Align High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_051305669.1 G494_RS0112690 amino acid ABC transporter ATP-binding protein
Query= TCDB::P21630 (233 letters) >NCBI__GCF_000429965.1:WP_051305669.1 Length = 247 Score = 115 bits (288), Expect = 8e-31 Identities = 71/219 (32%), Positives = 116/219 (52%), Gaps = 3/219 (1%) Query: 9 TYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRYEGEELVGL 68 TY G ++AL D +V VK+GE+V ++G +G+GKST L L G + SGSI +G L Sbjct: 16 TYPGNLKALDDFTVRVKRGEVVVVVGPSGSGKSTFLRCLNGLEEIDSGSITVDGIPLDDR 75 Query: 69 PSSTI-MRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMDKVLELFPRL--KE 125 + +R+ + +V + +F +TV EN+ + + + L L ++ E Sbjct: 76 EEHRLEIRREVGMVFQAFNLFPHMTVLENVNLAQQLVRRRSRSEATEFSLALLDKVGVSE 135 Query: 126 RYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQLRREGVT 185 + +SGG+QQ +AI RAL PK++L DE + L P +I ++ +++ L EG+T Sbjct: 136 KARVYPDALSGGQQQRVAIARALALMPKVMLFDEATSALDPEMIGEVLDVMRSLAGEGMT 195 Query: 186 VFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNP 224 + +V A +++DR +E GRIV A T P Sbjct: 196 MVVVTHEMGFAREVSDRVVFMEQGRIVEEAATATFFTAP 234 Lambda K H 0.318 0.136 0.374 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: 125 Number of extensions: 7 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: 233 Length of database: 247 Length adjustment: 23 Effective length of query: 210 Effective length of database: 224 Effective search space: 47040 Effective search space used: 47040 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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