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 YP_427258.1 Rru_A2171 extracellular ligand-binding receptor
Query= TCDB::Q9L3M3 (381 letters) >NCBI__GCF_000013085.1:YP_427258.1 Length = 370 Score = 319 bits (818), Expect = 7e-92 Identities = 170/352 (48%), Positives = 227/352 (64%), Gaps = 2/352 (0%) Query: 8 AVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGINGEQIK 67 +V ++A+ A AD+ + +A LTG AA G Q ++GAE A A N AGG+ GE I Sbjct: 10 SVTVSALAISPLPALADIPVGLALGLTGQIAAIGEQSRRGAEAAIAAFNKAGGLKGETIT 69 Query: 68 IELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPGRDEPD 127 +++ DD DPKQG++VANKF + GV+ VIGH +G ++ AS VY+E I PD Sbjct: 70 LQVEDDACDPKQGVAVANKFVSAGVEAVIGHMCTGPTMAASTVYSEEEIPMVTASATGPD 129 Query: 128 LHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKKAMNAA 187 L GL N FR GRDDQQG IAGK +A+ F D A+VHDK YG+GLA+E KKAMNAA Sbjct: 130 LTERGLTNVFRATGRDDQQGTIAGKMIAERFADQTTAIVHDKQAYGRGLAEEAKKAMNAA 189 Query: 188 GVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKATLVSG 247 G E ++ I G++DFSALI+++K+AGV ++Y+GG + + G I+RQ+ QGL A V G Sbjct: 190 GKEEALFAAIVPGEQDFSALISRLKQAGVKVVYYGGYYNDLGQIVRQSRAQGLDAVFVGG 249 Query: 248 DGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAG-FNPEAYTLYSYAAMQ 306 DG+ S+E +I G+A GTL TF PD + NPA KE VE FKA G + + + Y YAA Q Sbjct: 250 DGLSSSEFWAITGEAGEGTLFTFTPDASTNPAAKEAVEAFKADGKGDADNFAYYYYAAAQ 309 Query: 307 TIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEW 358 + A AGS DPEAV KA+++ F TV G + FD KGD P ++ Y+W Sbjct: 310 VLTQAMAKAGSADPEAVTKALRD-NTFETVAGPMDFDAKGDLTAPAFVFYQW 360 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: 420 Number of extensions: 21 Number of successful extensions: 2 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: 370 Length adjustment: 30 Effective length of query: 351 Effective length of database: 340 Effective search space: 119340 Effective search space used: 119340 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