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_004321586.1 C665_RS15475 branched-chain amino acid ABC transporter substrate-binding protein
Query= TCDB::Q9L3M3 (381 letters) >NCBI__GCF_000310185.1:WP_004321586.1 Length = 364 Score = 337 bits (863), Expect = 4e-97 Identities = 176/359 (49%), Positives = 236/359 (65%), Gaps = 3/359 (0%) Query: 1 MKKSLLSAVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGG 60 MKK+LL A A+ A+ FS A AD+ +A+AGP+TG A+ G Q++KGAE A ADINA GG Sbjct: 1 MKKTLL-ATAVLALGGFSNAALADLAVAIAGPMTGQYASAGDQIRKGAEMAIADINARGG 59 Query: 61 INGEQIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNH 120 + G+++K+E+GDD DPKQ +SVAN G+ F+ GH+ S +IPASEVY E I Sbjct: 60 VLGQKLKLEVGDDACDPKQAVSVANTMVNKGIVFMHGHWCSSSTIPASEVYVEADIPMAT 119 Query: 121 PGRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADET 180 + P + GL N FR GRDDQQG +AG Y+ADHFK K+AVV DK+ YG+GLADE Sbjct: 120 VSTN-PQVTERGLKNVFRIMGRDDQQGLVAGGYIADHFKGKKVAVVDDKSAYGKGLADEM 178 Query: 181 KKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGL 240 KAM G+ + E I G+KD+S ++ K+K+AGV ++ +GG HTE LI+RQA GL Sbjct: 179 AKAMEGKGLKPALRESITAGEKDYSGIVTKLKQAGVEVMAYGGYHTEVALILRQAQAAGL 238 Query: 241 KATLVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEAYTLY 300 + T++ GD + ++EL + AG A + TF PD NP +VEKF+AA PE Y LY Sbjct: 239 QLTVMGGDTMTNSELVTAAGPAADNVMFTFSPDARKNPDAAPVVEKFRAAKTEPEGYVLY 298 Query: 301 SYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEWK 359 +YAAMQ AA A S + KAM+ G F TV+GD++FD KGD K PG+++Y W+ Sbjct: 299 AYAAMQLFEQAATTAKSTKYADLEKAMR-GGSFKTVIGDLAFDAKGDQKAPGFVVYRWQ 356 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: 450 Number of extensions: 21 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: 364 Length adjustment: 30 Effective length of query: 351 Effective length of database: 334 Effective search space: 117234 Effective search space used: 117234 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: 49 (23.5 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