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_020176259.1 A3OQ_RS0115155 ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >NCBI__GCF_000385335.1:WP_020176259.1 Length = 255 Score = 199 bits (505), Expect = 6e-56 Identities = 111/260 (42%), Positives = 161/260 (61%), Gaps = 20/260 (7%) Query: 2 SRPILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGL 61 S P+L G+ RFGG A++ VN+ E ++ ++IGPNGAGK+T F+ L+G P+ G Sbjct: 3 SAPVLAAEGIGKRFGGFTALDDVNVAFERGRLTAIIGPNGAGKSTFFSLLSGAVAPSKGH 62 Query: 62 IRLDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENL-LVAQHRHLNTNFLAGLFKT 120 IR +G ++ G P H+ AR G+ R++Q LF ++T EN+ L Q H Sbjct: 63 IRFEGADVAGEPQHRFARMGIARSYQITNLFPQLTVHENVRLACQAMH-----------A 111 Query: 121 PAFRRSEREAMEY------AAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRI 174 PA R R+ Y A L +V LT R A +LA+G+QR LEIA + +RP++ Sbjct: 112 PARRSLWRDRTHYTGLADEADAALAQVGLTSRRKRLAASLAHGEQRALEIAVALASRPKL 171 Query: 175 LMLDEPAAGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLA 234 L+LDEP AG++P+ET ++ ALI +L +E TVLL+EH MK+VM ++D IVV++QG LA Sbjct: 172 LLLDEPTAGMSPEETKEMMALIGRLAAER--TVLLVEHKMKMVMGLADRIVVLHQGKLLA 229 Query: 235 DGTPEQIRDNPDVIKAYLGE 254 GTP++IR + V + YLGE Sbjct: 230 SGTPDEIRADASVRRVYLGE 249 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: 152 Number of extensions: 5 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: 255 Length adjustment: 24 Effective length of query: 231 Effective length of database: 231 Effective search space: 53361 Effective search space used: 53361 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 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