Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_090271761.1 BLU11_RS01725 ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_900105005.1:WP_090271761.1 Length = 236 Score = 92.4 bits (228), Expect = 8e-24 Identities = 69/224 (30%), Positives = 108/224 (48%), Gaps = 21/224 (9%) Query: 27 VNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTLRHADGKEFLLERMPGY 86 ++D+ GE+TA+IGP+G+GK+TL N I P+ G L L+ ++ Sbjct: 26 LHDIDLRLGRGELTALIGPSGSGKSTLLNLIGLLDVPSAGELYLQGQPTRDSDDATRTHL 85 Query: 87 RISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIAGLLGLPSYTRTEREAV 146 R ++ FQ L SVLEN+++ LI SG R EA+ Sbjct: 86 R---NQALGFVFQFHHLISAFSVLENVLMP----LIIRSG-------------RPSTEAI 125 Query: 147 DLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVMLCLDEPAAGLNPRESGE 206 DLA+ L V L + AD + + G Q+R+ IARA+ T P +L DEP L+ + + Sbjct: 126 DLARGLLREVGLEKMADKKPTEISGGQQQRVAIARALITRPPLLLADEPTGNLDTKTAES 185 Query: 207 LADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250 + DL I + +L++ HD + + V ++D GR +SD Sbjct: 186 VFDLFRRINSQFGCSILVVTHDPRLAASCPRTVQLVD-GRIVSD 228 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: 157 Number of extensions: 10 Number of successful extensions: 2 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: 236 Length adjustment: 25 Effective length of query: 269 Effective length of database: 211 Effective search space: 56759 Effective search space used: 56759 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