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 Ac3H11_1936 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)
Query= TCDB::P21630 (233 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1936 Length = 272 Score = 215 bits (547), Expect = 8e-61 Identities = 112/234 (47%), Positives = 158/234 (67%), Gaps = 2/234 (0%) Query: 1 MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60 +L V + YG I+A+ VS++V++GEI ++G+NGAGK+T+L T+ G GSI + Sbjct: 20 LLRLQNVESAYGPIKAIRGVSLQVRRGEIAAVLGSNGAGKTTILKTISGIIDPRKGSIEF 79 Query: 61 EGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFF-TDKDDYQVQMDKVLEL 119 +G+++ + I+R+ + VPEGR VF L+V +NL MG + DKD ++ V Sbjct: 80 QGQDITARDPAAIVRRGLMHVPEGREVFPLLSVRDNLLMGAYTRADKDGVARDIETVFGY 139 Query: 120 FPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQL 179 FP LKER Q AG +SGG+QQMLAI RALM+ P+L+LLDEPSLGL+P + ++IFEI+ ++ Sbjct: 140 FPILKERAAQDAGLLSGGQQQMLAISRALMAAPELILLDEPSLGLSPKLTKEIFEIVVRI 199 Query: 180 RRE-GVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLG 232 RE G T+ LVEQNAN AL +D YVLENGRIVM D+ L +++ YLG Sbjct: 200 NRERGTTILLVEQNANMALNASDYGYVLENGRIVMEDSCERLREKDDIKEFYLG 253 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: 168 Number of extensions: 5 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: 272 Length adjustment: 24 Effective length of query: 209 Effective length of database: 248 Effective search space: 51832 Effective search space used: 51832 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