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_068001888.1 PsAD2_RS02810 branched-chain amino acid ABC transporter substrate-binding protein
Query= TCDB::Q9L3M3 (381 letters) >NCBI__GCF_001623255.1:WP_068001888.1 Length = 366 Score = 380 bits (976), Expect = e-110 Identities = 197/363 (54%), Positives = 249/363 (68%), Gaps = 8/363 (2%) Query: 1 MKKSLLSAVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGG 60 MKK LL++VA A +A SG A AD+++ AGP+TG A+FGAQ++ GAEQA ADINAAGG Sbjct: 1 MKKYLLASVAGVAAMAISGAAMADIIVGTAGPMTGQYASFGAQMKAGAEQAVADINAAGG 60 Query: 61 INGEQIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNH 120 +NGE + +E+GDD DPKQ ++VAN+ V F+ GHF SG SIPAS+VYAE GI++ Sbjct: 61 VNGEMLVLEVGDDACDPKQAVAVANQMVGKNVAFMAGHFCSGSSIPASQVYAEEGIIQIT 120 Query: 121 PGRDEP----DLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGL 176 P P + G G TFR CGRDDQQG +AG LA F D IAV+HDKT YG+GL Sbjct: 121 PASTNPKYTDERAGPG---TFRVCGRDDQQGRVAGTTLATEFGDKNIAVIHDKTAYGKGL 177 Query: 177 ADETKKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAA 236 AD TK MNAAG E +YE G+KD++AL++K+K V ++Y GG HTEAGL+ RQ Sbjct: 178 ADATKAVMNAAGKEEALYEAYTAGEKDYTALVSKLKSEKVDVLYVGGYHTEAGLMKRQMV 237 Query: 237 DQGLKATLVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEA 296 DQG+ LVSGD +V++E SI G A AGTL TF PDP +N +V +AAG E Sbjct: 238 DQGMDTILVSGDALVTDEYWSITGPAGAGTLMTFPPDPRSNEEAAAVVAALEAAGKTTEG 297 Query: 297 YTLYSYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMY 356 Y LY+YAA+QT A AA AAGS D + V + + + F TVLG++SFDEKGD +PGY+ Y Sbjct: 298 YALYTYAAIQTWAKAAAAAGSTDYDTVVEKLNSE-KFDTVLGELSFDEKGDVTLPGYVWY 356 Query: 357 EWK 359 EWK Sbjct: 357 EWK 359 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: 469 Number of extensions: 25 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: 366 Length adjustment: 30 Effective length of query: 351 Effective length of database: 336 Effective search space: 117936 Effective search space used: 117936 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