# 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_1425.faa # target HMM database: Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 23726_FusoPortal_Gene_1425 [L=416] Description: # 1526852 # 1528099 # 1 # ID=1_1425;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.294 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-08 33.9 0.0 6.5e-08 33.0 0.0 1.5 1 Radical_SAM Radical SAM superfamily 2.1e-06 27.8 0.0 4.7e-06 26.7 0.0 1.5 1 HHH_3 Helix-hairpin-helix motif 0.0003 21.0 0.0 0.00059 20.0 0.0 1.4 1 Fer4_12 4Fe-4S single cluster domain 0.00072 19.2 0.0 0.0017 18.0 0.0 1.6 1 HHH Helix-hairpin-helix motif 0.0048 17.4 0.0 0.013 16.0 0.0 1.8 1 HHH_5 Helix-hairpin-helix domain ------ inclusion threshold ------ 0.099 12.7 0.0 0.18 11.8 0.0 1.4 1 HHH_2 Helix-hairpin-helix motif 0.83 10.1 4.1 0.35 11.4 1.6 1.6 2 ShK ShK domain-like Domain annotation for each model (and alignments): >> Radical_SAM Radical SAM superfamily # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 33.0 0.0 2.7e-11 6.5e-08 3 141 .. 62 199 .. 60 227 .. 0.80 Alignments for each domain: == domain 1 score: 33.0 bits; conditional E-value: 2.7e-11 EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC.......CCT CS xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxx RF Radical_SAM 3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla.......vpg 77 t+ C ++C++C+++++ + ++l+++ei+++ + ++++ +++++l++g + + d++++l +++++ + 23726_FusoPortal_Gene_1425 62 MTNYCIYDCKYCINRKD--NDIERAILTPDEIVKLTINF-YRRNyIEGLFLSSG-IIKNVDYTMELMIAVAKKlrleekfNGY 140 6899************8..********************.57777*********.9999************977777766666 PP EEEEEEECSSCH.HHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHCT CS xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF Radical_SAM 78 iritvetngtlpdeeklerllelg..vdrvslgleaaddekvlklmnrghtfeevlealeklreag 141 i++ v+ + + +++ e g vdrvs+++e a ++ lkl+ + + + ++ ++ ++r+++ 23726_FusoPortal_Gene_1425 141 IHMKVIPGASR------QLINEIGlyVDRVSVNIEFAENR-ALKLLAPDKKPTDISTSMGLIRKNM 199 66666666666......4555555666************9.8998887677666666666666555 PP >> HHH_3 Helix-hairpin-helix motif # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 26.7 0.0 2e-09 4.7e-06 5 36 .. 325 356 .. 323 370 .. 0.84 Alignments for each domain: == domain 1 score: 26.7 bits; conditional E-value: 2e-09 HHH_3 5 gvdiNtAsaeeLqklpglgpklAknIvayRek 36 ++ iN+As++eL ++pg+g + Ak+Iv R+ 23726_FusoPortal_Gene_1425 325 PIEINKASYKELLRVPGIGVTSAKRIVMTRKY 356 589**************************953 PP >> Fer4_12 4Fe-4S single cluster domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 20.0 0.0 2.5e-07 0.00059 9 116 .. 60 162 .. 50 179 .. 0.86 Alignments for each domain: == domain 1 score: 20.0 bits; conditional E-value: 2.5e-07 Fer4_12 9 slfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekp.ekdiwl 90 +l ++ C Ck+C+n++ + ++ +++e+ + i+ ++iegl l+ G +n++ +el+ v ++ e + 23726_FusoPortal_Gene_1425 60 ILMTNYCIYDCKYCINRKDNDIERAILTPDEIVKLTINFYRRNYIEGLFLSSG---IIKNVDYTMELMIAVAKKLRlE---EK 136 566899*********************************************99...4579999999999999988744...58 PP Fer4_12 91 ytgytleelskkekeellkeidvlvd 116 ++gy+ ++ + ++++l++ei vd 23726_FusoPortal_Gene_1425 137 FNGYIHMKVIPGASRQLINEIGLYVD 162 **********999******9997776 PP >> HHH Helix-hairpin-helix motif # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 18.0 0.0 7.2e-07 0.0017 5 27 .. 328 350 .. 326 351 .. 0.93 Alignments for each domain: == domain 1 score: 18.0 bits; conditional E-value: 7.2e-07 HHTSSHHHHHTSTT-SHHHHHHH CS HHH 5 lipasreeLlalPGVGpktAeaI 27 ++ as++eLl +PG+G A +I 23726_FusoPortal_Gene_1425 328 INKASYKELLRVPGIGVTSAKRI 350 789*****************998 PP >> HHH_5 Helix-hairpin-helix domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 16.0 0.0 5.4e-06 0.013 25 54 .. 324 353 .. 308 355 .. 0.81 Alignments for each domain: == domain 1 score: 16.0 bits; conditional E-value: 5.4e-06 SHHHHHCS-HHHHHTSTTS-HHHHHHHHHH CS HHH_5 25 svedlaaadveeLakipGiGkktAeriile 54 ++ ++ +a+ +eL ++pGiG A+ri++ 23726_FusoPortal_Gene_1425 324 FPIEINKASYKELLRVPGIGVTSAKRIVMT 353 5667888999*****************985 PP >> HHH_2 Helix-hairpin-helix motif # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.8 0.0 7.6e-05 0.18 29 53 .. 328 352 .. 326 360 .. 0.90 Alignments for each domain: == domain 1 score: 11.8 bits; conditional E-value: 7.6e-05 HHH_2 29 LkkasleeLlevddiGeeiAqsive 53 + kas++eLl v++iG + A+ iv 23726_FusoPortal_Gene_1425 328 INKASYKELLRVPGIGVTSAKRIVM 352 789*******************986 PP >> ShK ShK domain-like # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.7 0.0 7 1.7e+04 9 21 .. 15 25 .. 13 28 .. 0.61 2 ? 11.4 1.6 0.00015 0.35 6 38 .] 42 73 .. 40 73 .. 0.91 Alignments for each domain: == domain 1 score: -3.7 bits; conditional E-value: 7 ShK 9 CaswaalgfCtnp 21 a + C+++ 23726_FusoPortal_Gene_1425 15 AAKYDVS--CSSS 25 5556666..7765 PP == domain 2 score: 11.4 bits; conditional E-value: 0.00015 ShK 6 ssdCaswaalgfCtnptyrdfmkeqCpktCgfC 38 ++ C sw+a g C + + +m+ +C + C++C 23726_FusoPortal_Gene_1425 42 NGICHSWSADGRCISL-LKILMTNYCIYDCKYC 73 678**********766.69************** PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (416 residues searched) Target model(s): 16712 (2907032 nodes) Passed MSV filter: 530 (0.0317137); expected 334.2 (0.02) Passed bias filter: 395 (0.0236357); expected 334.2 (0.02) Passed Vit filter: 35 (0.0020943); expected 16.7 (0.001) Passed Fwd filter: 7 (0.000418861); 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: 0.28u 0.23s 00:00:00.51 Elapsed: 00:00:00.32 # Mc/sec: 3779.14 // [ok]