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_029133998.1 A3GO_RS0114445 ABC transporter ATP-binding protein
Query= TCDB::P21630 (233 letters) >NCBI__GCF_000428045.1:WP_029133998.1 Length = 271 Score = 190 bits (483), Expect = 2e-53 Identities = 105/228 (46%), Positives = 150/228 (65%), Gaps = 10/228 (4%) Query: 14 IQALHDVSVEVKKGEIVTLIGANGAGKSTLLMT---LCGSPQA--ASGSIRYEGEELVGL 68 I L VS+EV KG IV L+GANGAGKST L L G+ + G+I Y+GE + L Sbjct: 22 ILVLKGVSLEVPKGGIVALLGANGAGKSTTLKAISNLLGAERGDVTKGNILYKGEAVESL 81 Query: 69 PSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQV---QMDKVLELFPRLKE 125 S ++R+ + V EGR F LT+EENL G + T +D + ++ + + FPRL+E Sbjct: 82 NPSDLVRRGVVQVMEGRHCFEHLTIEENLLTGAY-TRRDGRKAIAQSLEMIYDYFPRLRE 140 Query: 126 RYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQL-RREGV 184 R +AG SGGEQQM AIGRA++++P+++LLDEPS+GLAP ++++IFEI+++L + EGV Sbjct: 141 RRSSQAGYTSGGEQQMCAIGRAMLAQPEMILLDEPSMGLAPQLVEEIFEIVKKLNQNEGV 200 Query: 185 TVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLG 232 + L EQN N AL+ +D Y++ENGR+VM L N V++ YLG Sbjct: 201 SFLLAEQNTNVALRYSDYGYIMENGRVVMEGNAKELSENEDVKEFYLG 248 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: 173 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: 271 Length adjustment: 24 Effective length of query: 209 Effective length of database: 247 Effective search space: 51623 Effective search space used: 51623 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 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