Align ABC transporter substrate-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 8500416 DvMF_1166 Extracellular ligand-binding receptor (RefSeq)
Query= TCDB::Q8DQI1 (386 letters) >FitnessBrowser__Miya:8500416 Length = 387 Score = 179 bits (455), Expect = 9e-50 Identities = 115/373 (30%), Positives = 188/373 (50%), Gaps = 20/373 (5%) Query: 32 AGNSVEEKTIKIGFNFEESGSLAAYGTAEQKGAQLAVDEINAAGGID--GKQ--IEVVDK 87 +G + TIK+GF +G + G A + A++ +EIN GG+D GK+ +E V + Sbjct: 16 SGQAFAADTIKLGFVIPLTGDIPKVGEASKFAAEMLREEINGKGGLDVGGKKYKLEFVFE 75 Query: 88 DNKSETAEAASVTTNLVTQSKVSAVVGPATSGATAAAVANATKAGVPLISPSATQDGLTK 147 DN+++ A + ++ + +V AVVGP +S A A P+ISP +T TK Sbjct: 76 DNEAKPESAVNAMLKVIERDQVLAVVGPQSSKQAVPAGGVANDNETPMISPWSTNPDTTK 135 Query: 148 GQDYLFIGTFQDSFQGKIISNYVSEKLNAKKVVLYTDNASDYAKGIAKSFRESYK----- 202 G+ ++F F D FQ +++N+ +++ AKK + D ++DY+KG+A+ F+ ++ Sbjct: 136 GRPWVFRAAFLDPFQAPVVANFATKQFKAKKAAVLFDISNDYSKGLAEFFKAEWEKMHGA 195 Query: 203 GEIVADETFVAGDTDFQAALTKMKGKDFDAIVVPGYYNEAGKIVNQARGMGIDKPIVGGD 262 G +V E+ D DF A LTK+ D I +P YN IV QAR +G P +G D Sbjct: 196 GSVVGMESHGTKDQDFSAQLTKVVAAKPDFIFLPENYNIVALIVKQARDLGYKGPFMGSD 255 Query: 263 GFNGEEFVQQATAEKASNIYFISGFSTTVEVSAKAKAFLDAYRAKYNEEPSTFAALAYDS 322 + E + E YF + ++ A K F+D Y KY P AAL +D+ Sbjct: 256 AWGSAELMDLCGKECVGQ-YFSTHYAAAGATGA-TKEFIDKYNNKYGYIPDDVAALTWDA 313 Query: 323 VHLVANAAKGA--------KNSGEIKNNLAKTKDFEGVTGQTSFDADHNTVKTAYMMTMN 374 LV A + K +++ + K F+G+TG+ SFD + + +K A ++ ++ Sbjct: 314 TRLVLQAIQSVGKVDSDTRKMRKAVRDAMVNIKSFDGITGKMSFDENRDPIKCAVVVKIS 373 Query: 375 -NGKVEAAEVVKP 386 G+ AE V P Sbjct: 374 EKGEFTFAESVCP 386 Lambda K H 0.310 0.126 0.337 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 327 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 386 Length of database: 387 Length adjustment: 30 Effective length of query: 356 Effective length of database: 357 Effective search space: 127092 Effective search space used: 127092 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory