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 8502037 DvMF_2750 Extracellular ligand-binding receptor (RefSeq)
Query= TCDB::Q9L3M3 (381 letters) >FitnessBrowser__Miya:8502037 Length = 375 Score = 181 bits (458), Expect = 4e-50 Identities = 118/362 (32%), Positives = 188/362 (51%), Gaps = 10/362 (2%) Query: 3 KSLLSAVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGIN 62 K+L A+A + ++A + A A V I + PLTG A+ G ++ A ++N AGGIN Sbjct: 6 KALTLALAASLLMAATAFA-APVKIGLMCPLTGKWASEGQDMRNIVTLLADELNKAGGIN 64 Query: 63 GEQIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPG 122 G ++++ + DD DP+ A K GV IG + S V+ + +Y E G+++ G Sbjct: 65 GNKVELVVEDDGGDPRTAALAAQKLTTSGVIAAIGTYGSAVTEASQSIYDEAGVVQIATG 124 Query: 123 RDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYL-ADHFKDAKIAVVHDKTPYGQGLADETK 181 L GL RT RDD+QG +A K + A +K +A++HD + Y +GLADETK Sbjct: 125 STAVRLTEKGLKRFLRTAPRDDEQGMVAAKLIKAKGYK--AVALLHDNSSYAKGLADETK 182 Query: 182 KAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLK 241 ++ AG V Y+ + G++D++A++ K+K A II+ G + E G+++RQ + Sbjct: 183 ALLDKAGTKIVFYDALTPGERDYTAILTKLKAANPDIIFCTGYYPEVGMLLRQKMEMKWN 242 Query: 242 ATLVSGDGIVSNELASIAGDAVAG---TLNTFGPDPTANPANKELVEKFKAA--GFNPEA 296 ++ GD +L I+G A L+ GP PA K ++ +KA G Sbjct: 243 VPMMGGDAANHADLVKISGKEAAKGYFFLSPPGPQDLDAPAAKSMLTAYKAKYNGVPGSV 302 Query: 297 YTLYSYAAMQTIAGAAKAAGSLDPEAVAKAMKEK-GPFPTVLGDISFDEKGDPKIPGYIM 355 +++ + A I A K+ G D A+A+ +K K +P G ISF+EKGD Y + Sbjct: 303 WSVLAGDAFNVIVEAVKSTGKADSGAIAEYLKTKLKNYPGFTGQISFNEKGDRVGDLYRV 362 Query: 356 YE 357 YE Sbjct: 363 YE 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: 356 Number of extensions: 18 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