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_088754101.1 CEJ45_RS04945 branched-chain amino acid ABC transporter substrate-binding protein
Query= TCDB::Q9L3M3 (381 letters) >NCBI__GCF_002213425.1:WP_088754101.1 Length = 373 Score = 284 bits (727), Expect = 2e-81 Identities = 155/363 (42%), Positives = 222/363 (61%), Gaps = 4/363 (1%) Query: 8 AVALTAMLAFSGNAWAD-VLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGINGEQI 66 A+A AF+G A A+ V IA+AGPLTG A +G ++ GA A INAAGG NG + Sbjct: 11 ALAAATFAAFAGVAHAETVKIAIAGPLTGAVAQYGDMVKAGALTAIEQINAAGGANGNKF 70 Query: 67 KIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPGRDEP 126 + + DD +PKQ ++VANK + G+K+VIGH SG +IPAS++Y G++ P P Sbjct: 71 EAVMMDDACEPKQAVAVANKIVSQGIKYVIGHVCSGSTIPASDIYENEGVVMITPSATAP 130 Query: 127 DLHGTGLWN-TFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKKAMN 185 L FRT GRDDQQG A +Y+ + K K+AV+HDK YGQG+A K A++ Sbjct: 131 QLTEAKPHKFIFRTIGRDDQQGPAAARYVIEKLKPKKVAVLHDKQSYGQGVASSVKSALD 190 Query: 186 AAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKATLV 245 AA V V++EGIN GD D+SA++ K+K GV +Y+GG H E GLI+RQA +QG+KA + Sbjct: 191 AAKVPVVVFEGINAGDSDYSAIVTKLKSQGVDFVYFGGYHPEMGLIMRQAREQGVKAVFM 250 Query: 246 SGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEA-YTLYSYAA 304 +G+ + ++ +IAG A G L T D A+PAN LV+ F AA + + + +Y+A Sbjct: 251 GPEGVGNKDITAIAGPASEGMLVTLPADFAADPANAALVKAFAAAKRDANGPFQMPAYSA 310 Query: 305 MQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEWKKVRTA 364 ++ IA A A S DP+ VA A F T +G++ +D+KGD K ++++ W K T Sbjct: 311 VKIIADAITGAKSTDPDKVA-AYIHGNSFKTPIGNVEYDKKGDLKAFKFVVFTWHKDATK 369 Query: 365 STA 367 + A Sbjct: 370 TEA 372 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: 487 Number of extensions: 26 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: 373 Length adjustment: 30 Effective length of query: 351 Effective length of database: 343 Effective search space: 120393 Effective search space used: 120393 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