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 GFF1279 Psest_1312 ABC-type branched-chain amino acid transport systems, periplasmic component
Query= TCDB::Q9L3M3 (381 letters) >FitnessBrowser__psRCH2:GFF1279 Length = 372 Score = 282 bits (722), Expect = 9e-81 Identities = 153/361 (42%), Positives = 216/361 (59%), Gaps = 3/361 (0%) Query: 8 AVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGINGEQIK 67 A+ALT +++ A + I +AGP+TGP A +G GAE A IN AGG+NG Q+K Sbjct: 13 AMALTGAASYTLAA-DTIRIGLAGPVTGPVAQYGDMQFIGAEMAIEQINKAGGVNGAQLK 71 Query: 68 IELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPGRDEPD 127 DD DPKQ ++VANK D VKFV+GH S + PAS++Y + GIL PD Sbjct: 72 GVRYDDACDPKQAVAVANKIVNDNVKFVVGHLCSSSTQPASDIYEDEGILMITAASTSPD 131 Query: 128 LHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKKAMNAA 187 + G FRT G D QG AG ++ADH K +AV+HDK YG+G+A K+ + Sbjct: 132 ITSRGYELIFRTIGLDSLQGPTAGNFIADHVKPKNVAVIHDKQQYGEGIATAVKQTLEGK 191 Query: 188 GVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKATLVSG 247 + ++EGIN GDKDFS+LIAK+K GV +Y+GG H E GL++RQ+ ++GL + Sbjct: 192 NIKVGLFEGINAGDKDFSSLIAKLKREGVDFVYYGGYHPELGLLLRQSKEKGLNVRFMGP 251 Query: 248 DGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEA-YTLYSYAAMQ 306 +G+ ++E+++IAG A G T +P NKELV+ FKA +P + +YAA+Q Sbjct: 252 EGVGNSEISAIAGPASEGMYVTLPKSFDQDPRNKELVDGFKAKKQDPSGPFVFPAYAAVQ 311 Query: 307 TIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEWKKVRTAST 366 IA + AGS D + VA+A++ F T G +SFDEKGD K +++YEW + T + Sbjct: 312 VIAEGIEKAGSTDTDKVAEALR-SNTFDTPTGMLSFDEKGDLKDFNFVVYEWHQDGTKTE 370 Query: 367 A 367 A Sbjct: 371 A 371 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: 420 Number of extensions: 20 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: 372 Length adjustment: 30 Effective length of query: 351 Effective length of database: 342 Effective search space: 120042 Effective search space used: 120042 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