Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_110208105.1 DNK54_RS16590 ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_003194585.1:WP_110208105.1 Length = 263 Score = 172 bits (437), Expect = 6e-48 Identities = 106/265 (40%), Positives = 146/265 (55%), Gaps = 22/265 (8%) Query: 10 PLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLT 69 PLL V + +RFGG+ AVN F+A+ IT +IGPNGAGKTT FN ITG PT G + Sbjct: 2 PLLEVNDVVVRFGGVTAVNQARFTADERRITGLIGPNGAGKTTCFNVITGLQRPTSGSVR 61 Query: 70 LRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSI 129 D + R + +ARTFQ + FG ++V +N+ VA I Sbjct: 62 FGGRDVTRTAVHR------RARRGMARTFQRLEAFGSLTVRDNVRVA----------LDI 105 Query: 130 AGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVM 189 AG G R+ VD A LDRV + E+A A ++P G R LE+AR + +P + Sbjct: 106 AG--GFGGLMRSSSARVDEA---LDRVGISEYAAERADSIPTGTARLLELARCLVGDPKL 160 Query: 190 LCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKIS 249 L LDEP++GL+ E+ +LL + E K +L++EHDM +VMT+ D + VLD+G I Sbjct: 161 LLLDEPSSGLDESETDAFGELLIALASEGK-AILMVEHDMDLVMTVCDDIHVLDFGEIIC 219 Query: 250 DGDPAFVKNDPAVIRAYLGEEEDEE 274 G PA V+ D V AYLG + +E Sbjct: 220 SGSPAEVRADARVQAAYLGASDTDE 244 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: 185 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: 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 Sep 24 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