Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_085770502.1 B1812_RS04380 ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_002117405.1:WP_085770502.1 Length = 293 Score = 195 bits (496), Expect = 9e-55 Identities = 115/264 (43%), Positives = 161/264 (60%), Gaps = 11/264 (4%) Query: 12 LTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTLR 71 L + ++++ FGG+ A++++ FS GEI +IIGPNGAGK++L N ITG Y P GR+ L Sbjct: 35 LALTNISLSFGGIQALSEIDFSVAAGEICSIIGPNGAGKSSLINVITGLYRPDWGRIQL- 93 Query: 72 HADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIAG 131 D F RMP R++ VARTFQN+ LF G+SV +N+ V ++ + Sbjct: 94 --DKNSF--SRMPTERLAS-LGVARTFQNLALFRGLSVFDNIAVG---RVSATRSHWLEQ 145 Query: 132 LLGLPSYTRTEREAVDL-AKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190 + GLP R +R A ++ + L + L + + AG LPYG Q+R+E+ARA+ P +L Sbjct: 146 VFGLPR-ARADRLATEIIVEEMLVFLGLGQVRNRIAGTLPYGMQKRVELARALAIRPRLL 204 Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250 LDEP AG+ E E+ + + RD ++LIEHD+ VVM +SD V VLDYGRKI+D Sbjct: 205 LLDEPMAGMTAGEKAEMGEFIQLTRDRFGASIVLIEHDIGVVMELSDRVAVLDYGRKIAD 264 Query: 251 GDPAFVKNDPAVIRAYLGEEEDEE 274 G P+ V ND AVI AYLG D E Sbjct: 265 GPPSDVMNDEAVIDAYLGVAHDIE 288 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: 206 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: 293 Length adjustment: 26 Effective length of query: 268 Effective length of database: 267 Effective search space: 71556 Effective search space used: 71556 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