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 BPHYT_RS31715 BPHYT_RS31715 branched-chain amino acid ABC transporter substrate-binding protein
Query= TCDB::Q9L3M3 (381 letters) >FitnessBrowser__BFirm:BPHYT_RS31715 Length = 380 Score = 206 bits (524), Expect = 9e-58 Identities = 131/362 (36%), Positives = 186/362 (51%), Gaps = 12/362 (3%) Query: 6 LSAVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAG-GINGE 64 ++A++ AF+ + + I A P TG A G + + GA A D+N G ING+ Sbjct: 11 VAALSAACNAAFAADDITVIKIGSAAPTTGAIANLGKENENGARLAVEDVNRRGLVINGK 70 Query: 65 QIKIELG--DDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPG 122 +IK+EL DD +DP+QG VA + DGV V+GH NSGVSI AS +Y + IL+ P Sbjct: 71 KIKLELDAVDDQADPRQGTQVAQRLVDDGVVAVVGHLNSGVSIAASRIYHDAQILQISPD 130 Query: 123 RDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKK 182 P G T+R D QQ + Y + K K+A+V D T YGQGLAD+ Sbjct: 131 STNPKFTQQGFNTTYRLVATDAQQSPVLAHYALETLKAKKVAIVDDSTAYGQGLADQFSS 190 Query: 183 AMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKA 242 A+ + G T V E N DF +I K+K +I++GG+ AG I+Q A GL A Sbjct: 191 AVKSGGATVVAREATNDKTIDFKGVITKIKGQSPDVIFYGGMDATAGPFIKQVAQLGLNA 250 Query: 243 TLVSGDGIVSNELASIAGDAVAGTLNTFGPDP----TANPA-NKELVEKFKAAGFNPEAY 297 ++ GDG S+E+ ++AG AV + + P A PA KE ++F G + Y Sbjct: 251 KVLGGDGTCSDEVIALAGPAVDRLVCSIAGLPLSRMKAGPAFEKEYQQRF---GMPVQIY 307 Query: 298 TLYSYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYE 357 Y+Y A+ I A K +GS D A A + + G I FD+KGD + P +Y Sbjct: 308 APYAYDAVMVIVDAMKKSGSTD-HAKILAAASATDYQGLTGQIQFDDKGDVRSPRLTLYG 366 Query: 358 WK 359 +K Sbjct: 367 YK 368 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: 356 Number of extensions: 15 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: 380 Length adjustment: 30 Effective length of query: 351 Effective length of database: 350 Effective search space: 122850 Effective search space used: 122850 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