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_085770499.1 B1812_RS04360 ABC transporter ATP-binding protein
Query= TCDB::P21630 (233 letters) >NCBI__GCF_002117405.1:WP_085770499.1 Length = 266 Score = 188 bits (477), Expect = 1e-52 Identities = 103/236 (43%), Positives = 154/236 (65%), Gaps = 8/236 (3%) Query: 5 DKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLL-----MTLCGSPQAASGSIR 59 D ++Y I AL DVS++V++GEIV L+GANG+GK+T+L + Q SG I Sbjct: 12 DVEASYNQAIVALRDVSLKVRRGEIVALLGANGSGKTTILNATSRLLAAERGQITSGKIL 71 Query: 60 YEGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFF--TDKDDYQVQMDKVL 117 ++G ++ + +K + V EGRRVF LTVEENLA G +++ + + +D V Sbjct: 72 FDGRSTSKSSTAELAQKGLVQVLEGRRVFRSLTVEENLASGALARRSNRRELRDDLDYVY 131 Query: 118 ELFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIE 177 +FP+LK R AG +SGGEQQM AIGRA+M+ P+LL+LDEPS+GLAP+++++I++++ Sbjct: 132 GVFPQLKHRRRSLAGLLSGGEQQMTAIGRAMMTHPRLLILDEPSMGLAPLVVEEIYQVLG 191 Query: 178 QLRR-EGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLG 232 L R +G+++ + EQNA AL+ A R YV+ENG +V+ A L V+D YLG Sbjct: 192 ALNRMKGLSLLVAEQNAYVALRHAHRGYVVENGVVVLEGAAATLQEREDVKDFYLG 247 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: 164 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: 266 Length adjustment: 24 Effective length of query: 209 Effective length of database: 242 Effective search space: 50578 Effective search space used: 50578 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 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