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 BWI76_RS26335 BWI76_RS26335 ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >FitnessBrowser__Koxy:BWI76_RS26335 Length = 255 Score = 373 bits (957), Expect = e-108 Identities = 180/255 (70%), Positives = 216/255 (84%) Query: 1 MSRPILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGG 60 MS+P+L V+GL MRFGGLLAVN V+L++ E+++VS+IGPNGAGKTTVFNCLTGFY+PTGG Sbjct: 1 MSQPLLSVNGLMMRFGGLLAVNNVSLELREREIVSLIGPNGAGKTTVFNCLTGFYKPTGG 60 Query: 61 LIRLDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKT 120 I L + ++GLPG +IAR GVVRTFQ+VRLF+EMT +ENLLVAQH+ L T +GL KT Sbjct: 61 TIMLRDQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGVFSGLLKT 120 Query: 121 PAFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEP 180 P+FRR++ EA++ AA WLE + L E ANR A LAYG QRRLEIARCM+T+P ILMLDEP Sbjct: 121 PSFRRAQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEP 180 Query: 181 AAGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQ 240 AAGLNPKET +L LIA+LRS HN T+LLIEHDMKLVM ISD I V+NQG PLA+GTPE+ Sbjct: 181 AAGLNPKETKELDELIAELRSHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEE 240 Query: 241 IRDNPDVIKAYLGEA 255 IR+NPDVI+AYLGEA Sbjct: 241 IRNNPDVIRAYLGEA 255 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: 259 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: 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 17 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