Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate N515DRAFT_3950 N515DRAFT_3950 lipopolysaccharide export system ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__Dyella79:N515DRAFT_3950 Length = 239 Score = 115 bits (288), Expect = 9e-31 Identities = 79/260 (30%), Positives = 127/260 (48%), Gaps = 24/260 (9%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 +L+ E L RF V D +FS GE+ ++GPNGAGKTT F + G G + L Sbjct: 1 MLSAEGLQKRFRTRQVVRDFAFSIREGEVVGLLGPNGAGKTTCFYMVVGLIEADAGTIKL 60 Query: 71 RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130 D + +P + + K + Q +F ++V +N++ Sbjct: 61 DKYD-----ITGLPMHARA-KLGIGYLPQEPSVFRRLTVADNIMA--------------- 99 Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190 +L L ++ A +L LD +++ AD +L G +RR+EIARA+ EP + Sbjct: 100 -VLELRENLSAKQRAGELESL-LDELKIAHIADQRGISLSGGERRRVEIARALAAEPRYM 157 Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250 LDEP AG++P GE+ ++ +++ E IGVL+ +H++ + I D +L+ G +S Sbjct: 158 LLDEPFAGVDPISVGEIQRIVRHLK-ERGIGVLITDHNVRETLGICDRAYILNDGEVLSR 216 Query: 251 GDPAFVKNDPAVIRAYLGEE 270 G PA + D V YLG E Sbjct: 217 GTPAHILADEKVREVYLGRE 236 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: 172 Number of extensions: 13 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: 239 Length adjustment: 25 Effective length of query: 269 Effective length of database: 214 Effective search space: 57566 Effective search space used: 57566 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