Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate Dsui_2058 Dsui_2058 ABC-type branched-chain amino acid transport systems, ATPase component
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__PS:Dsui_2058 Length = 260 Score = 197 bits (502), Expect = 2e-55 Identities = 118/262 (45%), Positives = 162/262 (61%), Gaps = 10/262 (3%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 LL++ ++ FGGL + DVSF G I +IGPNGAGKTT+FN ITG TP+ G++ Sbjct: 9 LLSIRNVGKHFGGLHVLQDVSFEVPAGSIYGLIGPNGAGKTTVFNLITGLLTPSAGQI-- 66 Query: 71 RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130 D + L + +RI+ + +ARTFQNIR+F M +LEN++V H+ L GF I Sbjct: 67 ---DFQGQTLIGLEPHRITHQ-GIARTFQNIRIFKEMDLLENVMVGMHDHL-NYGGFGI- 120 Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190 L P+ E++A + A L V L AD A NL YG QR+LE ARA+ TEP +L Sbjct: 121 -FLNSPACRAAEKKARERALELLSWVGLDHKADMLADNLSYGDQRKLEFARALATEPKLL 179 Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250 LDEP AG+NP E L + + IR+ GV +IEHDM VM + D + VL++GR I++ Sbjct: 180 LLDEPVAGMNPSEKTILMEEINNIRN-RGYGVFMIEHDMRFVMGLCDRIAVLNFGRIIAE 238 Query: 251 GDPAFVKNDPAVIRAYLGEEED 272 G P V+N+P VI AYLG+E++ Sbjct: 239 GTPDEVRNNPDVIEAYLGKEDE 260 Lambda K H 0.319 0.137 0.397 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: 215 Number of extensions: 12 Number of successful extensions: 4 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: 294 Length of database: 260 Length adjustment: 25 Effective length of query: 269 Effective length of database: 235 Effective search space: 63215 Effective search space used: 63215 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