Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate 8500738 DvMF_1481 ABC transporter related (RefSeq)
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__Miya:8500738 Length = 259 Score = 212 bits (540), Expect = 6e-60 Identities = 122/262 (46%), Positives = 162/262 (61%), Gaps = 10/262 (3%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 LL V L++ FGG+ A++ SF+A G ITA+IGPNGAGKTTL NC+TG P G + Sbjct: 3 LLAVRDLSVAFGGIRALDAASFTAQAGAITALIGPNGAGKTTLVNCVTGMVRPDSGNVAF 62 Query: 71 RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130 D R+P + +ARTFQ++R+FG MS+LEN++V H + ++ Sbjct: 63 DGRDITGMAAHRLP------RLGLARTFQHLRVFGSMSLLENVMVGLHGHVRTGM---LS 113 Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190 +L LP RTER D A LD L + AD AG LPYG Q+RL +ARA+ +P M+ Sbjct: 114 SMLRLPGVRRTERAMRDAAMRALDFTGLADRADGAAGLLPYGDQKRLVLARALVGDPRMI 173 Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250 LDEP AGLNP E+ E+ L+ +R + VLLIEHDMS+VM +SD VVVL G KI++ Sbjct: 174 LLDEPVAGLNPAETHEMGGLILALR-ARGVAVLLIEHDMSLVMRVSDAVVVLCSGAKIAE 232 Query: 251 GDPAFVKNDPAVIRAYLGEEED 272 G P VK +P V+ AYLG E+ Sbjct: 233 GAPGEVKRNPEVVNAYLGGGEE 254 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: 220 Number of extensions: 9 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: 259 Length adjustment: 25 Effective length of query: 269 Effective length of database: 234 Effective search space: 62946 Effective search space used: 62946 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