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_088755389.1 CEJ45_RS12295 branched-chain amino acid ABC transporter substrate-binding protein
Query= TCDB::Q9L3M3 (381 letters) >NCBI__GCF_002213425.1:WP_088755389.1 Length = 381 Score = 211 bits (536), Expect = 4e-59 Identities = 135/370 (36%), Positives = 194/370 (52%), Gaps = 17/370 (4%) Query: 3 KSLLSAVALTAMLAFSGNAWADVLIAVA--GPLTGPNAAFGAQLQKGAEQAAADINAAG- 59 K + A AL A +F+G A A +I + PLTGPNA G + GA A ++NA G Sbjct: 5 KMIPVATALVAAFSFAGAAQAQEVIKIGHVAPLTGPNAHIGKDNENGARMAVDELNAKGF 64 Query: 60 GINGEQIKIEL--GDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGIL 117 I G+++ +L DD SDPKQ +VA VK V+GH NSG +IPAS++Y + GI Sbjct: 65 EIGGKKVTFQLVPQDDASDPKQATTVAQALVDAKVKGVVGHMNSGTTIPASKIYYDAGIP 124 Query: 118 RNHPGRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLA 177 + P P G FR D Q G + G+Y + K +AV+ D+T YGQG+A Sbjct: 125 QISPSATNPKYTQQGFNTAFRVVANDGQLGGVLGRYAVNELKGKNVAVIDDRTAYGQGVA 184 Query: 178 DETKKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAAD 237 +E +K+ AAG T V + DF+A++ +K ++++GG+ AG ++RQ Sbjct: 185 EEFRKSALAAGATIVATQYTTDKATDFNAILTSVKSKKPDLVFFGGMDAVAGPMLRQMDQ 244 Query: 238 QGLKATLVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAA---GFNP 294 G+ A + GDGI + EL S+AG + + A K+ +E FKAA FN Sbjct: 245 LGVAAKFMGGDGICTTELPSLAGAGLKDSEVVCAEAGGVTEAGKKPLEDFKAAYKKKFNQ 304 Query: 295 EA--YTLYSYAAMQTIAGAAKAAGSLDPEA---VAKAMKEKGPFPTVLGDISFDEKGDPK 349 + Y Y+Y A+ T+A A K AGS DP+ V +K KG V G+I+FD KGD Sbjct: 305 DVVIYAPYTYDALMTLADAMKQAGSSDPKVYLPVLAKIKHKG----VTGEIAFDAKGDIL 360 Query: 350 IPGYIMYEWK 359 +Y +K Sbjct: 361 NGTLTLYTYK 370 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: 378 Number of extensions: 23 Number of successful extensions: 4 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: 381 Length adjustment: 30 Effective length of query: 351 Effective length of database: 351 Effective search space: 123201 Effective search space used: 123201 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