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_045585058.1 AL072_RS29535 branched-chain amino acid ABC transporter substrate-binding protein
Query= TCDB::Q9L3M3 (381 letters) >NCBI__GCF_001305595.1:WP_045585058.1 Length = 366 Score = 395 bits (1014), Expect = e-114 Identities = 198/357 (55%), Positives = 254/357 (71%), Gaps = 3/357 (0%) Query: 2 KKSLLSAVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGI 61 K SLL+A+A TA+ A + A AD+ +A AGP+TG A FG Q++KG EQA ADINAAGG+ Sbjct: 4 KLSLLAAIAATALSATA--AKADIAVATAGPITGQYATFGEQMKKGMEQAVADINAAGGV 61 Query: 62 NGEQIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHP 121 G+++K+E+GDD DPKQ ++VAN+ A GVKFV GHF SG SIPAS+VYAE G+L+ P Sbjct: 62 LGQKLKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGMLQISP 121 Query: 122 GRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETK 181 P L GL N FR CGRDDQQG IAGKYL + +K +A++HDK+ YG+GLADET+ Sbjct: 122 ASTNPKLTEQGLKNVFRVCGRDDQQGMIAGKYLLEKYKGKNVAILHDKSAYGKGLADETQ 181 Query: 182 KAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLK 241 KA+NA G E IYE G+KD+SAL++K+K+A V +Y GG HTEAGL+ RQ DQGLK Sbjct: 182 KALNAGGQKEAIYEAYTAGEKDYSALVSKLKQANVDAVYVGGYHTEAGLLARQMKDQGLK 241 Query: 242 ATLVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEAYTLYS 301 A +VSGD +V+NE +I GDA T+ TFGPDP K +VEKF+ AG+ PE YTLY+ Sbjct: 242 APIVSGDALVTNEYWAITGDAGEDTMMTFGPDPREKADAKAVVEKFRKAGYEPEGYTLYT 301 Query: 302 YAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEW 358 YAA+Q A A K A S D V++ ++ KG + TV+G I FD KGD P Y+ Y+W Sbjct: 302 YAALQIWAEAVKQAKSTDAAKVSEVLR-KGSYETVIGKIGFDAKGDVTSPAYVWYKW 357 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: 19 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