Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_009545830.1 CCE_RS09615 LPS export ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >NCBI__GCF_000017845.1:WP_009545830.1 Length = 238 Score = 124 bits (311), Expect = 2e-33 Identities = 78/236 (33%), Positives = 132/236 (55%), Gaps = 19/236 (8%) Query: 21 VNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRLDGEEIQGLPGHKIARK 80 VN VNLKV ++V ++GPNGAGKTT F TG +P G + L+ +E+ LP +K AR Sbjct: 18 VNRVNLKVAPGEIVGLLGPNGAGKTTTFYIATGLIKPNKGRVWLNQQEVTRLPLNKRARL 77 Query: 81 GVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFRRSEREAMEYAAHWLEE 140 G+ Q +F+ ++ EN+ VA + TN P +R +R L+E Sbjct: 78 GIGYMTQQPSIFRHLSVAENIQVALEQ---TN-------VPFRQRPQR-----LHTLLKE 122 Query: 141 VNLTEFANRSAGTLAYGQQRRLEIARCM---MTRPRILMLDEPAAGLNPKETDDLKALIA 197 L + A+ ++ G++RR E+AR + P L+LDEP AG++P +++ +IA Sbjct: 123 FRLEKIAHTKGSQVSGGERRRTELARSLAVGQQGPDFLLLDEPFAGVDPIAVSEIQTMIA 182 Query: 198 KLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDNPDVIKAYLG 253 +L + + +L+ +H+++ ++I++ ++ G LA G+ E+I +NP V + YLG Sbjct: 183 QL-CDRQMGILITDHNVQATLAITNRAYIMRDGQILAAGSAEEIYNNPLVRQYYLG 237 Lambda K H 0.320 0.137 0.391 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: 140 Number of extensions: 7 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: 255 Length of database: 238 Length adjustment: 24 Effective length of query: 231 Effective length of database: 214 Effective search space: 49434 Effective search space used: 49434 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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