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 AO353_13340 AO353_13340 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q9L3M3 (381 letters) >FitnessBrowser__pseudo3_N2E3:AO353_13340 Length = 377 Score = 325 bits (832), Expect = 2e-93 Identities = 171/354 (48%), Positives = 228/354 (64%), Gaps = 4/354 (1%) Query: 8 AVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGINGEQIK 67 A+A+ A L S ADV + VAGP+TGP+A+FG Q KGA+ AA INA GGINGE+I Sbjct: 12 ALAVAAALGVSSFVQADVKLGVAGPMTGPSASFGLQYMKGAQAAADAINAKGGINGEKIV 71 Query: 68 IELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPGRDEPD 127 + GDD +PKQ ++VANK D V V+GHF S +IPASEVY++ GI+ PG P Sbjct: 72 LVQGDDACEPKQAVAVANKMVQDKVIGVVGHFCSSSTIPASEVYSDAGIIAITPGSTNPT 131 Query: 128 LHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKKAMNAA 187 + GL R CGRDDQQG +AG Y+ D K K+AV++DK YG+GLAD T K + A Sbjct: 132 VTERGLPAMMRMCGRDDQQGIVAGNYIVDVLKGKKVAVINDKDTYGKGLADATAKQLTAR 191 Query: 188 GVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLK-ATLVS 246 GV V+ EG+ G+KDFSALI K++ G ++Y+GGLH EAG ++ Q +QGLK +S Sbjct: 192 GVKPVLEEGLTRGEKDFSALITKVRSVGADVLYFGGLHPEAGPLVHQLREQGLKDVKFMS 251 Query: 247 GDGIVSNELASIAGDA--VAGTLNTFGPDPTANPANKELVEKFKAAGFNPEAYTLYSYAA 304 DGIV++E+ + AG A V G TFG DP P +K +V+ F+ +G+ PE YTLY+YA+ Sbjct: 252 DDGIVTDEMVTTAGGAPYVDGVYMTFGADPRLIPDSKAVVDTFRKSGYEPEGYTLYAYAS 311 Query: 305 MQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEW 358 +Q +A A S E AK +K P TV+G +D KGD KI Y++Y+W Sbjct: 312 VQALAAGFNGAKSNKGEEAAKWLKAH-PVETVMGKKEWDSKGDLKISDYVVYQW 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: 428 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: 377 Length adjustment: 30 Effective length of query: 351 Effective length of database: 347 Effective search space: 121797 Effective search space used: 121797 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