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_067078017.1 MCUHO_RS10540 ATP-binding cassette domain-containing protein
Query= TCDB::P21630 (233 letters) >NCBI__GCF_001602375.1:WP_067078017.1 Length = 316 Score = 113 bits (283), Expect = 4e-30 Identities = 70/212 (33%), Positives = 118/212 (55%), Gaps = 5/212 (2%) Query: 11 YGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRYEGEELVGLPS 70 +G A+ +S VKKGEI + +G NGAGKST + L G++R G ++ P Sbjct: 16 FGDFTAVRGISFTVKKGEIFSFLGPNGAGKSTTINILTTLLPVQKGAVRVAGYDVAREPR 75 Query: 71 STIMRKSIAVVPEGRRVFSRLTVEENLAMGG--FFTDKDDYQVQMDKVLELFPRLKERYE 128 +RK+I +V + + LTV E + G + +++ + ++D +L + L+ + + Sbjct: 76 K--VRKAIGIVFQDDVLDRDLTVRETMEFHGRLYGIPREERRRRIDDLLRIV-ELEFKRD 132 Query: 129 QRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQLRREGVTVFL 188 +R +SGG ++ L I R LM++P +L LDEP+ GL P +I++ I Q+ G T+FL Sbjct: 133 ERTKNLSGGMKRRLQIARGLMTQPGVLFLDEPTQGLDPQTRMRIWDYIRQVNEAGTTIFL 192 Query: 189 VEQNANQALKLADRAYVLENGRIVMHDTGAAL 220 +A L+DR ++++GRIV+ T A L Sbjct: 193 TTHYMEEADMLSDRISIIDHGRIVVSGTPAEL 224 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: 162 Number of extensions: 14 Number of successful extensions: 2 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: 316 Length adjustment: 25 Effective length of query: 208 Effective length of database: 291 Effective search space: 60528 Effective search space used: 60528 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 Sep 24 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