# 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_1040.faa # target HMM database: Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 23726_FusoPortal_Gene_1040 [L=419] Description: # 1150084 # 1151340 # 1 # ID=1_1040;partial=00;start_type=GTG;rbs_motif=AGGAGG;rbs_spacer=5-10bp;gc_cont=0.304 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-23 81.6 1.4 3.1e-23 81.6 1.4 3.1 3 Sigma70_r3 Sigma-70 region 3 1.1e-21 76.2 0.0 2.3e-21 75.2 0.0 1.5 1 Sigma70_r2 Sigma-70 region 2 2.9e-18 65.0 4.1 4.6e-18 64.4 0.7 2.8 3 Sigma70_r4 Sigma-70, region 4 2.9e-15 55.9 1.4 2.9e-15 55.9 1.4 2.9 3 Sigma70_r1_2 Sigma-70 factor, region 1.2 1.7e-08 34.3 14.2 1.7e-08 34.3 14.2 3.3 3 Sigma70_r1_1 Sigma-70 factor, region 1.1 ------ inclusion threshold ------ 0.18 12.1 1.7 37 4.8 0.0 3.3 3 B12-binding_2 B12 binding domain 1.8 8.3 3.6 6.4 6.5 0.3 2.9 3 FrhB_FdhB_C Coenzyme F420 hydrogenase/dehydrogenase, beta Domain annotation for each model (and alignments): >> Sigma70_r3 Sigma-70 region 3 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.4 5.0 4.2 9.9e+03 57 73 .. 79 94 .. 58 108 .. 0.78 2 ! 81.6 1.4 1.3e-26 3.1e-23 1 76 [. 263 338 .. 263 340 .. 0.97 3 ? -1.8 0.0 1.3 3.2e+03 22 40 .. 377 395 .. 376 399 .. 0.84 Alignments for each domain: == domain 1 score: -3.4 bits; conditional E-value: 4.2 STTXBSTTTXBXSSSXX CS Sigma70_r3 57 eedtelgdlleddeaes 73 +++ e+ dlledd e+ 23726_FusoPortal_Gene_1040 79 TDNEEHDDLLEDD-SED 94 5677788888888.444 PP == domain 2 score: 81.6 bits; conditional E-value: 1.3e-26 XHHHHHHHHHHHHHHHHSSXXXHHHHHHHHTXXHHHHHHHHHHHXXXEETTXBSSSSTTXBSTTTXBXSSSXXHHH CS Sigma70_r3 1 EklnkikraqreLeqelgrePtpeEiAeeLglseekVrevleaarepvSldlpvgeeedtelgdlleddeaespee 76 E++nkik+ +r qe+g++++pe +Ae+Lg++++k++ + e+++ep+Sl++pvg+eed+elgd++ed++ +sp e 23726_FusoPortal_Gene_1040 263 ETINKIKKESRIYLQETGKDASPEILAERLGMEVDKIKAIQEMNQEPISLETPVGSEEDSELGDFVEDQKTTSPYE 338 89*******************************************************************9999976 PP == domain 3 score: -1.8 bits; conditional E-value: 1.3 XHHHHHHHHTXXHHHHHHH CS Sigma70_r3 22 tpeEiAeeLglseekVrev 40 t eE+ + +++ e++r++ 23726_FusoPortal_Gene_1040 377 TLEEVGKIFNVTRERIRQI 395 5689999999999999886 PP >> Sigma70_r2 Sigma-70 region 2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 75.2 0.0 9.6e-25 2.3e-21 1 70 [. 184 253 .. 184 254 .. 0.98 Alignments for each domain: == domain 1 score: 75.2 bits; conditional E-value: 9.6e-25 HHHHHHHHHHHHHHHCT-THHHHHHHHHHHHHHHHHHGGGTSTTTCHHHHHHHHHHHHHHHHHHHHTSST CS Sigma70_r2 1 lverylplvkrlarrllgsgadaeDlvQeaflrlwraverfdpergvsfsawllriarnaaidrlRkrrr 70 l+e++l+lv+++a++ +++g+ Dl+Qe++++l++ave+f+ ++g++fs+++++++r+a+ +++ +++r 23726_FusoPortal_Gene_1040 184 LIESNLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGR 253 79****************************************************************9998 PP >> Sigma70_r4 Sigma-70, region 4 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 0.4 0.1 0.19 4.5e+02 8 40 .. 9 44 .. 7 51 .. 0.62 2 ? -3.5 0.0 3.1 7.5e+03 24 38 .. 286 300 .. 279 303 .. 0.68 3 ! 64.4 0.7 1.9e-21 4.6e-18 1 50 [] 352 405 .. 352 405 .. 0.98 Alignments for each domain: == domain 1 score: 0.4 bits; conditional E-value: 0.19 HHHHHHHHHH.TTT--HHHHHHHHT..S-HHHHHHH CS Sigma70_r4 8 rerevlelrf.geelTleEIgerlg..iSrerVrqi 40 + r ++ + T+eEI e+lg + e + q+ 23726_FusoPortal_Gene_1040 9 KARALIKKAVeEGIITYEEINEELGddFPAENIEQL 44 556666666644446999999999744555555555 PP == domain 2 score: -3.5 bits; conditional E-value: 3.1 HHHHHHHTS-HHHHH CS Sigma70_r4 24 eEIgerlgiSrerVr 38 e ++erlg+ ++ 23726_FusoPortal_Gene_1040 286 EILAERLGMEVDKIK 300 557899997665555 PP == domain 3 score: 64.4 bits; conditional E-value: 1.9e-21 HHHHS-HHHHHHHHHHH....TTT--HHHHHHHHTS-HHHHHHHHHHHHHHHHH CS Sigma70_r4 1 aLasLpererevlelrf....geelTleEIgerlgiSrerVrqiekrAlrkLRk 50 +L++L++re +vl++r+ + TleE+g++++++rer+rqie +AlrkLR+ 23726_FusoPortal_Gene_1040 352 VLKTLSPREEKVLRYRYglddSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRH 405 599*****************999******************************7 PP >> Sigma70_r1_2 Sigma-70 factor, region 1.2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 55.9 1.4 1.2e-18 2.9e-15 2 34 .] 147 179 .. 146 179 .. 0.97 2 ? 0.9 0.1 0.19 4.5e+02 4 12 .. 273 281 .. 273 281 .. 0.91 3 ? -3.0 0.0 3.2 7.6e+03 16 24 .. 356 364 .. 355 364 .. 0.85 Alignments for each domain: == domain 1 score: 55.9 bits; conditional E-value: 1.2e-18 HHHHHHHHHHHS---THHHHHHHHHHHHHHHHH CS Sigma70_r1_2 2 pvrlYLrEIGriPLLtaeEEveLAkrieaGdea 34 p+++YLrEIG++PLLt+eEE+++Ak++ +Gde+ 23726_FusoPortal_Gene_1040 147 PIKMYLREIGQVPLLTHEEEIDYAKKAYEGDEE 179 9******************************96 PP == domain 2 score: 0.9 bits; conditional E-value: 0.19 HHHHHHHHH CS Sigma70_r1_2 4 rlYLrEIGr 12 r+YL+E G+ 23726_FusoPortal_Gene_1040 273 RIYLQETGK 281 89****997 PP == domain 3 score: -3.0 bits; conditional E-value: 3.2 -THHHHHHH CS Sigma70_r1_2 16 LtaeEEveL 24 L++ EE+ L 23726_FusoPortal_Gene_1040 356 LSPREEKVL 364 99****866 PP >> Sigma70_r1_1 Sigma-70 factor, region 1.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 34.3 14.2 7.1e-12 1.7e-08 5 76 .. 8 80 .. 5 86 .. 0.73 2 ? -5.5 11.1 7 1.7e+04 57 81 .. 81 105 .. 78 116 .. 0.54 3 ? -0.7 1.1 0.59 1.4e+03 23 42 .. 104 125 .. 102 129 .. 0.77 Alignments for each domain: == domain 1 score: 34.3 bits; conditional E-value: 7.1e-12 HHHHHHHHHHHHHSS-BHHHHHHH-SS-S--HHHHHHHHHHHHTT----B--S-............-S-SSS--XX CS Sigma70_r1_1 5 aavkeLikkgKkkGyLtyeEindaLpddeldseqiediiemLedmgIdvveeae....dedellleeeaedaeeed 76 ++ ++Likk+ + G +tyeEin+ L d++ +e+ie++i + ++gI++v+e++ edel e+e ed+ d 23726_FusoPortal_Gene_1040 8 EKARALIKKAVEEGIITYEEINEELG-DDFPAENIEQLINEMLEQGIKIVDEEQldelGEDEL-REKELEDDYT-D 80 67789********************9.888*********************999643222222.2222222222.2 PP == domain 2 score: -5.5 bits; conditional E-value: 7 S-.........-S-SSS--XXXXXXX CS Sigma70_r1_1 57 aededell.leeeaedaeeedeeaae 81 +e+ d+ll +++e++ +e+ede+ +e 23726_FusoPortal_Gene_1040 81 NEEHDDLLeDDSEDKIDENEDEN-DE 105 45556665333333333333333.22 PP == domain 3 score: -0.7 bits; conditional E-value: 0.59 HHHHHH-S..S-S--HHHHHHH CS Sigma70_r1_1 23 eEindaLp..ddeldseqiedi 42 +E ++++ dde+++e ied+ 23726_FusoPortal_Gene_1040 104 DETEEHFTefDDEFNPEYIEDV 125 56677776558899******98 PP >> B12-binding_2 B12 binding domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 3.7 0.0 0.034 81 14 33 .. 38 57 .. 34 58 .. 0.85 2 ? 4.8 0.0 0.016 37 6 47 .. 170 222 .. 167 230 .. 0.89 3 ? -3.4 0.0 5.4 1.3e+04 17 37 .. 240 264 .. 239 265 .. 0.57 Alignments for each domain: == domain 1 score: 3.7 bits; conditional E-value: 0.034 B12-binding_2 14 kegieelidealaqgsaavd 33 e ie+li+e+l+qg + vd 23726_FusoPortal_Gene_1040 38 AENIEQLINEMLEQGIKIVD 57 689*********99988765 PP == domain 2 score: 4.8 bits; conditional E-value: 0.016 B12-binding_2 6 hwaivhgdkegieelideala...........qgsaavdvlndvllpamkeVG 47 +++ +gd+e+ ++li+ l+ +g +++d+++++ + +mk V 23726_FusoPortal_Gene_1040 170 AKKAYEGDEEASKKLIESNLRlvvsiakkhtnRGLKLLDLIQEGNIGLMKAVE 222 6788899**********9999999999999889999*************9995 PP == domain 3 score: -3.4 bits; conditional E-value: 5.4 B12-binding_2 17 ieelideal.aqgsa...avdvlnd 37 i+++i +a+ +qg +v+ +++ 23726_FusoPortal_Gene_1040 240 IRQAITRAIaDQGRTiriPVHMIET 264 4566667773344446667776665 PP >> FrhB_FdhB_C Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 6.5 0.3 0.0027 6.4 128 154 .. 4 30 .. 4 31 .. 0.93 2 ? 1.3 0.0 0.11 2.6e+02 27 74 .. 188 236 .. 172 277 .. 0.74 3 ? -1.4 0.0 0.73 1.7e+03 41 70 .. 374 403 .. 370 417 .. 0.61 Alignments for each domain: == domain 1 score: 6.5 bits; conditional E-value: 0.0027 FrhB_FdhB_C 128 lvrtekgeellekaveageleleelde 154 l+++ek+++l++kave+g +++ee++e 23726_FusoPortal_Gene_1040 4 LIKNEKARALIKKAVEEGIITYEEINE 30 589*********************987 PP == domain 2 score: 1.3 bits; conditional E-value: 0.11 FrhB_FdhB_C 27 killtiglfCggnfspealrklleelgvd.pedvkklefrgk.gkfrvel 74 + +l++ + ++ +l +l++e ++ ++ v+k+e+ +k +kf + 23726_FusoPortal_Gene_1040 188 NLRLVVSIAKKHTNRGLKLLDLIQEGNIGlMKAVEKFEY-TKgYKFSTYA 236 556666666666666667777888889998999999999.8988887744 PP == domain 3 score: -1.4 bits; conditional E-value: 0.73 FrhB_FdhB_C 41 spealrklleelgvdpedvkklefrgk.gkf 70 sp+ l+++ + +v e ++++e++ k+ 23726_FusoPortal_Gene_1040 374 SPKTLEEVGKIFNVTRERIRQIEVK-AlRKL 403 7777777777777777788877774.22332 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (419 residues searched) Target model(s): 16712 (2907032 nodes) Passed MSV filter: 1467 (0.0877812); expected 334.2 (0.02) Passed bias filter: 620 (0.0370991); expected 334.2 (0.02) Passed Vit filter: 67 (0.0040091); expected 16.7 (0.001) Passed Fwd filter: 13 (0.000777884); expected 0.2 (1e-05) Initial search space (Z): 16712 [actual number of targets] Domain search space (domZ): 7 [number of targets reported over threshold] # CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.34 # Mc/sec: 3582.49 // [ok]