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 206137 DVU0712 amino acid ABC transporter, periplasmic-binding protein
Query= TCDB::Q9L3M3 (381 letters) >MicrobesOnline__882:206137 Length = 376 Score = 172 bits (437), Expect = 1e-47 Identities = 114/360 (31%), Positives = 181/360 (50%), Gaps = 9/360 (2%) Query: 6 LSAVALTAMLAFSGNAWA--DVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGING 63 L AV + L + A+A V + + PLTG A+ G ++ E A ++N AGGING Sbjct: 7 LLAVCMVTSLLMAATAFAAGPVRVGLMCPLTGKWASEGQDMRNIVELLAEEVNKAGGING 66 Query: 64 EQIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPGR 123 ++++ + DD DP+ A K + GV VIG + S V+ + +Y E GI + G Sbjct: 67 NKVELIVEDDGGDPRTAALAAQKLSTSGVTAVIGTYGSAVTEASQNIYDEAGIAQIATGS 126 Query: 124 DEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKKA 183 L GL RTC RDD+QG +A K + + A +A++HD + Y +GLADETK Sbjct: 127 TNVRLTEKGLKLFLRTCPRDDEQGRVAAKVIKNKGYKA-VALLHDNSSYAKGLADETKAL 185 Query: 184 MNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKAT 243 ++ G V Y+ + G++D++A++ K+K A II++ G + E G+++RQ + Sbjct: 186 LDKDGTKIVFYDALTPGERDYTAILTKLKAANPDIIFFTGYYPEVGMLLRQKMEMKWNVP 245 Query: 244 LVSGDGIVSNELASIAGDAVA-GTLNTFGPDP----TANPANKELVEKFKAAGFNPEAYT 298 ++ GD + +L IAG A A G P P TA K K ++ Sbjct: 246 MMGGDAANNLDLVKIAGKAAAKGYFFLSPPVPQDFDTAEAKAFLAAYKAKHNALPNSVWS 305 Query: 299 LYSYAAMQTIAGAAKAAGSLDPEAVAKAMK-EKGPFPTVLGDISFDEKGDPKIPGYIMYE 357 + + A + I A + G D +A +K + +P + G ISF+EKGD Y +Y+ Sbjct: 306 VLAGDAFKVIVEAVQKGGKADGAGIATYLKTQLKNYPGLSGQISFNEKGDRVGDLYRVYD 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: 351 Number of extensions: 16 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: 376 Length adjustment: 30 Effective length of query: 351 Effective length of database: 346 Effective search space: 121446 Effective search space used: 121446 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