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 AO356_05320 AO356_05320 leucine ABC transporter substrate-binding protein
Query= TCDB::Q9L3M3 (381 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_05320 Length = 375 Score = 283 bits (723), Expect = 7e-81 Identities = 152/356 (42%), Positives = 212/356 (59%), Gaps = 2/356 (0%) Query: 4 SLLSAVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGING 63 S L A + A +A A + I +AGP TGP A +G GA+ A INA GG++G Sbjct: 9 SKLFAAMVLAGVASHSFAADTIKIGIAGPKTGPVAQYGDMQFSGAKMAIEQINAKGGVDG 68 Query: 64 EQIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPGR 123 +Q+ DD DPKQ ++VANK DGVKFV+GH S + PAS++Y + G++ P Sbjct: 69 KQLVAVEYDDACDPKQAVAVANKVVNDGVKFVVGHLCSSSTQPASDIYEDEGVIMITPAA 128 Query: 124 DEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKKA 183 PD+ G FRT G D QG AG Y+ADH K +AV+HDK YG+G+A KK Sbjct: 129 TSPDITARGYKMIFRTIGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGEGIASAVKKT 188 Query: 184 MNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKAT 243 + GV ++EG+N GDKDFS++IAK+K+A V +Y+GG H E GLI+RQ+ ++GLKA Sbjct: 189 LEGKGVKVAVFEGVNAGDKDFSSMIAKLKQANVDFVYYGGYHPELGLILRQSQEKGLKAK 248 Query: 244 LVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEA-YTLYSY 302 + +G+ ++ ++ IA ++ G L T +PAN L + FKA +P + SY Sbjct: 249 FMGPEGVGNDSISQIAKESSEGLLVTLPKSFDQDPANVALADAFKAKKEDPSGPFVFPSY 308 Query: 303 AAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEW 358 +A+ IA A KAA S D VA+A+ G F T GD+SFD KGD K +++YEW Sbjct: 309 SAVTVIADAIKAAKSEDAGKVAEAI-HAGTFKTPTGDLSFDAKGDLKDFKFVVYEW 363 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: 448 Number of extensions: 22 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: 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 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