Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_086511522.1 BZY95_RS19340 ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_002151265.1:WP_086511522.1 Length = 264 Score = 143 bits (361), Expect = 4e-39 Identities = 90/267 (33%), Positives = 140/267 (52%), Gaps = 20/267 (7%) Query: 9 TPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRL 68 TPLL + LT RFGGLVAVNDV F+ GEI AI+GPNGAGK+TL N ++G + P+ G + Sbjct: 13 TPLLETKGLTRRFGGLVAVNDVDFTLRQGEIHAILGPNGAGKSTLINLLSGEFPPSEGEI 72 Query: 69 TLRHADGKEFLLERMPGYRISQ--KASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASG 126 F + + G + Q + + R+ Q +F ++ L+N + A+ Sbjct: 73 L--------FQGQPIQGRKARQIARMGIGRSHQKTNIFPRLTCLQNCQL--------AAR 116 Query: 127 FSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTE 186 + G+ G RE + A L+ +L+ A A + YG QR+L+IA + T Sbjct: 117 IHLGGVFGSWRSRHRAREVDERALEVLETCQLVHRAHTPASAMSYGEQRQLQIAMVLATA 176 Query: 187 PVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGR 246 P ++ LDEP AG+ E+ ++ +LL + D + + +LIEHDM V ++D + V+ G Sbjct: 177 PKLMLLDEPMAGMGREETAQVTELLKGLSDRYPL--VLIEHDMDSVFRLADRITVMVDGC 234 Query: 247 KISDGDPAFVKNDPAVIRAYLGEEEDE 273 + G A ++ V YLG +E Sbjct: 235 VLETGPTAQIRASERVRDVYLGRHHEE 261 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: 164 Number of extensions: 5 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: 294 Length of database: 264 Length adjustment: 25 Effective length of query: 269 Effective length of database: 239 Effective search space: 64291 Effective search space used: 64291 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 Apr 09 2024. 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