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_011654660.1 RL_RS25315 ABC transporter ATP-binding protein
Query= TCDB::P21630 (233 letters) >NCBI__GCF_000009265.1:WP_011654660.1 Length = 238 Score = 187 bits (476), Expect = 1e-52 Identities = 102/230 (44%), Positives = 148/230 (64%), Gaps = 7/230 (3%) Query: 11 YGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRYEGE----ELV 66 YG +Q LH +S+E ++GE V L+G NG GKSTL+ L G + GSI E + +L Sbjct: 9 YGTVQVLHGLSIEAREGETVVLLGTNGNGKSTLMKCLIGDVRPTQGSITLELDGQAIDLT 68 Query: 67 GLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFF-TDKDDYQVQMDKVLELFPRLKE 125 L + I+ I++VPEGRR+F +LTVEENL +G + + ++ FP LKE Sbjct: 69 HLGTDQIVEYGISIVPEGRRLFPQLTVEENLLLGAYRKAARSKIAANLEFCYGAFPILKE 128 Query: 126 RYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQLRRE-GV 184 R Q +G+MSGG+QQMLA+GRA+MS P++LL+DEPS+GLAPI++ Q I +L+ + G+ Sbjct: 129 RRRQLSGSMSGGQQQMLALGRAIMSSPRILLVDEPSVGLAPIMVSQAIAKIGELKEQFGL 188 Query: 185 TVFLVEQNANQALKLADRAYVLENGRIVMH-DTGAALLTNPKVRDAYLGG 233 TV + EQN +A+++ADR YVL +G + +T A L + + YLGG Sbjct: 189 TVVMAEQNFQEAMRIADRGYVLVHGEVAFSAETAAELRDSELISQLYLGG 238 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: 147 Number of extensions: 9 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: 238 Length adjustment: 23 Effective length of query: 210 Effective length of database: 215 Effective search space: 45150 Effective search space used: 45150 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