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 WP_023430731.1 N177_RS02905 branched-chain amino acid ABC transporter substrate-binding protein
Query= TCDB::Q9L3M3 (381 letters) >NCBI__GCF_000496075.1:WP_023430731.1 Length = 375 Score = 133 bits (334), Expect = 9e-36 Identities = 112/350 (32%), Positives = 163/350 (46%), Gaps = 9/350 (2%) Query: 6 LSAVALTAMLAF-SGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGINGE 64 ++A+AL A++A + +A V I GPL+G N+ G + G + A NA + G Sbjct: 13 VAAIALAAVVATGAADAQETVKIGFIGPLSGGNSQQGLTARNGFQLAIDQANAREDL-GF 71 Query: 65 QIKIELGDDVSDPKQGISVANKFAAD-GVKFVIGHFNSGVSIPASEVYAENGILRNHPGR 123 +I+ + DD S+P+ G+S A K D V V GH+NS V++ + V GI G Sbjct: 72 KIEGVIQDDASNPQTGVSAALKLTNDPAVIAVTGHWNSPVALATAPVITRAGIPFVIWGA 131 Query: 124 DEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKKA 183 P + T R + A+ IA+V D + YG +K Sbjct: 132 ISPKITETNNPLLARVVPTLVNTNEPLAAWAAEEIGQ-NIAIVSDTSDYGMANVAAFRKP 190 Query: 184 MNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKAT 243 AG T E VG DF A + K+K IY+GG+ TEAGL+ +Q + GL Sbjct: 191 FEEAGGTITSVETAPVGTTDFRATLTKIKSDNPDAIYFGGVVTEAGLVRQQMKEVGLDVP 250 Query: 244 LVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPE--AYTLYS 301 ++ DG E IAGDA GT++ + T N E+ E + AAGF YT + Sbjct: 251 MIGVDGFHDPEFIKIAGDAAEGTISGIMKE-TENEKLVEMNEAYAAAGFAEPVGTYTKNA 309 Query: 302 YAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIP 351 Y A I A + AG+ D AV +A++ + +G SFDE G K+P Sbjct: 310 YDAANIIIAAIEEAGT-DRAAVGEAIRAM-EYDGAMGHTSFDENGQTKLP 357 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: 336 Number of extensions: 17 Number of successful extensions: 5 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 24 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