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_084005217.1 BEN30_RS07660 ABC transporter ATP-binding protein
Query= TCDB::P21630 (233 letters) >NCBI__GCF_001746755.1:WP_084005217.1 Length = 262 Score = 167 bits (422), Expect = 2e-46 Identities = 94/225 (41%), Positives = 136/225 (60%), Gaps = 5/225 (2%) Query: 9 TYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLC--GSPQAASGSIRYEGEELV 66 +YYG+ + V+ ++ +GEIV L+G NGAGK++ L T+ PQ G I + + L Sbjct: 39 SYYGESYIVQGVNFDIHEGEIVALLGRNGAGKTSTLRTIARMDDPQLRHGEIWLDHQPLH 98 Query: 67 GLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMDKVLELFPRLKER 126 + S R + +VPE R + LTVEENL + ++++ E FPRL ER Sbjct: 99 TMQSWQAARLGVGLVPEDRSIIPGLTVEENLTLSQI---APPIGWSIERIYEHFPRLAER 155 Query: 127 YEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQLRREGVTV 186 Q T+SGGEQQMLA+ RAL KLLLLDEP GLAP+I+ +I I+E +++ G+T Sbjct: 156 RMQEGVTLSGGEQQMLAVARALARDIKLLLLDEPYEGLAPVIVHEIESILEGVKKLGITT 215 Query: 187 FLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYL 231 +VEQNA AL L+DRA +L+ G +V + + +L N ++RD YL Sbjct: 216 IIVEQNAIAALHLSDRAIILDMGEVVFNGSAQEVLDNKELRDEYL 260 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: 178 Number of extensions: 7 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: 233 Length of database: 262 Length adjustment: 24 Effective length of query: 209 Effective length of database: 238 Effective search space: 49742 Effective search space used: 49742 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