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 GFF250 PGA1_c02620 high-affinity branched-chain amino acid transport ATP-binding protein LivF
Query= TCDB::P21630 (233 letters) >FitnessBrowser__Phaeo:GFF250 Length = 257 Score = 221 bits (564), Expect = 8e-63 Identities = 117/235 (49%), Positives = 164/235 (69%), Gaps = 4/235 (1%) Query: 1 MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60 +L + ++YG I A+ VS+ V+ G+IVT++GANGAGKSTLL T+ G GS+ + Sbjct: 5 LLDIRNLESFYGPIMAIRGVSLSVQAGQIVTVLGANGAGKSTLLKTISGIMDPEKGSVSF 64 Query: 61 EGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMDK--VLE 118 GEE+ G I+R+ I VPEGR VF L+VEENL +G +T +D +++ D+ V + Sbjct: 65 NGEEIQGEEPHRIVRRGIVHVPEGREVFPLLSVEENLTLGA-YTRRDQAEIERDRQMVFD 123 Query: 119 LFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQ 178 FP L ER Q AGT+SGG+QQMLAIGR LM +P+++LLDEPSLGL+P+++Q+IF I+++ Sbjct: 124 YFPILAERRHQEAGTLSGGQQQMLAIGRGLMLRPRIMLLDEPSLGLSPLLVQEIFGILKR 183 Query: 179 LRR-EGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLG 232 L R EGVT+ LVEQNA AL+LA YV+E GRIVM + L+ + ++ YLG Sbjct: 184 LNRDEGVTMMLVEQNARIALELAHVGYVMEIGRIVMDGSADRLMESEDIKSFYLG 238 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: 154 Number of extensions: 3 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: 257 Length adjustment: 24 Effective length of query: 209 Effective length of database: 233 Effective search space: 48697 Effective search space used: 48697 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