# 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_1959.faa # target HMM database: Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 23726_FusoPortal_Gene_1959 [L=198] Description: # 2107048 # 2107641 # -1 # ID=1_1959;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.293 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.2e-24 83.7 0.1 2.1e-23 82.6 0.1 1.6 1 Toprim_4 Toprim domain 2e-15 56.0 4.4 3.4e-15 55.2 4.4 1.4 1 RecR RecR protein 2.2e-07 31.0 0.2 7.6e-07 29.2 0.1 1.8 2 Toprim Toprim domain ------ inclusion threshold ------ 0.17 10.9 0.5 1 8.4 0.5 1.9 1 Memo Memo-like protein Domain annotation for each model (and alignments): >> Toprim_4 Toprim domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 82.6 0.1 4.9e-27 2.1e-23 2 89 .] 80 170 .. 79 170 .. 0.97 Alignments for each domain: == domain 1 score: 82.6 bits; conditional E-value: 4.9e-27 Toprim_4 2 eiiiVEgyaDvlaleka.giknavavlggalspldgirpeklksenlve..aekkvkevilaldgDaeGeataerlaelllee 81 i++VE D + le++ ++++++vl g+l+pl+gi p +l++++l+e a++ ++e+ila+++ eGe+ta++la+l+++ 23726_FusoPortal_Gene_1959 80 IICVVEESKDIMILERTtKYRGVYHVLNGRLDPLNGITPNELNIKSLLEriAKDDIEEIILATNPNIEGETTAMYLAKLMKNF 162 69******************************************99*99*****************************999** PP Toprim_4 82 gvkvtrva 89 g+k+t++a 23726_FusoPortal_Gene_1959 163 GIKITKLA 170 *****986 PP >> RecR RecR protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 55.2 4.4 8.1e-19 3.4e-15 1 40 [] 38 77 .. 38 77 .. 0.97 Alignments for each domain: == domain 1 score: 55.2 bits; conditional E-value: 8.1e-19 HHHHHHHHHHHHHHH-EE-TTT--EESSSS-CCCCSTTSE CS RecR 1 eaeeLaeaLqeakekvrhCsrCgnlteedlCaICsdprRD 40 +++++aeaL ++k++v+ C +Cgn++e+d C+ICsd+ RD 23726_FusoPortal_Gene_1959 38 DVKNFAEALLAVKKNVKKCHICGNYCESDTCHICSDNARD 77 5899***********************************9 PP >> Toprim Toprim domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.1 0.0 0.5 2.1e+03 31 60 .. 30 46 .. 12 73 .. 0.58 2 ! 29.2 0.1 1.8e-10 7.6e-07 2 96 .. 81 162 .. 80 171 .. 0.76 Alignments for each domain: == domain 1 score: -1.1 bits; conditional E-value: 0.5 SSEEECSTTEEEEEEETTTHHHHHHHHHHH CS Toprim 31 hildletefkpvyeeiedkkkvlkalkela 60 hil++ + + +k ++e + 23726_FusoPortal_Gene_1959 30 HILNQSE-------------EDVKNFAEAL 46 4444444.............2222222222 PP == domain 2 score: 29.2 bits; conditional E-value: 1.8e-10 EEEESSHHHHHHHHTTCCSTCEEEEEESSSSEEECSTTEEEEEEETTTHHHHHHHHHHH..HHHSEEEEES-SSHHHHHHHHH CS Toprim 2 lvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkela..kradeiilatDpDreGeaiawe 82 +++vE +d + ++++ ++ v+++l ld + i +++ ++k+l e+ + +eiilat+p eGe++a++ 23726_FusoPortal_Gene_1959 81 ICVVEESKDIMILERT--TKYRGVYHVLNGRLDPLN-------GITPNELNIKSLLERIakDDIEEIILATNPNIEGETTAMY 154 79**************..566677777666666666.......6778888888866666255556****************** PP HHHHHTCHHTTCEE CS Toprim 83 llevlkellenkig 96 l++++k n + 23726_FusoPortal_Gene_1959 155 LAKLMK----N--F 162 **5554....4..3 PP >> Memo Memo-like protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 8.4 0.5 0.00024 1 201 246 .. 121 167 .. 28 172 .. 0.61 Alignments for each domain: == domain 1 score: 8.4 bits; conditional E-value: 0.00024 Memo 201 evika.leelneeelkeylektnnticGekpiavilkalkklgakka 246 ik le+ +++++e + tn i Ge + + + k++k++g+k 23726_FusoPortal_Gene_1959 121 LNIKSlLERIAKDDIEEIILATNPNIEGETTAMYLAKLMKNFGIKIT 167 34444045558899999999999999999999999999999997544 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (198 residues searched) Target model(s): 16712 (2907032 nodes) Passed MSV filter: 996 (0.0595979); expected 334.2 (0.02) Passed bias filter: 603 (0.0360819); expected 334.2 (0.02) Passed Vit filter: 58 (0.00347056); 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: 0.24u 0.23s 00:00:00.47 Elapsed: 00:00:00.30 # Mc/sec: 1918.64 // [ok]