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 350453 BT0925 ABC transporter, ATP-binding protein (NCBI ptt file)
Query= TCDB::P21630 (233 letters) >FitnessBrowser__Btheta:350453 Length = 247 Score = 110 bits (276), Expect = 2e-29 Identities = 67/213 (31%), Positives = 119/213 (55%), Gaps = 12/213 (5%) Query: 6 KVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRYEGEEL 65 +++ YGK A+ + + ++KGEI L+G NGAGKST ++ + G + SG + E+ Sbjct: 10 ELTKQYGKFTAVDHIRLSIRKGEIFGLLGPNGAGKSTTILMMMGLTEPTSGIV-----EI 64 Query: 66 VGLPSST---IMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMDKVLELFPR 122 G+ S+T +++ I +PE + +T ENL D + ++ K LEL R Sbjct: 65 CGINSTTHPIEVKRKIGYLPEDVGFYDDMTGLENLMYTARLNGIPDKEAKV-KALELMKR 123 Query: 123 --LKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQL- 179 L+++ +++ G S G +Q L + L+ P++++LDEP+ G+ P +Q+ E+I L Sbjct: 124 VGLEDQLKKKTGKYSRGMRQRLGLADVLIKNPEIIILDEPTSGIDPAGVQEFIELIRWLS 183 Query: 180 RREGVTVFLVEQNANQALKLADRAYVLENGRIV 212 + EG+TV + +QA K+ DR + NG+I+ Sbjct: 184 KEEGLTVLFSSHHLDQAQKVCDRVGLFSNGKIL 216 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: 134 Number of extensions: 8 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: 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 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