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_154652424.1 A1QA_RS0111820 ATP-binding cassette domain-containing protein
Query= TCDB::P21629 (255 letters) >NCBI__GCF_000295095.1:WP_154652424.1 Length = 613 Score = 104 bits (259), Expect = 5e-27 Identities = 68/223 (30%), Positives = 109/223 (48%), Gaps = 16/223 (7%) Query: 24 VNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRLDGEEIQGLPGHKIA-RKGV 82 V+L++ + +++IGPNG+GK+T G TGG +RL + G A R+ V Sbjct: 273 VSLEIGAGRALALIGPNGSGKSTACLVAAGLLDATGGEVRLGERVLDGAEDFVPAGRRDV 332 Query: 83 VRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFRRSEREAMEYAAHWLEEVN 142 Q +F M+ +EN+ F + REA E A L V Sbjct: 333 ALLSQVPGVFTHMSVLENVA---------------FGPRCQGQGRREARERAWAELAAVG 377 Query: 143 LTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGLNPKETDDLKALIAKLRSE 202 A RS L+ GQ R+ +AR + T PR+L+LDEP A L+ +++ L+A+ +E Sbjct: 378 AEHLAGRSGAELSGGQAARVALARALATSPRVLILDEPMAALDVGARQEMRDLVARRSAE 437 Query: 203 HNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDNP 245 +TVLL+ HD+ + S++D +VV+ G + G ++ P Sbjct: 438 EGLTVLLVTHDVLDIASLADDVVVLEAGRVVESGEAARVLSAP 480 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: 314 Number of extensions: 16 Number of successful extensions: 2 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: 613 Length adjustment: 31 Effective length of query: 224 Effective length of database: 582 Effective search space: 130368 Effective search space used: 130368 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: 50 (23.9 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