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 GFF3277 PS417_16775 branched-chain amino acid ABC transporter ATP-binding protein
Query= TCDB::P21630 (233 letters) >FitnessBrowser__WCS417:GFF3277 Length = 255 Score = 197 bits (502), Expect = 1e-55 Identities = 113/241 (46%), Positives = 153/241 (63%), Gaps = 9/241 (3%) Query: 1 MLSFDKVSTYY-GKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQA-----A 54 +LS + + Y G I A+ VS+ V KG V L+GANGAGKST L + G +A + Sbjct: 13 LLSVNDIEVIYDGAILAVAGVSLSVPKGATVALLGANGAGKSTTLKAISGLVRAERAEVS 72 Query: 55 SGSIRYEGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFT--DKDDYQVQ 112 G+I Y G +L G+ S +R+ + V EGR VF +L+VE+NL GGF + + + Sbjct: 73 RGTIEYAGTDLAGIDPSQRVRQGMVHVLEGRHVFGQLSVEDNLRSGGFVRRLSRQEMEHD 132 Query: 113 MDKVLELFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQI 172 ++++ FPRLK + RAG SGGEQQM+AIGRALM++P L+LLDEPS+GLAP+I+Q+I Sbjct: 133 LERLYAWFPRLKTKRHTRAGLTSGGEQQMVAIGRALMTRPTLVLLDEPSMGLAPMIVQEI 192 Query: 173 FEIIEQLRREGVTVFLV-EQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYL 231 FEII QL RE FL+ EQN N AL A YVL+ GR+ + + A LL + D YL Sbjct: 193 FEIIGQLNREQQVSFLIAEQNINVALNYASHGYVLDTGRVALSGSAAELLARGDLHDIYL 252 Query: 232 G 232 G Sbjct: 253 G 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: 142 Number of extensions: 6 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: 255 Length adjustment: 24 Effective length of query: 209 Effective length of database: 231 Effective search space: 48279 Effective search space used: 48279 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