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 GFF1302 PS417_06615 leucine ABC transporter substrate-binding protein
Query= TCDB::Q9L3M3 (381 letters) >FitnessBrowser__WCS417:GFF1302 Length = 375 Score = 281 bits (718), Expect = 3e-80 Identities = 147/359 (40%), Positives = 215/359 (59%), Gaps = 4/359 (1%) Query: 3 KSLLSAVALTAMLAFSGNAWA--DVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGG 60 K + A + +G+++A + I +AGP TGP +G GA+QA ADINA GG Sbjct: 6 KQISKLFAAMVLAGVAGHSFAADTIKIGIAGPKTGPVTQYGDMQFMGAKQAIADINAKGG 65 Query: 61 INGEQIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNH 120 ++G+ ++ + DD DPKQ ++VANK DGVKFV+GH S + PAS++Y + G++ Sbjct: 66 VDGKMLEAKEYDDACDPKQAVAVANKVVNDGVKFVVGHLCSSSTQPASDIYEDEGVIMIT 125 Query: 121 PGRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADET 180 P P++ G FRT G D QG AG Y+ADH K +AV+HDK YG+G+A Sbjct: 126 PAATSPEITARGYKLIFRTIGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGEGIATAV 185 Query: 181 KKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGL 240 K+ + G ++EG+N GDKDFS++I K+K+A V +Y+GG H E GLI+RQA ++GL Sbjct: 186 KQTLEKKGTKVAVFEGLNAGDKDFSSIIQKLKQANVDFVYYGGYHPELGLILRQAKEKGL 245 Query: 241 KATLVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEA-YTL 299 A + +G+ ++ ++ IA A G L T +PANK +VE+F +P + Sbjct: 246 NAKFMGPEGVGNDSISQIAQGASEGLLVTLPKSFDTDPANKAIVEEFAKNKQDPTGPFVF 305 Query: 300 YSYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEW 358 +Y+A++ IAG KAA S D VA+A+ G F T GD+SFD KGD K +++YEW Sbjct: 306 PAYSAIEVIAGGIKAAKSEDTAKVAEAI-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: 466 Number of extensions: 28 Number of successful extensions: 3 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