 .. 722 740 .. 720 752 .. 0.74 Alignments for each domain: == domain 1 score: 13.3 bits; conditional E-value: 2.8e-05 Toprim_C_rpt 4 tgepikvkeGRfGPYvkh....gkknasLpkg 31 +g+p+ k+GRfG Y+ k n sL+ 23726_FusoPortal_Gene_1306 579 NGKPMIMKIGRFGRYLASqdteSKENISLKGI 610 79***************766666699999755 PP == domain 2 score: 7.6 bits; conditional E-value: 0.0017 Toprim_C_rpt 5 gepikvkeGRfGPYvkh...gk..knasLpkg 31 g +k GRfG Y+ ++ + ++pk+ 23726_FusoPortal_Gene_1306 647 GSRLLLKYGRFGAYLESenyKEdnIRKTIPKE 678 66667899*******96433224455666665 PP == domain 3 score: 4.1 bits; conditional E-value: 0.02 Toprim_C_rpt 5 gepikvkeGRfGPYvkhgk 23 g+p k+ +GR+G ++ +++ 23726_FusoPortal_Gene_1306 722 GRPFKISNGRWGKFLACTG 740 78889*******9998754 PP >> Toprim_4 Toprim domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 15.8 0.1 6.7e-06 0.014 45 83 .. 70 109 .. 8 115 .. 0.74 2 ? -2.8 0.0 4.3 8.9e+03 7 45 .. 193 224 .. 189 241 .. 0.46 Alignments for each domain: == domain 1 score: 15.8 bits; conditional E-value: 6.7e-06 Toprim_4 45 enlveaekkvkevilaldgDaeGeataerlaelll.eegv 83 ++l+ea kk+++++la d+D eGe a ++a++l+ ++++ 23726_FusoPortal_Gene_1306 70 KQLKEASKKADKIYLASDPDREGESIAWHIANTLKlDHNE 109 445559999***********************55445544 PP == domain 2 score: -2.8 bits; conditional E-value: 4.3 Toprim_4 7 EgyaDvlaleka.giknavavlggalspldgirpeklkse 45 E y Dv + ++ n++ ++ ++ klk e 23726_FusoPortal_Gene_1306 193 EKYWDVKGIFDTkYSLNLYKIDNKKID--------KLKDE 224 555555555555333455555544442........33332 PP >> O-FucT GDP-fucose protein O-fucosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 8.1 0.0 0.00087 1.8 232 272 .. 64 101 .. 50 158 .. 0.72 2 ? 3.2 0.0 0.027 57 243 301 .. 491 545 .. 461 551 .. 0.78 3 ? -1.8 0.1 0.89 1.9e+03 77 129 .. 673 721 .. 600 731 .. 0.72 Alignments for each domain: == domain 1 score: 8.1 bits; conditional E-value: 0.00087 O-FucT 232 slegialqakgllkeltsvyvAtdeiyggeelkeLkkefpn 272 + ++++q+k+++k++ ++y+A+d +++ge + ++ n 23726_FusoPortal_Gene_1306 64 GKGEVIKQLKEASKKADKIYLASDPDREGE---SIAWHIAN 101 56789*******************777665...33333333 PP == domain 2 score: 3.2 bits; conditional E-value: 0.027 O-FucT 243 llkeltsvyvAtdeiyggeelkeLkkefpnlvkvtketlaskeeleklkdgssaaiDqi 301 + ++ +v t y+ +L k fpn++++ k+t + ++el++++ g+ + iD++ 23726_FusoPortal_Gene_1306 491 VEL-QNKSFVPTEIGYE--VKTQLDKFFPNIMNI-KFTAKLEDELDEVDSGDKNWIDLL 545 333.4788888886675..4799*******8888.99999*************999985 PP == domain 3 score: -1.8 bits; conditional E-value: 0.89 O-FucT 77 kelppelksaekrksvckeakpsyyleeilpllkkkkviqlakfqklrCrskq 129 k++p+e+k + +k++ k+ ++ yl++i+++++k+++ l+k +C k 23726_FusoPortal_Gene_1306 673 KTIPKEIKTK-IEKNTIKKENDILYLKDIFDKIEKEEAEILKKA--GKCE-KC 721 3566555554.335556777777888888888887777444443..4555.44 PP >> Toprim_2 Toprim-like # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.0 0.0 0.0002 0.41 32 71 .. 68 106 .. 35 126 .. 0.72 Alignments for each domain: == domain 1 score: 11.0 bits; conditional E-value: 0.0002 Toprim_2 32 teaalkllerypekkvvlalDnDkaGrkaakrlaellrea 71 ++lk+ +++ ++k++la D D+ G+ a +a+ l+ + 23726_FusoPortal_Gene_1306 68 VIKQLKEASKK-ADKIYLASDPDREGESIAWHIANTLKLD 106 33444444444.467*****************99999733 PP >> Trans_coact Phage late-transcription coactivator # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -2.8 1.2 3.2 6.8e+03 31 52 .. 212 233 .. 208 249 .. 0.75 2 ? 14.0 2.0 1.8e-05 0.037 26 56 .. 660 690 .. 658 694 .. 0.93 Alignments for each domain: == domain 1 score: -2.8 bits; conditional E-value: 3.2 Trans_coact 31 dieeeqvpklIskpLkeKikaE 52 i+ +++ kl ++L ++ k++ 23726_FusoPortal_Gene_1306 212 KIDNKKIDKLKDEKLLDRVKKD 233 6777777777777777777765 PP == domain 2 score: 14.0 bits; conditional E-value: 1.8e-05 Trans_coact 26 wceendieeeqvpklIskpLkeKikaEAiel 56 ++e +++ e++++k+I+k +k Ki++++i++ 23726_FusoPortal_Gene_1306 660 YLESENYKEDNIRKTIPKEIKTKIEKNTIKK 690 99*************************9985 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (754 residues searched) Target model(s): 16712 (2907032 nodes) Passed MSV filter: 1187 (0.0710268); expected 334.2 (0.02) Passed bias filter: 467 (0.027944); expected 334.2 (0.02) Passed Vit filter: 54 (0.00323121); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.41 # Mc/sec: 5346.10 // [ok]