Align BraC, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC (characterized)
to candidate BWI76_RS26350 BWI76_RS26350 branched chain amino acid ABC transporter substrate-binding protein
Query= TCDB::Q9L3M3 (381 letters) >FitnessBrowser__Koxy:BWI76_RS26350 Length = 369 Score = 259 bits (663), Expect = 6e-74 Identities = 141/360 (39%), Positives = 212/360 (58%), Gaps = 3/360 (0%) Query: 1 MKKSLLSAVALTAMLAFSGNAWA-DVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAG 59 MK++ + +A LA S A+A D+ +AV G ++GP A +G GA QA DINA G Sbjct: 1 MKRNAKTVIAGLVALAMSQAAFAKDIKVAVVGAMSGPVAQWGDMEFNGARQAIKDINAQG 60 Query: 60 GINGEQIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRN 119 GI G+++ DD DPKQ ++VANK DG+++VIGH S + PAS++Y + GIL Sbjct: 61 GIKGDKLVAVEYDDACDPKQAVAVANKIVNDGIQYVIGHLCSSSTQPASDIYEDEGILMI 120 Query: 120 HPGRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADE 179 PG P+L G RT G D QG A KY+ + K +IA++HDK YG+GLA Sbjct: 121 SPGATNPELTQRGYQYIMRTAGLDSSQGPTAAKYIMETVKPQRIAIIHDKQQYGEGLARS 180 Query: 180 TKKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQG 239 ++++ G V ++GI G+KDFSAL+A++K+ + +Y+GG + E G ++RQA G Sbjct: 181 VQESLKKGGANIVFFDGITAGEKDFSALLARLKKENIDFVYYGGYYPEMGQMLRQARSVG 240 Query: 240 LKATLVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEA-YT 298 LK + +G+ + L++IAGDA G L T +PAN +V+ KA +P Y Sbjct: 241 LKTVFMGPEGVGNASLSNIAGDAAEGMLVTMPKRYDQDPANSAIVDALKAEKKDPSGPYV 300 Query: 299 LYSYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEW 358 +YAA+Q++A A A S +P + K +K G TV+G +++DEKGD K + +++W Sbjct: 301 WITYAAVQSLAQAMDRAASQEPLDLIKDLKAHGA-KTVIGPLNWDEKGDLKGFEFGVFQW 359 Lambda K H 0.314 0.132 0.383 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: 391 Number of extensions: 20 Number of successful extensions: 2 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: 381 Length of database: 369 Length adjustment: 30 Effective length of query: 351 Effective length of database: 339 Effective search space: 118989 Effective search space used: 118989 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 (22.0 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