Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_013403238.1 CALHY_RS06840 ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_000166355.1:WP_013403238.1 Length = 234 Score = 106 bits (265), Expect = 4e-28 Identities = 79/261 (30%), Positives = 126/261 (48%), Gaps = 31/261 (11%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 +L V + + +G + A+ VS GEI +IG NGAGK+TL I+G P G + Sbjct: 1 MLKVNGIDVYYGAIQALFSVSLDVQKGEIVTLIGANGAGKSTLLKTISGLIRPRTGSIYF 60 Query: 71 RHAD-GKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSI 129 D K+ +E + K ++ + R+F M+VLEN Sbjct: 61 EDIDITKKSSMEIV-------KLGISHVPEGRRVFPEMTVLEN----------------- 96 Query: 130 AGLLGLPSYTRTEREAV--DLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEP 187 L L +Y R +++ + DL K + RL E + AG L G Q+ L I RA+ + P Sbjct: 97 ---LELGAYLRKDKQGIKEDLKKVFERFPRLYERKNQLAGTLSGGEQQMLAIGRALMSRP 153 Query: 188 VMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRK 247 +L LDEP+ GL P E+ ++ I + +LLIE + + ++I+D V++ G+ Sbjct: 154 KLLLLDEPSMGLAPILVTEIFKIIKEINSQGTT-ILLIEQNAHMALSIADRAYVIETGKI 212 Query: 248 ISDGDPAFVKNDPAVIRAYLG 268 + GD + +P V +AYLG Sbjct: 213 VLSGDAKEIAANPEVKKAYLG 233 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: 125 Number of extensions: 6 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: 234 Length adjustment: 25 Effective length of query: 269 Effective length of database: 209 Effective search space: 56221 Effective search space used: 56221 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