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 209486 DVU0547 high-affinity branched chain amino acid ABC transporter, periplasmic branched chain amino acid-binding protein
Query= TCDB::Q9L3M3 (381 letters) >MicrobesOnline__882:209486 Length = 372 Score = 176 bits (445), Expect = 1e-48 Identities = 111/354 (31%), Positives = 175/354 (49%), Gaps = 7/354 (1%) Query: 9 VALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGINGEQIKI 68 VA+ A F+G+ + + V G +G A++G A+ A N GGING+ +++ Sbjct: 15 VAVMAGPVFAGDT---IKLGVPGAHSGDLASYGLPSANAAKIVAKMFNDKGGINGKMVEV 71 Query: 69 ELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPGRDEPDL 128 DD P+ + A K +DGV V+GH SG + A +Y E + P P L Sbjct: 72 IPQDDQCKPEMATNAATKLVSDGVDIVLGHICSGATKAALPIYKEANKVVMSPSATTPAL 131 Query: 129 HGTGLWNT-FRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKKAMNAA 187 +G + FRT DDQQ + + D KIAV+HDK YG+G A+ K+ + + Sbjct: 132 TQSGDYPMFFRTISSDDQQAKLGVDFAIDKLGAKKIAVLHDKGDYGKGYAEYAKQFIEQS 191 Query: 188 G-VTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKATLVS 246 G T V++EG+ G D+SA++ K++ G + +GG H EA I+ Q + + +S Sbjct: 192 GKATVVLFEGVTPGAVDYSAVVQKVRSEGADAVMFGGYHPEASKIVAQMRKKRMTTPFIS 251 Query: 247 GDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAA-GFNPEAYTLYSYAAM 305 DG+ + +AG G + D + P KE +E K G P A+ ++AA Sbjct: 252 DDGVKDDTFIKVAGKDAEGVYASSSKDVSMLPMYKEAIELHKKEFGTEPGAFYKEAFAAA 311 Query: 306 QTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEWK 359 Q + A + AGS + V A++ T +G I FD++GD + G+ MY+ K Sbjct: 312 QALLTAVQRAGSTETPKVVDALRNNF-VETAIGKIKFDKRGDAEGTGFSMYQVK 364 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: 374 Number of extensions: 32 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: 381 Length of database: 372 Length adjustment: 30 Effective length of query: 351 Effective length of database: 342 Effective search space: 120042 Effective search space used: 120042 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