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_086510700.1 BZY95_RS14915 ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >NCBI__GCF_002151265.1:WP_086510700.1 Length = 256 Score = 180 bits (456), Expect = 3e-50 Identities = 92/249 (36%), Positives = 147/249 (59%) Query: 5 ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64 I++V + FGGL +N +++VE+ + +IGPNGAGK+T+FN + G G + L Sbjct: 4 IIDVRHVYKAFGGLKVINDCSIQVEKGSITGLIGPNGAGKSTLFNIIAGALPLDSGQVLL 63 Query: 65 DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFR 124 DGE+I P +++ KG++RTFQ F +MTA+ENL++ + + + K Sbjct: 64 DGEDITNRPANELFHKGLLRTFQIAHEFSQMTALENLMMVPPKQAGESLFSAWLKPGLVN 123 Query: 125 RSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184 + E + A ++ + L N AG L+ GQ++ LE+ R MMT R+++LDE AAG+ Sbjct: 124 QQETAVRQKALEVIDFIGLHHVRNELAGNLSGGQKKLLELGRTMMTDARVVLLDEIAAGV 183 Query: 185 NPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDN 244 N DL I +L E T L+IEHDM ++ + D ++V+ QG+ + +GT E+I++N Sbjct: 184 NRTLLGDLVENIERLNREMGYTFLVIEHDMDMIARLCDPVIVLAQGSVMVEGTIEEIQNN 243 Query: 245 PDVIKAYLG 253 P VI+AY G Sbjct: 244 PQVIEAYFG 252 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: 157 Number of extensions: 5 Number of successful extensions: 1 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: 256 Length adjustment: 24 Effective length of query: 231 Effective length of database: 232 Effective search space: 53592 Effective search space used: 53592 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