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 WP_029133947.1 A3GO_RS0114160 branched-chain amino acid ABC transporter substrate-binding protein
Query= TCDB::Q9L3M3 (381 letters) >NCBI__GCF_000428045.1:WP_029133947.1 Length = 375 Score = 199 bits (507), Expect = 8e-56 Identities = 119/361 (32%), Positives = 190/361 (52%), Gaps = 5/361 (1%) Query: 1 MKKSLLSAVALTAMLAFSGNAWADVL-IAVAGPLTGPNAAFGAQLQKGAEQAAADINAAG 59 +KK L + V L+ + A D + + VAG +G A++G A+ AD+NA G Sbjct: 6 VKKLLAATVGLSLAIPTMAIAADDTIKLGVAGAHSGDLASYGLPTVNAAKLVVADVNARG 65 Query: 60 GINGEQIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRN 119 GING+Q+++ + DDV P+ + A K + GV V+GH SG + A +Y G++ Sbjct: 66 GINGKQVELLVEDDVCKPEVATNTATKLVSSGVHVVLGHICSGATKAALPIYKNAGVIVM 125 Query: 120 HPGRDEPDLHGTGLW-NTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLAD 178 P P+L +G + N FRT DD Q + D+ KIAV+HDK YG+GLA+ Sbjct: 126 SPSATNPELTQSGDYPNFFRTIASDDAQAKTQVDFALDNRNLKKIAVIHDKGDYGKGLAE 185 Query: 179 ETKKAMNAAGVTEVI-YEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAAD 237 K+ + +G EV+ +EG+ G D+SA++ K+K +G + +GG H EA I+ Q Sbjct: 186 FAKQFIEKSGNAEVVLFEGVTPGAVDYSAVVQKIKRSGADGVIYGGYHPEASKIVTQMRK 245 Query: 238 QGLKATLVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAA-GFNPEA 296 + + +SGDG+ + +AG + G T D ++NP +E K G +P A Sbjct: 246 KRIDIDFISGDGVKDDTFIKVAGKSAEGVYATGAKDNSSNPLYTAAIEAHKKTYGEDPGA 305 Query: 297 YTLYSYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMY 356 + ++AA + A + AGS D A+ A+ + T +G+I FDE+GD G+ +Y Sbjct: 306 FFDSAHAAAAALLNAVEKAGSTDTAAITNAL-QANDVATTVGNIHFDERGDAVGVGFAVY 364 Query: 357 E 357 + Sbjct: 365 Q 365 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: 369 Number of extensions: 22 Number of successful extensions: 4 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: 375 Length adjustment: 30 Effective length of query: 351 Effective length of database: 345 Effective search space: 121095 Effective search space used: 121095 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 24 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