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 1937025 b3460 leucine/isoleucine/valine transporter subunit (NCBI)
Query= TCDB::Q9L3M3 (381 letters) >FitnessBrowser__Keio:1937025 Length = 367 Score = 258 bits (658), Expect = 2e-73 Identities = 144/355 (40%), Positives = 207/355 (58%), Gaps = 5/355 (1%) Query: 15 LAFSGNAWA-DVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGINGEQIKIELGDD 73 LAFS A A D+ +AV G ++GP A +G Q GAEQA ADINA GGI G +++I DD Sbjct: 15 LAFSNMALAEDIKVAVVGAMSGPVAQYGDQEFTGAEQAVADINAKGGIKGNKLQIVKYDD 74 Query: 74 VSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPGRDEPDLHGTGL 133 DPKQ ++VANK DG+K+VIGH S + PAS++Y + GIL P P+L G Sbjct: 75 ACDPKQAVAVANKVVNDGIKYVIGHLCSSSTQPASDIYEDEGILMITPAATAPELTARGY 134 Query: 134 WNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKKAMNAAGVTEVI 193 RT G D QG A KY+ + K +IA+VHDK YG+GLA + + V Sbjct: 135 QLILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGEGLARAVQDGLKKGNANVVF 194 Query: 194 YEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKATLVSGDGIVSN 253 ++GI G+KDFS L+A++K+ + +Y+GG H E G I+RQA GLK + +G+ + Sbjct: 195 FDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQARAAGLKTQFMGPEGVANV 254 Query: 254 ELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPE-AYTLYSYAAMQTIAGAA 312 L++IAG++ G L T + PANK +V+ KA +P A+ +YAA+Q++ Sbjct: 255 SLSNIAGESAEGLLVTKPKNYDQVPANKPIVDAIKAKKQDPSGAFVWTTYAALQSLQAGL 314 Query: 313 KAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEWKKVRTASTA 367 S DP +AK +K TV+G +++DEKGD K + +++W TA+ A Sbjct: 315 NQ--SDDPAEIAKYLKANS-VDTVMGPLTWDEKGDLKGFEFGVFDWHANGTATDA 366 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: 405 Number of extensions: 17 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: 367 Length adjustment: 30 Effective length of query: 351 Effective length of database: 337 Effective search space: 118287 Effective search space used: 118287 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