Align glucose transporter, ATPase component (characterized)
to candidate WP_069957998.1 BEN30_RS08935 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF3641 (260 letters) >NCBI__GCF_001746755.1:WP_069957998.1 Length = 233 Score = 100 bits (250), Expect = 2e-26 Identities = 71/230 (30%), Positives = 129/230 (56%), Gaps = 16/230 (6%) Query: 13 TPLVEMKDISISFGG----IKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMD 68 +PL+E+K IS +G + A+ VS+++YPG+V+GLLG +G+GK+TL+ ++ + Sbjct: 7 SPLIELKHISKHYGEGETRVDALRDVSLEVYPGQVIGLLGPSGSGKTTLLNIIGCIVEAS 66 Query: 69 AGEIRVNGDKVEI-----TNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGL 123 +G +++GD + ++ R R + I+Q L L++ N+ + +L G+ Sbjct: 67 SGWAKLDGDVIYDNAWMKSDLRRLRLDKVGFIFQFHNLLPFLNSMENVSVVLDLA---GV 123 Query: 124 VDDSAMEAECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAA 183 D A + ++++ L ++ + P LSGG+ Q VAIARA+ N +I++ DEPTAA Sbjct: 124 PADRAKQ-RAQELLEYLEVGHRRDAYPAH-LSGGEAQRVAIARALANNPRIILADEPTAA 181 Query: 184 LGPHETQMVAELIQQLKA-QGIGIFLIDHDVNAVMELCDRASVMKNGQLV 232 L +V +L+++L Q + + HD + + DR +++GQLV Sbjct: 182 LDSERALIVMKLLRKLAVEQDAAVLAVTHD-EKIYDQFDRIFHVRDGQLV 230 Lambda K H 0.317 0.135 0.373 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: 134 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: 260 Length of database: 233 Length adjustment: 24 Effective length of query: 236 Effective length of database: 209 Effective search space: 49324 Effective search space used: 49324 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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