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_003944041.1 C1M55_RS16615 ABC transporter ATP-binding protein
Query= TCDB::P21630 (233 letters) >NCBI__GCF_002893965.1:WP_003944041.1 Length = 268 Score = 186 bits (472), Expect = 4e-52 Identities = 98/226 (43%), Positives = 144/226 (63%), Gaps = 1/226 (0%) Query: 7 VSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRYEGEELV 66 V+ Y + L + + +K+GEIV +IG NGAGKSTLL +L G GS+ + + Sbjct: 36 VAGYIPGVNILRECNFFLKEGEIVGIIGPNGAGKSTLLKSLFGLIPVREGSVTLREDNIT 95 Query: 67 GLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMDKVLELFPRLKER 126 P+ +++K + VP+ + VF LT+EENL MG + K + + V ELFP L ER Sbjct: 96 SAPAHVLVQKGVGYVPQTQNVFQTLTIEENLEMGIYLRPKA-FAERFAFVSELFPLLSER 154 Query: 127 YEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQLRREGVTV 186 + +AG +SGGE+QM+A+GRALM P +LLLDEPS GL+P+ ++F +++ GV+V Sbjct: 155 RKVKAGALSGGERQMVAMGRALMMDPSVLLLDEPSAGLSPMFQDEVFIRCKKINAAGVSV 214 Query: 187 FLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLG 232 +VEQNA + L++ DR YVL+ G+ DTGA L+ +PKV + YLG Sbjct: 215 IMVEQNARRCLQICDRGYVLDQGKNAYTDTGANLMNDPKVIELYLG 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: 164 Number of extensions: 8 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: 268 Length adjustment: 24 Effective length of query: 209 Effective length of database: 244 Effective search space: 50996 Effective search space used: 50996 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