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_086511522.1 BZY95_RS19340 ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >NCBI__GCF_002151265.1:WP_086511522.1 Length = 264 Score = 172 bits (435), Expect = 8e-48 Identities = 96/253 (37%), Positives = 145/253 (57%), Gaps = 7/253 (2%) Query: 1 MSRPILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGG 60 + P+LE GLT RFGGL+AVN V+ + + ++ +++GPNGAGK+T+ N L+G + P+ G Sbjct: 11 LETPLLETKGLTRRFGGLVAVNDVDFTLRQGEIHAILGPNGAGKSTLINLLSGEFPPSEG 70 Query: 61 LIRLDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKT 120 I G+ IQG +IAR G+ R+ Q +F +T ++N +A H L G+F + Sbjct: 71 EILFQGQPIQGRKARQIARMGIGRSHQKTNIFPRLTCLQNCQLAARIH-----LGGVFGS 125 Query: 121 PAFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEP 180 R RE E A LE L A+ A ++YG+QR+L+IA + T P++++LDEP Sbjct: 126 WRSRHRAREVDERALEVLETCQLVHRAHTPASAMSYGEQRQLQIAMVLATAPKLMLLDEP 185 Query: 181 AAGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQ 240 AG+ +ET + L+ L + ++LIEHDM V ++D I V+ G L G Q Sbjct: 186 MAGMGREETAQVTELLKGLSDRY--PLVLIEHDMDSVFRLADRITVMVDGCVLETGPTAQ 243 Query: 241 IRDNPDVIKAYLG 253 IR + V YLG Sbjct: 244 IRASERVRDVYLG 256 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: 166 Number of extensions: 8 Number of successful extensions: 3 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: 264 Length adjustment: 24 Effective length of query: 231 Effective length of database: 240 Effective search space: 55440 Effective search space used: 55440 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: 47 (22.7 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