# 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_248.faa # target HMM database: Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 23726_FusoPortal_Gene_248 [L=269] Description: # 267472 # 268278 # -1 # ID=1_248;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.239 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-17 63.9 0.1 1e-17 63.9 0.1 2.2 3 MerR_1 MerR HTH family regulatory protein 3.6e-12 45.7 0.4 8.9e-12 44.5 0.4 1.7 1 MerR MerR family regulatory protein 0.0091 16.4 0.0 0.016 15.6 0.0 1.4 1 MerR-DNA-bind MerR, DNA binding ------ inclusion threshold ------ 0.016 14.8 0.6 0.016 14.8 0.6 1.8 2 YL1_C YL1 nuclear protein C-terminal domain 0.041 14.0 0.0 0.089 12.9 0.0 1.6 1 HTH_17 Helix-turn-helix domain 0.22 11.4 3.7 0.42 10.5 3.3 1.7 1 P4Ha_N Prolyl 4-Hydroxylase alpha-subunit, N-terminal Domain annotation for each model (and alignments): >> MerR_1 MerR HTH family regulatory protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 63.9 0.1 3.6e-21 1e-17 1 68 [. 5 74 .. 5 75 .. 0.98 2 ? -3.5 0.0 3.8 1.1e+04 17 31 .. 125 139 .. 123 142 .. 0.74 3 ? -2.7 0.1 2.1 6e+03 39 54 .. 156 171 .. 152 175 .. 0.71 Alignments for each domain: == domain 1 score: 63.9 bits; conditional E-value: 3.6e-21 EEHHHHHHHHTS-HHHHHHHHHHTT-S-EE..-TTS-EEEEHHHHHHHHHHHHHHHTT--GGG---XXXX CS MerR_1 1 ysigevakilgvtthtlrywekegllkpkr..teggrryYtdedierLklikyLlkrGltlkgikkllns 68 ysigev++i gv++ tlry+ + l+ pk ++g+ryY+ ++ + +ikyL+k Gl lk+ik++l++ 23726_FusoPortal_Gene_248 5 YSIGEVSEIMGVSVQTLRYYSNINLILPKYvnPSTGYRYYSVDQFHFIDRIKYLQKLGLCLKEIKEILSE 74 9************************999999************************************986 PP == domain 2 score: -3.5 bits; conditional E-value: 3.8 HHHHHHHTT-S-EE- CS MerR_1 17 lrywekegllkpkrt 31 + ++ek++++ k+ 23726_FusoPortal_Gene_248 125 ILHFEKRYVVAVKIL 139 568899999888774 PP == domain 3 score: -2.7 bits; conditional E-value: 2.1 EHHHHHHHHHHHHHHH CS MerR_1 39 tdedierLklikyLlk 54 ++e ++Lk ++++l+ 23726_FusoPortal_Gene_248 156 NNEKYKNLKYMRQFLY 171 5666777888888776 PP >> MerR MerR family regulatory protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 44.5 0.4 3.2e-15 8.9e-12 1 38 [] 6 44 .. 6 44 .. 0.97 Alignments for each domain: == domain 1 score: 44.5 bits; conditional E-value: 3.2e-15 EHHHHHHHHTTTHHHHHHHHHTT.SSTTCEETTTSSEEE CS MerR 1 tIgevAeltGvsprtLRyYEreG.LipppeRtegGyRlY 38 +Igev+e+ Gvs++tLRyY ++ +p+ + +++GyR+Y 23726_FusoPortal_Gene_248 6 SIGEVSEIMGVSVQTLRYYSNINlILPKYVNPSTGYRYY 44 7**********************8889***********9 PP >> MerR-DNA-bind MerR, DNA binding # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 15.6 0.0 5.7e-06 0.016 6 62 .. 54 105 .. 50 108 .. 0.90 Alignments for each domain: == domain 1 score: 15.6 bits; conditional E-value: 5.7e-06 HHHHHHHTT--HHHHHHHHHHHHSCCTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS MerR-DNA-bind 6 fIrrarrlGFsLdeIrelLalyddrappcqdvrallarklaeleeriaeLqalraeL 62 I+ ++ lG+ L+eI+e+L ++ + + l++ + +ee i++L+ + + + 23726_FusoPortal_Gene_248 54 RIKYLQKLGLCLKEIKEIL-----SENNISTLIKYLDKYKNYIEEEINKLKDTIDSI 105 5999***************.....7889999999*************9999998876 PP >> YL1_C YL1 nuclear protein C-terminal domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -3.5 0.2 3.1 8.8e+03 18 22 .. 21 25 .. 20 26 .. 0.72 2 ? 14.8 0.6 5.8e-06 0.016 10 29 .] 33 52 .. 33 52 .. 0.94 Alignments for each domain: == domain 1 score: -3.5 bits; conditional E-value: 3.1 YL1_C 18 LpYan 22 L+Y++ 23726_FusoPortal_Gene_248 21 LRYYS 25 78875 PP == domain 2 score: 14.8 bits; conditional E-value: 5.8e-06 YL1_C 10 rYrDPkTgLpYanveaykvI 29 +Y P+Tg +Y++v+ + I 23726_FusoPortal_Gene_248 33 KYVNPSTGYRYYSVDQFHFI 52 8***************9877 PP >> HTH_17 Helix-turn-helix domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 12.9 0.0 3.2e-05 0.089 1 21 [. 4 24 .. 4 46 .. 0.86 Alignments for each domain: == domain 1 score: 12.9 bits; conditional E-value: 3.2e-05 HTH_17 1 lltveEaAelLgvsrstvyrl 21 l+++ E++e+ gvs++t++ + 23726_FusoPortal_Gene_248 4 LYSIGEVSEIMGVSVQTLRYY 24 79****************987 PP >> P4Ha_N Prolyl 4-Hydroxylase alpha-subunit, N-terminal region # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 10.5 3.3 0.00015 0.42 14 97 .. 79 157 .. 64 167 .. 0.86 Alignments for each domain: == domain 1 score: 10.5 bits; conditional E-value: 0.00015 P4Ha_N 14 elveeLesyieeeekkleklkrfleelekehesakedkeeylsnPlnaFklikRltsdWeeleklleeseseelieqlealkkr 97 +l++ L++y + +e++++klk ++++e + + y++ ++ + i ++ + + k+le++++e++ +l++l+++ 23726_FusoPortal_Gene_248 79 TLIKYLDKYKNYIEEEINKLKDTIDSIEWYK-----NYFTYIGENVDDHSYILHFEKRYVVAVKILENEPKEDFHIRLNELRNN 157 6999**********************98776.....5678*******************9889999999999988888655444 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (269 residues searched) Target model(s): 16712 (2907032 nodes) Passed MSV filter: 1050 (0.0628291); expected 334.2 (0.02) Passed bias filter: 477 (0.0285424); expected 334.2 (0.02) Passed Vit filter: 68 (0.00406893); expected 16.7 (0.001) Passed Fwd filter: 6 (0.000359023); expected 0.2 (1e-05) Initial search space (Z): 16712 [actual number of targets] Domain search space (domZ): 6 [number of targets reported over threshold] # CPU time: 0.25u 0.22s 00:00:00.47 Elapsed: 00:00:00.30 # Mc/sec: 2606.64 // [ok]