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_011869254.1 MMARC5_RS07655 daunorubicin resistance protein DrrA family ABC transporter ATP-binding protein
Query= TCDB::P21630 (233 letters) >NCBI__GCF_000016125.1:WP_011869254.1 Length = 323 Score = 109 bits (272), Expect = 7e-29 Identities = 73/209 (34%), Positives = 118/209 (56%), Gaps = 6/209 (2%) Query: 11 YGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRYEGEELVGLPS 70 + K A+++VS VKKGEI +G NGAGKST + L +A SGS G + P Sbjct: 13 FDKNVAVNNVSFNVKKGEIFAFLGPNGAGKSTTINMLTTLLKATSGSAIISGFDASKDPK 72 Query: 71 STIMRKSIAVVPEGRRVFSRLTVEENLAMGG--FFTDKDDYQVQMDKVLELFPRLKERYE 128 +RK+I +V + + ++LT ENL + G + + + ++D++LE F L E + Sbjct: 73 K--VRKTIGIVFQDSTLDNQLTAYENLYIHGKIYGYKGEALKTRIDELLE-FVELLEVKD 129 Query: 129 QRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQLR-REGVTVF 187 SGG + L I R+L+ +P++L LDEP++GL P I+E I+ +R R +T+F Sbjct: 130 TVVKNFSGGMVRRLEIARSLIHEPEVLFLDEPTIGLDPQTRSHIWEYIQNMRKRNNMTIF 189 Query: 188 LVEQNANQALKLADRAYVLENGRIVMHDT 216 L ++A LAD+ +++NG+I+ T Sbjct: 190 LTTHYMDEAELLADKVAIIDNGKIIAEGT 218 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: 176 Number of extensions: 11 Number of successful extensions: 4 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: 323 Length adjustment: 25 Effective length of query: 208 Effective length of database: 298 Effective search space: 61984 Effective search space used: 61984 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 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