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_011841979.1 RSPH17029_RS14860 ABC transporter ATP-binding protein
Query= TCDB::P21630 (233 letters) >NCBI__GCF_000015985.1:WP_011841979.1 Length = 231 Score = 179 bits (454), Expect = 4e-50 Identities = 99/211 (46%), Positives = 132/211 (62%), Gaps = 2/211 (0%) Query: 1 MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60 ML+ + V YG++Q L +S E + GE+ ++G NGAGK+T+L ++ G +G I Sbjct: 1 MLTLEHVDAGYGRVQVLRGLSFEARAGEVTCVMGRNGAGKTTMLRSIMGQVAVTAGRILL 60 Query: 61 EGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMDKVLELF 120 +G L GL I + I VP+GRR+F LTV ENL +G + ++VLELF Sbjct: 61 DGAALEGLAPHRIPQLGIGYVPQGRRLFGPLTVAENLEIGLMTRGRGSRT--RERVLELF 118 Query: 121 PRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQLR 180 PRL+ER +Q A T+SGGEQQMLAIGRAL +PKLLLLDEP+ GL P +I I + + +LR Sbjct: 119 PRLRERLDQAASTLSGGEQQMLAIGRALCLEPKLLLLDEPTEGLQPSMIALIRDTVRRLR 178 Query: 181 REGVTVFLVEQNANQALKLADRAYVLENGRI 211 GV V LVEQ L LADR +E GR+ Sbjct: 179 GMGVAVVLVEQRIEAVLDLADRVAFVETGRV 209 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: 165 Number of extensions: 2 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: 231 Length adjustment: 23 Effective length of query: 210 Effective length of database: 208 Effective search space: 43680 Effective search space used: 43680 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 Apr 10 2024. 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