# 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_1488.faa # target HMM database: Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 23726_FusoPortal_Gene_1488 [L=141] Description: # 1586121 # 1586543 # -1 # ID=1_1488;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-24 84.6 0.0 9.3e-24 83.5 0.0 1.6 2 Rrf2 Transcriptional regulator 6.3e-05 22.4 0.2 0.00075 18.9 0.1 2.2 2 HTH_24 Winged helix-turn-helix DNA-binding ------ inclusion threshold ------ 0.049 13.4 0.0 0.072 12.9 0.0 1.4 1 TrmB Sugar-specific transcriptional regulator TrmB 0.11 12.4 0.0 1.1 9.2 0.0 2.0 2 MarR_2 MarR family Domain annotation for each model (and alignments): >> Rrf2 Transcriptional regulator # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 83.5 0.0 2.2e-27 9.3e-24 1 83 [] 1 83 [. 1 83 [. 0.99 2 ? -2.2 0.0 1.2 5.1e+03 67 81 .. 119 133 .. 118 134 .. 0.83 Alignments for each domain: == domain 1 score: 83.5 bits; conditional E-value: 2.2e-27 X---HHHHHHHHHHHHHHCSTTCC.--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT.TCEEESS-CCC-BHHHHHHHH CS Rrf2 1 MklsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLakppeeItlldvvrav 83 Mk++++++yal++++yL++++++ +ss+ei+++ ni++ ++ +i++kL+kag+vk rG++GGy+L+++p++ t+ d+++ + 23726_FusoPortal_Gene_1488 1 MKIKNEVRYALQIIYYLTLNRDKDIISSNEISAEENIPRLFCLRIIKKLEKAGVVKIFRGAKGGYVLTRDPKRLTFRDIIEII 83 9*******************************************************************************975 PP == domain 2 score: -2.2 bits; conditional E-value: 1.2 ESS-CCC-BHHHHHH CS Rrf2 67 LakppeeItlldvvr 81 L + ++I+++d v+ 23726_FusoPortal_Gene_1488 119 LLDDFDKINFYDLVE 133 6678899****9987 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 ! 18.9 0.1 1.8e-07 0.00075 14 48 .] 21 56 .. 10 56 .. 0.87 2 ? 1.1 0.0 0.065 2.7e+02 12 27 .. 67 83 .. 65 85 .. 0.80 Alignments for each domain: == domain 1 score: 18.9 bits; conditional E-value: 1.8e-07 HTH_24 14 knpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48 ++ + is +e++ + ++++ ++r +k+Le++G++k 23726_FusoPortal_Gene_1488 21 RDKDiISSNEISAEENIPRLFCLRIIKKLEKAGVVK 56 455559****************************97 PP == domain 2 score: 1.1 bits; conditional E-value: 0.065 HTH_24 12 Lqknpr.isqreLAerl 27 L ++p+ ++ r++ e + 23726_FusoPortal_Gene_1488 67 LTRDPKrLTFRDIIEII 83 77888889999998875 PP >> TrmB Sugar-specific transcriptional regulator TrmB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 12.9 0.0 1.7e-05 0.072 25 58 .. 28 61 .. 13 79 .. 0.86 Alignments for each domain: == domain 1 score: 12.9 bits; conditional E-value: 1.7e-05 HCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS TrmB 25 adeiaeelgvprskvYevLrsLedkGlVerekgr 58 +ei+ e ++pr + +++++Le++G+V++ +g 23726_FusoPortal_Gene_1488 28 SNEISAEENIPRLFCLRIIKKLEKAGVVKIFRGA 61 579**************************98876 PP >> MarR_2 MarR family # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 9.2 0.0 0.00025 1.1 15 54 .. 18 58 .. 10 64 .. 0.76 2 ? 1.1 0.0 0.086 3.6e+02 14 29 .. 66 81 .. 64 83 .. 0.78 Alignments for each domain: == domain 1 score: 9.2 bits; conditional E-value: 0.00025 HCTTTSEE.EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS MarR_2 15 grrpgrdl.tvselarrlglsksavsrilkrLvaaGLverr 54 + ++d+ + +e++++ ++++ ri+k+L++aG v 23726_FusoPortal_Gene_1488 18 TLNRDKDIiSSNEISAEENIPRLFCLRIIKKLEKAGVVKIF 58 55555555588899999999999999**********99765 PP == domain 2 score: 1.1 bits; conditional E-value: 0.086 HHCTTTSEEEHHHHHH CS MarR_2 14 lgrrpgrdltvselar 29 + r++++lt +++ + 23726_FusoPortal_Gene_1488 66 VLTRDPKRLTFRDIIE 81 56678888*****976 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (141 residues searched) Target model(s): 16712 (2907032 nodes) Passed MSV filter: 423 (0.0253112); expected 334.2 (0.02) Passed bias filter: 338 (0.020225); expected 334.2 (0.02) Passed Vit filter: 38 (0.00227382); expected 16.7 (0.001) Passed Fwd filter: 4 (0.000239349); expected 0.2 (1e-05) Initial search space (Z): 16712 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 0.23u 0.23s 00:00:00.46 Elapsed: 00:00:00.34 # Mc/sec: 1205.56 // [ok]