Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_078715619.1 B5D49_RS00080 ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_900167125.1:WP_078715619.1 Length = 263 Score = 238 bits (606), Expect = 1e-67 Identities = 132/266 (49%), Positives = 175/266 (65%), Gaps = 8/266 (3%) Query: 10 PLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRL- 68 P L V L M FGGL A+N V GEI A+IGPNGAGKTT FNCITG Y PT G + Sbjct: 4 PALDVRGLCMDFGGLRALNKVDLEVRQGEIAALIGPNGAGKTTFFNCITGIYAPTEGDIH 63 Query: 69 TLRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFS 128 L + + + R P + + +ARTFQNIRLF M+VLEN+++ +H + + S Sbjct: 64 VLPDGENRVRINGRKPNH--VTELGMARTFQNIRLFPSMTVLENVMIGRHCR----NRSS 117 Query: 129 IAGLLGLPSYTRTEREAVDLAKY-WLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEP 187 I G + +TR + + V Y L+ V L +A+ A NLPYGAQRRLEIARAM TEP Sbjct: 118 ILGAVLRDGHTRRQEDEVISRSYEMLELVGLERWANELATNLPYGAQRRLEIARAMATEP 177 Query: 188 VMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRK 247 +L LDEPAAG+NP+E+ L DL+ +IR+ + I VLLIEHDM +VM++SD + V+DYG++ Sbjct: 178 FLLLLDEPAAGMNPQETRRLKDLIDHIRETYHIAVLLIEHDMKMVMSVSDRIYVMDYGQR 237 Query: 248 ISDGDPAFVKNDPAVIRAYLGEEEDE 273 I+ G P V +P VI+AYLGE+ D+ Sbjct: 238 IAAGSPEEVSKNPEVIKAYLGEDADD 263 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: 222 Number of extensions: 7 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: 263 Length adjustment: 25 Effective length of query: 269 Effective length of database: 238 Effective search space: 64022 Effective search space used: 64022 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