# 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_616.faa # target HMM database: Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 23726_FusoPortal_Gene_616 [L=230] Description: # 687988 # 688677 # 1 # ID=1_616;partial=00;start_type=ATG;rbs_motif=GGxGG;rbs_spacer=3-4bp;gc_cont=0.248 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-32 109.7 2.6 1.2e-31 108.9 2.6 1.4 1 PAS_6 YheO-like PAS domain 1.7e-21 76.0 0.8 3.8e-21 74.8 0.1 1.9 2 HTH_22 HTH domain 0.00034 20.0 2.7 0.00065 19.1 2.7 1.4 1 DUF4747 Domain of unknown function (DUF4747) 0.00035 20.5 0.0 0.00096 19.1 0.0 1.8 1 HTH_7 Helix-turn-helix domain of resolvase 0.0013 18.3 0.0 0.0037 16.9 0.0 1.7 1 HTH_38 Helix-turn-helix domain ------ inclusion threshold ------ 0.017 15.0 0.0 0.081 12.8 0.0 2.1 2 HTH_11 HTH domain 0.019 14.6 0.1 0.14 11.9 0.0 2.4 2 HTH_23 Homeodomain-like domain Domain annotation for each model (and alignments): >> PAS_6 YheO-like PAS domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 108.9 2.6 4.8e-35 1.2e-31 1 113 [. 6 117 .. 6 119 .. 0.97 Alignments for each domain: == domain 1 score: 108.9 bits; conditional E-value: 4.8e-35 PAS_6 1 LeslkqlveglaellgencEvvlhdledpehsivaiaNghvtgRkvGdpltdlvlellkeeeeeeedvlvnyktktkdgkilks 84 L+++k lv++l+++lg+++E+vlh++++ e +++aiaNg++++R++++++++ +l++lk++++++e+ +vn + k+gk+++s 23726_FusoPortal_Gene_616 6 LNQYKILVNFLGKTLGPSFEIVLHEIKSEEVKMIAIANGEISNRTLENSISSETLDILKNKSYHNEESMVNHTVLLKNGKKVRS 89 789********************************************************************************* PP PAS_6 85 stifirdekgkliglLCiNldiskleaae 113 s++fi++ ++k+ig+LCiN+d sk+++++ 23726_FusoPortal_Gene_616 90 SSMFIKE-NQKIIGMLCINFDDSKFHDIN 117 ******9.567*************99875 PP >> HTH_22 HTH domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.8 0.0 1.3 3.2e+03 10 30 .. 80 102 .. 72 104 .. 0.56 2 ! 74.8 0.1 1.6e-24 3.8e-21 2 61 .. 163 222 .. 162 223 .. 0.98 Alignments for each domain: == domain 1 score: -1.8 bits; conditional E-value: 1.3 HTH_22 10 ladlgkp..verltkeekieivr 30 l ++gk+ +++ +e+++i+ 23726_FusoPortal_Gene_616 80 LLKNGKKvrSSSMFIKENQKIIG 102 35555552245666788888876 PP == domain 2 score: 74.8 bits; conditional E-value: 1.6e-24 HTH_22 2 lesiieevladlgkpverltkeekieivraLdekGiFllkgavekvAekLgiSraTvYry 61 +e+i+++v + + p+erltk+e+ +iv+aL+ekGiF+lk+a+++vA+kL++S TvYry 23726_FusoPortal_Gene_616 163 MEKIFQDVNLKFNYPLERLTKQEREKIVKALYEKGIFNLKDAINFVAKKLSCSPTTVYRY 222 799********************************************************* PP >> DUF4747 Domain of unknown function (DUF4747) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 19.1 2.7 2.7e-07 0.00065 85 175 .. 118 207 .. 106 209 .. 0.89 Alignments for each domain: == domain 1 score: 19.1 bits; conditional E-value: 2.7e-07 DUF4747 85 inipenlkpnlkefefvFdpktHrLaiitkdkknlslspkqikalleeifnraeiatkygsvevtvlteresleriLslpkikk 168 +i + p+++ +++ d++ +L+ ++kd++n + s ++i+a++e+if++++ +++y +e ere + + L ++ i + 23726_FusoPortal_Gene_616 118 CQILRIIHPDMFVKNYLSDISYNILVDENKDQSNEENSTDNIEAFMEKIFQDVNLKFNY-PLERLTKQEREKIVKALYEKGIFN 200 56677789999999*********************************************.89999999*******999999999 PP DUF4747 169 lkieitf 175 lk i+f 23726_FusoPortal_Gene_616 201 LKDAINF 207 9988876 PP >> HTH_7 Helix-turn-helix domain of resolvase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 19.1 0.0 4e-07 0.00096 14 41 .. 190 222 .. 180 225 .. 0.85 Alignments for each domain: == domain 1 score: 19.1 bits; conditional E-value: 4e-07 GGSSTTTT-.....-STTTSSSS---SSSS--S CS HTH_7 14 vvkLleeGi.....siskIAkevnisRsTvYRy 41 v++L+e+Gi +i+ +Ak + +s++TvYRy 23726_FusoPortal_Gene_616 190 VKALYEKGIfnlkdAINFVAKKLSCSPTTVYRY 222 788888887777778999**************9 PP >> HTH_38 Helix-turn-helix domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 16.9 0.0 1.5e-06 0.0037 4 39 .. 180 221 .. 179 224 .. 0.89 Alignments for each domain: == domain 1 score: 16.9 bits; conditional E-value: 1.5e-06 HTH_38 4 hLsleeReeIerl.laeG.lslr....eIArrLgrspsTIsR 39 +L+ +eRe+I + +++G +l+ +A++L +sp+T++R 23726_FusoPortal_Gene_616 180 RLTKQEREKIVKAlYEKGiFNLKdainFVAKKLSCSPTTVYR 221 79********88757999***99877779************9 PP >> HTH_11 HTH domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -2.7 0.0 2.4 5.7e+03 26 36 .. 45 55 .. 45 57 .. 0.80 2 ? 12.8 0.0 3.4e-05 0.081 22 40 .. 209 227 .. 204 228 .. 0.89 Alignments for each domain: == domain 1 score: -2.7 bits; conditional E-value: 2.4 HTH_11 26 nvSrrtvrrdI 36 ++S rt + I 23726_FusoPortal_Gene_616 45 EISNRTLENSI 55 68999998887 PP == domain 2 score: 12.8 bits; conditional E-value: 3.4e-05 HTH_11 22 AeeLnvSrrtvrrdIkaLe 40 A++L++S +tv+r++ ++e 23726_FusoPortal_Gene_616 209 AKKLSCSPTTVYRYVGKIE 227 9**************9987 PP >> HTH_23 Homeodomain-like domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.4 0.0 0.85 2e+03 19 35 .. 35 52 .. 26 56 .. 0.79 2 ? 11.9 0.0 5.8e-05 0.14 23 40 .. 208 225 .. 180 229 .. 0.69 Alignments for each domain: == domain 1 score: -1.4 bits; conditional E-value: 0.85 HTH_23 19 svreIAreLg.vsrrTvy 35 v+ IA + g +s rT+ 23726_FusoPortal_Gene_616 35 EVKMIAIANGeISNRTLE 52 578899999889999986 PP == domain 2 score: 11.9 bits; conditional E-value: 5.8e-05 HTH_23 23 IAreLgvsrrTvyrwlkr 40 +A++L +s+ Tvyr++ + 23726_FusoPortal_Gene_616 208 VAKKLSCSPTTVYRYVGK 225 8*************9865 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (230 residues searched) Target model(s): 16712 (2907032 nodes) Passed MSV filter: 1170 (0.0700096); expected 334.2 (0.02) Passed bias filter: 499 (0.0298588); expected 334.2 (0.02) Passed Vit filter: 59 (0.0035304); 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: 0.24u 0.23s 00:00:00.47 Elapsed: 00:00:00.31 # Mc/sec: 2156.83 // [ok]