# 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_1502.faa # target HMM database: Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 23726_FusoPortal_Gene_1502 [L=236] Description: # 1600624 # 1601331 # 1 # ID=1_1502;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.257 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-21 76.2 0.0 3.4e-21 75.9 0.0 1.1 1 FCD FCD domain 1.4e-14 53.3 0.0 2.5e-14 52.6 0.0 1.4 1 GntR Bacterial regulatory proteins, gntR family 0.00018 20.9 0.0 0.00049 19.5 0.0 1.7 1 HTH_24 Winged helix-turn-helix DNA-binding 0.00019 21.3 0.0 0.00033 20.5 0.0 1.4 1 HTH_Crp_2 Crp-like helix-turn-helix domain 0.00078 19.6 2.7 0.00093 19.4 1.6 1.6 1 Acetyltransf_4 Acetyltransferase (GNAT) domain 0.0027 17.6 0.0 0.0059 16.5 0.0 1.5 1 HTH_46 Winged helix-turn-helix DNA binding ------ inclusion threshold ------ 0.012 15.5 0.0 0.029 14.2 0.0 1.6 1 HTH_36 Helix-turn-helix domain 0.025 14.8 0.0 0.051 13.8 0.0 1.4 1 Rrf2 Transcriptional regulator 0.038 14.1 0.1 0.15 12.2 0.0 2.0 2 Fe_dep_repress Iron dependent repressor, N-terminal DNA bind 0.049 13.5 1.3 0.22 11.4 0.1 2.3 2 HTH_11 HTH domain 0.11 12.0 0.0 0.23 11.0 0.0 1.5 1 HTH_41 Helix-turn-helix domain 0.13 12.3 0.3 0.13 12.3 0.3 1.9 2 FlaG FlaG protein Domain annotation for each model (and alignments): >> FCD FCD domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 75.9 0.0 2.4e-24 3.4e-21 1 123 [. 90 213 .. 90 215 .. 0.96 Alignments for each domain: == domain 1 score: 75.9 bits; conditional E-value: 2.4e-24 FCD 1 dlyelRalLEpeaarlaarratdadlaeleellealeeaaaegdleefaeadraFHralaeaagnpvlaelleelrarlrrlr 83 d++e+R E a laa+r+ d+d++ l+e +e+le ++ d + ++++d++FHr++a+a++n ++ + e + + r++ 23726_FusoPortal_Gene_1502 90 DILEVRIFYEKNNAFLAAKRIKDEDIKLLKECIEKLESNLSTFDSQLLYRIDHQFHRLVAKATQNNWMYKETELILDNYLRFE 172 79********************************************************************9999999999988 PP FCD 84 rlals.sperleeslaeHraildAirardadaAraamrrHl 123 + + + + + +++eH ai++Ai+++d+++A++ m+ Hl 23726_FusoPortal_Gene_1502 173 NKSVYnNSIDGQLVFKEHLAIFNAIKDKDSEKAKKMMEKHL 213 887777999*******************************9 PP >> GntR Bacterial regulatory proteins, gntR family # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 52.6 0.0 1.8e-17 2.5e-14 3 64 .] 20 80 .. 18 80 .. 0.98 Alignments for each domain: == domain 1 score: 52.6 bits; conditional E-value: 1.8e-17 HHHHHHHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEEEE CS GntR 3 eqvyerLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgrGtfV 64 eq+y+ +++ Il + +r G++ s+++++ e+g+srt+vReAL++L+ eg++++ +grG+ V 23726_FusoPortal_Gene_1502 20 EQAYDLIKDAILFNKFRIGAIY-SQESICNELGISRTPVREALIELQKEGYITILRGRGIEV 80 89********************.************************************987 PP >> HTH_24 Winged helix-turn-helix DNA-binding # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 19.5 0.0 3.5e-07 0.00049 19 48 .] 42 71 .. 41 71 .. 0.96 Alignments for each domain: == domain 1 score: 19.5 bits; conditional E-value: 3.5e-07 HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlIk 48 sq ++ +lg+S+++v++ l +L++eG+I+ 23726_FusoPortal_Gene_1502 42 SQESICNELGISRTPVREALIELQKEGYIT 71 8999*************************6 PP >> HTH_Crp_2 Crp-like helix-turn-helix domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 20.5 0.0 2.4e-07 0.00033 22 60 .. 41 81 .. 15 84 .. 0.86 Alignments for each domain: == domain 1 score: 20.5 bits; conditional E-value: 2.4e-07 CHHHHHHHHTTS-HHHHHHHHHHHHHTTSEE..ETEEEEES CS HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkreglie..rgrriril 60 +qe + + lG++r v +l eL++eg+i+ rgr+i+++ 23726_FusoPortal_Gene_1502 41 YSQESICNELGISRTPVREALIELQKEGYITilRGRGIEVT 81 79*****************************8445559985 PP >> Acetyltransf_4 Acetyltransferase (GNAT) domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 19.4 1.6 6.6e-07 0.00093 3 93 .. 82 178 .. 80 186 .. 0.83 Alignments for each domain: == domain 1 score: 19.4 bits; conditional E-value: 6.6e-07 Acetyltransf_4 3 aatqeDleailrlyaeyrvntait..feyevssveefekrlesl.dsek.....qylflvfe.sgrlvGyatlrqfkkakdwk 76 ++t+eD+++il+++ +y+ n+a+ +++++ ++ +++ +e+l + q+l+ +++ rlv+ at + + k+ 23726_FusoPortal_Gene_1502 82 PVTEEDAKDILEVRIFYEKNNAFLaaKRIKDEDIKLLKECIEKLeSN-LstfdsQLLYRIDHqFHRLVAKATQNNWMY-KETE 162 689**************99997764567789*************532.235667********99********998888.**** PP Acetyltransf_4 77 aelsvylardnnkeglg 93 +l +yl+ +n k +++ 23726_FusoPortal_Gene_1502 163 LILDNYLRFEN-KSVYN 178 *******9744.55555 PP >> HTH_46 Winged helix-turn-helix DNA binding # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 16.5 0.0 4.2e-06 0.0059 32 63 .. 49 80 .. 35 83 .. 0.87 Alignments for each domain: == domain 1 score: 16.5 bits; conditional E-value: 4.2e-06 HTH_46 32 rTnLSRSsilkvLseLkkggyIeierGkLvki 63 +SR + + L eL+k+gyI+i rG+ +++ 23726_FusoPortal_Gene_1502 49 ELGISRTPVREALIELQKEGYITILRGRGIEV 80 5679***********************97766 PP >> HTH_36 Helix-turn-helix domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 14.2 0.0 2.1e-05 0.029 24 55 .] 39 70 .. 31 70 .. 0.90 Alignments for each domain: == domain 1 score: 14.2 bits; conditional E-value: 2.1e-05 HTH_36 24 cfpsqetlakrlglsknTvsraikeLeqlGyi 55 + sqe +++ lg+s+ v+ a+ eL + Gyi 23726_FusoPortal_Gene_1502 39 AIYSQESICNELGISRTPVREALIELQKEGYI 70 5569***************************8 PP >> Rrf2 Transcriptional regulator # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 13.8 0.0 3.7e-05 0.051 27 62 .. 42 77 .. 31 82 .. 0.91 Alignments for each domain: == domain 1 score: 13.8 bits; conditional E-value: 3.7e-05 -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT. CS Rrf2 27 sseeiaerqnispsylekilakLrkaglvksvrGkg 62 s e+i ++ +is++ ++ l +L+k+g+++ rG+g 23726_FusoPortal_Gene_1502 42 SQESICNELGISRTPVREALIELQKEGYITILRGRG 77 678999****************************94 PP >> Fe_dep_repress Iron dependent repressor, N-terminal DNA binding domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 12.2 0.0 0.00011 0.15 24 54 .. 42 72 .. 37 78 .. 0.86 2 ? -2.5 0.1 4.2 5.8e+03 6 19 .. 217 230 .. 212 233 .. 0.68 Alignments for each domain: == domain 1 score: 12.2 bits; conditional E-value: 0.00011 -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS Fe_dep_repress 24 ktkdlaerLnvspssVsemlkkLekdGyvey 54 ++ + +L++s V e l +L+k+Gy+ 23726_FusoPortal_Gene_1502 42 SQESICNELGISRTPVREALIELQKEGYITI 72 6788999*********************976 PP == domain 2 score: -2.5 bits; conditional E-value: 4.2 HHHHHHHHHHHHHH CS Fe_dep_repress 6 tEdYLetIYtlsee 19 L+ I+ ++e 23726_FusoPortal_Gene_1502 217 YYRTLKKIWNTEKE 230 55569999998874 PP >> HTH_11 HTH domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.4 0.1 0.00015 0.22 17 54 .. 42 78 .. 39 79 .. 0.90 2 ? 0.3 0.1 0.47 6.6e+02 35 48 .. 114 127 .. 94 128 .. 0.89 Alignments for each domain: == domain 1 score: 11.4 bits; conditional E-value: 0.00015 HTH_11 17 sgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgrGY 54 s e + eL++Sr+ vr + +L++ g I+ +grG+ 23726_FusoPortal_Gene_1502 42 SQESICNELGISRTPVREALIELQKEG-YITILRGRGI 78 5678999********************.8888888885 PP == domain 2 score: 0.3 bits; conditional E-value: 0.47 HTH_11 35 dIkaLeelgvpIes 48 dIk L+e ++es 23726_FusoPortal_Gene_1502 114 DIKLLKECIEKLES 127 99999999887776 PP >> HTH_41 Helix-turn-helix domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.0 0.0 0.00016 0.23 10 40 .. 44 74 .. 38 77 .. 0.90 Alignments for each domain: == domain 1 score: 11.0 bits; conditional E-value: 0.00016 HTH_41 10 eelskeleLSvGlvQkALklLeddkavtler 40 e++++el++S+ v +AL L++++ +t+ r 23726_FusoPortal_Gene_1502 44 ESICNELGISRTPVREALIELQKEGYITILR 74 689************************9865 PP >> FlaG FlaG protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 12.3 0.3 9.5e-05 0.13 24 66 .. 108 150 .. 99 155 .. 0.83 2 ? -1.2 0.2 1.6 2.2e+03 23 32 .. 202 211 .. 194 234 .. 0.45 Alignments for each domain: == domain 1 score: 12.3 bits; conditional E-value: 9.5e-05 -------HHHHHHHHHHHHHHHTTSS--EEEEEEEETTEEEEE CS FlaG 24 eeekevseeeleeaveklnkklsslnteleFsvdedtkrvvVk 66 ++ k+++ + l+e +ekl+++ls+++++l +++d++ +r+v k 23726_FusoPortal_Gene_1502 108 KRIKDEDIKLLKECIEKLESNLSTFDSQLLYRIDHQFHRLVAK 150 44455556669****************************9866 PP == domain 2 score: -1.2 bits; conditional E-value: 1.6 S-------HH CS FlaG 23 aeeekevsee 32 +e++k+ e+ 23726_FusoPortal_Gene_1502 202 SEKAKKMMEK 211 2222222222 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (236 residues searched) Target model(s): 16712 (2907032 nodes) Passed MSV filter: 1204 (0.072044); expected 334.2 (0.02) Passed bias filter: 454 (0.0271661); expected 334.2 (0.02) Passed Vit filter: 57 (0.00341072); expected 16.7 (0.001) Passed Fwd filter: 12 (0.000718047); expected 0.2 (1e-05) Initial search space (Z): 16712 [actual number of targets] Domain search space (domZ): 12 [number of targets reported over threshold] # CPU time: 0.26u 0.24s 00:00:00.50 Elapsed: 00:00:00.32 # Mc/sec: 2143.94 // [ok]