Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_058929663.1 AU252_RS04335 ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_001484605.1:WP_058929663.1 Length = 345 Score = 145 bits (367), Expect = 1e-39 Identities = 101/283 (35%), Positives = 155/283 (54%), Gaps = 22/283 (7%) Query: 10 PLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLT 69 P++ E++T FGG+ AV+ +ITA+IGPNGAGKTTLFN +TGF P G+ Sbjct: 37 PIVVAENVTRSFGGINAVDVEYLEIPRHKITALIGPNGAGKTTLFNLLTGFDMPNSGKWQ 96 Query: 70 LRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENL-IVAQHNKLIRASGFS 128 +G L + Y++++ V RTFQ ++ G ++V+EN+ + R S Sbjct: 97 F---EGNS--LAGISPYKVARMGMV-RTFQLTKVMGKLTVMENMRLGGSEQPGERLSKAL 150 Query: 129 IAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPV 188 GL G E+E A L++ +L D A +L G ++ LE+AR++ P Sbjct: 151 FKGLWG-----GREKEITAQANVLLEKFKLDAKKDDYAASLSGGQRKLLEMARSLMVRPK 205 Query: 189 MLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKI 248 ++ LDEP AG+NP + L D + ++ E + VL +EHDM++V I+D VVV+ G+ + Sbjct: 206 LVMLDEPMAGVNPALTQSLLDHIKNLKAE-GMTVLFVEHDMNMVRHIADWVVVMAEGKIV 264 Query: 249 SDGDPAFVKNDPAVIRAYLGEEED---------EELPPEIKAD 282 ++G P V +PAVI AYLG D +EL E++AD Sbjct: 265 AEGPPGEVMKNPAVIDAYLGAHHDVDLGDTEGIKELAAELEAD 307 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: 256 Number of extensions: 17 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: 345 Length adjustment: 27 Effective length of query: 267 Effective length of database: 318 Effective search space: 84906 Effective search space used: 84906 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: 48 (23.1 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