Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate 8502040 DvMF_2753 ABC transporter related (RefSeq)
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__Miya:8502040 Length = 255 Score = 204 bits (520), Expect = 1e-57 Identities = 122/263 (46%), Positives = 165/263 (62%), Gaps = 10/263 (3%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 LL + +LT FGGLVAVN+V+F G I +IGPNGAGKTT+FN ITG Y P G + Sbjct: 3 LLALRNLTKTFGGLVAVNNVTFDVAEGSIVGLIGPNGAGKTTVFNLITGNYKPDSGDIFF 62 Query: 71 RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130 DG+ ++ +P +RI Q+ +ARTFQ IRLF MSV+EN++ H R ++ Sbjct: 63 ---DGR--TIKGLPTHRIVQQ-GIARTFQTIRLFQNMSVIENVLAGCH---CRMQSGMLS 113 Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190 +L P+ E+ A+ A L+ V L A NL YG QR LEIARA+ T+P + Sbjct: 114 AMLRTPAQRAEEQRALLRATRELEFVGLANEHANLAKNLSYGNQRLLEIARALATDPRFI 173 Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250 LDEPA G+N +E+ L D + IRD I VLLIEHDMS+VM + + +VVL+YG +++ Sbjct: 174 ILDEPAGGMNDQETAALIDTIRAIRD-RGITVLLIEHDMSLVMKVCEKLVVLEYGALLAE 232 Query: 251 GDPAFVKNDPAVIRAYLGEEEDE 273 G PA +K+DP VI AYLG + D+ Sbjct: 233 GVPAAIKDDPRVIEAYLGADTDD 255 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: 203 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: 255 Length adjustment: 25 Effective length of query: 269 Effective length of database: 230 Effective search space: 61870 Effective search space used: 61870 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