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 CA265_RS25230 CA265_RS25230 LPS export ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >FitnessBrowser__Pedo557:CA265_RS25230 Length = 246 Score = 135 bits (339), Expect = 1e-36 Identities = 76/249 (30%), Positives = 137/249 (55%), Gaps = 16/249 (6%) Query: 5 ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64 IL L ++ VN V+ V + ++V ++GPNGAGKTT F + G +P G I L Sbjct: 2 ILRAENLVKKYKQRTVVNNVSFNVSQGEIVGLLGPNGAGKTTSFYMIVGLIKPNEGRIFL 61 Query: 65 DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFR 124 + E+I P ++ A+KG+ Q +F+++T +N+ LA L + + Sbjct: 62 EDEDITEDPMYRRAQKGIGYLAQEASVFRKLTVEDNI------------LAILEMSNMSK 109 Query: 125 RSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184 +R+ +E + E +L + L+ G++RR EIAR + P ++LDEP AG+ Sbjct: 110 EEQRDKLE---ELINEFSLHKVRKNRGDLLSGGERRRTEIARALAANPNFILLDEPFAGV 166 Query: 185 NPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDN 244 +P +++++++AKL+ + N+ +L+ +H+++ +SI+D ++ +G L G PE + +N Sbjct: 167 DPIAVEEIQSIVAKLKHK-NIGILITDHNVQETLSITDRAYLLFEGKILEQGVPEVLAEN 225 Query: 245 PDVIKAYLG 253 V K YLG Sbjct: 226 EMVRKVYLG 234 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: 169 Number of extensions: 9 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: 246 Length adjustment: 24 Effective length of query: 231 Effective length of database: 222 Effective search space: 51282 Effective search space used: 51282 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: 46 (22.3 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