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 Ac3H11_2396 Extracellular ligand-binding receptor precursor
Query= TCDB::Q9L3M3 (381 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2396 Length = 375 Score = 166 bits (421), Expect = 8e-46 Identities = 123/368 (33%), Positives = 175/368 (47%), Gaps = 14/368 (3%) Query: 3 KSLLSAVALTAMLAFSGNAWADVL-IAVAGPLTGPNAAFGAQLQKGAEQAAADINAAG-G 60 K L+ VA A A +A V+ I P++G A +G + GA A ++NA G Sbjct: 4 KLKLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVT 63 Query: 61 INGEQIKIEL--GDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILR 118 I G++IK EL DD +DPKQG + A K V V+GH NSG +IPAS+VY + GI Sbjct: 64 IGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPH 123 Query: 119 NHPGRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLAD 178 P+L G TFR D+ GA Y D K +A++ D+T YGQG+AD Sbjct: 124 VTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVAD 183 Query: 179 ETKKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQ 238 KK A G+ V + DF A++ +K I++GG+ + G ++RQ Sbjct: 184 VFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQL 243 Query: 239 GL-KATLVSGDGIVSNELASIAGDAVAGTLNTF-----GPDPTANPANKELVEKFKAAGF 292 G+ GDGI ++E+A +A A A TL G P K+ A Sbjct: 244 GMGNVKYFGGDGICTSEIAKLA--AGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYP 301 Query: 293 NP-EAYTLYSYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIP 351 N + Y+ Y+Y A I A K A S+DP+ + K F V I+F+ G+ K P Sbjct: 302 NQFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPEL-AKSSFKGVTSTIAFEPNGEMKNP 360 Query: 352 GYIMYEWK 359 +Y +K Sbjct: 361 AITLYVYK 368 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: 376 Number of extensions: 24 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