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 8500412 DvMF_1162 ABC transporter related (RefSeq)
Query= TCDB::P21630 (233 letters) >FitnessBrowser__Miya:8500412 Length = 241 Score = 218 bits (556), Expect = 6e-62 Identities = 112/240 (46%), Positives = 165/240 (68%), Gaps = 7/240 (2%) Query: 1 MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCG-----SPQAAS 55 +LS + + YG I+ALH +S V +GEIVTLIGANGAGKST L ++ +P+ + Sbjct: 2 LLSIENLYVKYGNIEALHGLSFHVNEGEIVTLIGANGAGKSTTLKSIMRLPPPEAPKVSG 61 Query: 56 GSIRYEGEELVGL-PSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDD-YQVQM 113 G I ++G+ L+ + P + + +A+VPEGR +F LTV ENL + + D + Sbjct: 62 GDILFKGKSLLNVEPHDVVSKLHVALVPEGRHIFGNLTVMENLMLATYARKNDPAISRDL 121 Query: 114 DKVLELFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIF 173 +++ +LFPRL ER QR+ T+SGGEQQMLA+GRALM+ ++LLLDEPS+GLAP+++ ++F Sbjct: 122 ERIFDLFPRLAERRTQRSDTLSGGEQQMLAVGRALMTSCEVLLLDEPSMGLAPLLMYEMF 181 Query: 174 EIIEQLRREGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLGG 233 +++L REG+T+ +VEQNA AL++A R YVL+ G IV +LL +P+V+ AYLGG Sbjct: 182 RTLKELNREGLTIIVVEQNARLALQVASRGYVLDTGEIVAQGPSESLLNDPEVKKAYLGG 241 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: 158 Number of extensions: 6 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: 241 Length adjustment: 23 Effective length of query: 210 Effective length of database: 218 Effective search space: 45780 Effective search space used: 45780 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