# 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_1665.faa # target HMM database: Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 23726_FusoPortal_Gene_1665 [L=235] Description: # 1784968 # 1785672 # 1 # ID=1_1665;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.264 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-40 137.5 0.2 5.1e-40 137.3 0.2 1.0 1 ThiF ThiF family ------ inclusion threshold ------ 0.027 14.4 0.7 0.32 11.0 0.1 2.2 2 Shikimate_DH Shikimate / quinate 5-dehydrogenase 0.071 13.5 0.9 0.96 9.8 0.9 2.3 1 NAD_binding_7 Putative NAD(P)-binding Domain annotation for each model (and alignments): >> ThiF ThiF family # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 137.3 0.2 9.2e-44 5.1e-40 7 208 .. 9 231 .. 3 234 .. 0.80 Alignments for each domain: == domain 1 score: 137.3 bits; conditional E-value: 9.2e-44 HHHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGCCTBTTS-GGGTTSBHHHHHHHHHHHT-TTSE CS xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF ThiF 7 llgedgqeklrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaealqeinpdve 89 l+++ + ekl++s v + G+Gg+G ++L+++G+g+l +vD+D+i+++NlnRq++ +++ iGkpK++va++++ +inp+++ 23726_FusoPortal_Gene_1665 9 LISSNNVEKLKNSNVIVFGLGGVGGATVEALVRAGIGNLSIVDFDTIDKTNLNRQIITTQSVIGKPKVDVAKDRILSINPNIN 91 4677999**************************************************************************** PP EEEEES-CCGCCS-HHHHTT-..SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEE....EECCS-ECTSS-.. CS xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxx.. RF ThiF 90 veayteritdetvleellesv..DlVvdalDniearrlvnracvkkgiplieagtlgfkgqvvvi....ipgktgcyeCld.. 164 ++ y+e++ +e+ + ++++ D++vda+D ++a++ + +++ +++ip+i+ + g k + + i++++ c 23726_FusoPortal_Gene_1665 92 LTIYNEKFLKEK-IDLFFKDKkyDYIVDAIDLVTAKLDLIEFATNSKIPIISCMGTGNKLNPAQFkvvdINKTSVCPLAKIir 173 ********9987.4678875444*****************************8888888777777432333566666666533 PP .........TGGS.EECCCCEEHHH..................HHHCTE-B-HHHHHHHHHHHHHHHHHHH CS .........xxxxxxxxxxxxxxxx..................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF ThiF 165 .........psstedptekkvplct..................siagnipaiatttavvaglaalellkll 208 + + a+n+ i++++ v+++l+a e++k + 23726_FusoPortal_Gene_1665 174 kelkkrrinK----------L---KvvysdetprkplnldgdrEKAKNVGSISFVPPVAGMLLASEVIKDI 231 3332222220..........2...122355566666666666644555669*****************966 PP >> Shikimate_DH Shikimate / quinate 5-dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.0 0.1 5.7e-05 0.32 5 43 .. 13 51 .. 9 80 .. 0.87 2 ? 1.8 0.0 0.038 2.1e+02 66 99 .. 117 150 .. 86 163 .. 0.73 Alignments for each domain: == domain 1 score: 11.0 bits; conditional E-value: 5.7e-05 HHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEE CS Shikimate_DH 5 kkleslkekkvlliGaGemaelvakhLlakgvkkvvvaN 43 +++e+lk+++v++ G G ++ ++++L+++g+ ++ ++ 23726_FusoPortal_Gene_1665 13 NNVEKLKNSNVIVFGLGGVGGATVEALVRAGIGNLSIVD 51 67899****************************999986 PP == domain 2 score: 1.8 bits; conditional E-value: 0.038 GCGHHHHHHT-SEEEE-SSSSS-SB-HHHHHCCH CS Shikimate_DH 66 leelkellaeadvvisataseepilekeeveeal 99 ++ ++ + a+ d++ at+s+ pi++ + l 23726_FusoPortal_Gene_1665 117 VDAIDLVTAKLDLIEFATNSKIPIISCMGTGNKL 150 45666777899*************9876655555 PP >> NAD_binding_7 Putative NAD(P)-binding # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 9.8 0.9 0.00017 0.96 4 46 .. 17 74 .. 15 138 .. 0.62 Alignments for each domain: == domain 1 score: 9.8 bits; conditional E-value: 0.00017 NAD_binding_7 4 dlkgkkvlvvGgGevAarkvrklleag.akvtvvapevkeele..............e 46 +lk+ +v+v+G G v+ v+ l++ag ++ +v+ ++ ++++ 23726_FusoPortal_Gene_1665 17 KLKNSNVIVFGLGGVGGATVEALVRAGiGNLSIVDFDTIDKTNlnrqiittqsvigkP 74 68999*********************96688888877422222333333343344441 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (235 residues searched) Target model(s): 16712 (2907032 nodes) Passed MSV filter: 559 (0.033449); expected 334.2 (0.02) Passed bias filter: 382 (0.0228578); expected 334.2 (0.02) Passed Vit filter: 32 (0.00191479); expected 16.7 (0.001) Passed Fwd filter: 3 (0.000179512); expected 0.2 (1e-05) Initial search space (Z): 16712 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.24u 0.23s 00:00:00.47 Elapsed: 00:00:00.31 # Mc/sec: 2203.72 // [ok]