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 RR42_RS16980 RR42_RS16980 branched-chain amino acid ABC transporter substrate-binding protein
Query= TCDB::Q9L3M3 (381 letters) >FitnessBrowser__Cup4G11:RR42_RS16980 Length = 401 Score = 209 bits (532), Expect = 1e-58 Identities = 132/355 (37%), Positives = 187/355 (52%), Gaps = 8/355 (2%) Query: 10 ALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAG-GINGEQIKI 68 A TA A SG+ V I A PLTG A G + GA A ++N G ING++IK+ Sbjct: 38 AATAPAAGSGDVV--VKIGHAAPLTGGIAHLGKDNENGARLAVEEVNKTGLEINGKKIKL 95 Query: 69 EL--GDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPGRDEP 126 EL DD DPK G +VA K V V+GH NSGVSIPAS++Y++ GI++ P P Sbjct: 96 ELVGEDDAGDPKTGTAVAQKLVDAKVVAVVGHLNSGVSIPASKIYSDAGIVQISPSSTNP 155 Query: 127 DLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKKAMNA 186 D G TFR D QQG Y +A+V D T YG+GLADE +K A Sbjct: 156 DYTKQGFKTTFRVVATDAQQGPALANYATKSLHAKSVAIVDDATAYGKGLADEFEKTAKA 215 Query: 187 AGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKATLVS 246 +GV V E N DF A++ K+K +I +GG+ G +QA + G+ + +V Sbjct: 216 SGVNVVAREATNDKATDFKAILTKIKGKKPDVIMYGGMDATGGPFAKQAKELGISSKIVG 275 Query: 247 GDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNP--EAYTLYSYAA 304 GDG+ ++++A +AGDAV+ + + + +K A FN + Y ++Y A Sbjct: 276 GDGVCTDKVAELAGDAVSNIICSEAGLALSKMEQGADFDKRYQARFNAPVQIYAPFTYDA 335 Query: 305 MQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEWK 359 + I A K A S +P A+ M K + ++G+I+FDEKGD K +YE+K Sbjct: 336 VMVIVDAMKRANSTEPAAILAEM-PKTNYKGLIGNIAFDEKGDMKEGTITLYEYK 389 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: 412 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: 401 Length adjustment: 31 Effective length of query: 350 Effective length of database: 370 Effective search space: 129500 Effective search space used: 129500 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