Align glucose transporter, ATPase component (characterized)
to candidate WP_089136535.1 CES79_RS05345 methionine ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF3641 (260 letters) >NCBI__GCF_002217945.1:WP_089136535.1 Length = 344 Score = 116 bits (291), Expect = 5e-31 Identities = 75/230 (32%), Positives = 133/230 (57%), Gaps = 14/230 (6%) Query: 15 LVEMKDISISF----GGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAG 70 ++E K+++ +F G + AV V++++ GE+ G++G++GAGKSTL ++L+G +G Sbjct: 1 MIEFKNVTKTFTTKDGDVTAVSDVNLNIDDGEIYGIVGYSGAGKSTLTRMLNGLETPTSG 60 Query: 71 EIRVNGDKVEITNPRDARS--HNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSA 128 EI +NGD + + + R I I+Q L + N+ E+ V S Sbjct: 61 EIDINGDPITALSGPELRKKRQKIGMIFQHFNLLWSRTVIQNIMFPLEVAG----VSRSD 116 Query: 129 MEAECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHE 188 + + + +++ + ++ S P S LSGGQ+Q V +ARA+ + +ILI DE T+AL P Sbjct: 117 RKKKAQHLVDLVGLTGREHSYP-SELSGGQKQRVGVARALANDPEILISDEATSALDPQT 175 Query: 189 TQMVAELIQQL-KAQGIGIFLIDHDVNAVMELCDRASVMKNGQLV--GTV 235 T V +L+ ++ K + I LI H+++A+ ++CD +VM +G++V GTV Sbjct: 176 TDEVLDLLLEINKKMNLSIVLITHEMHAIRKICDHVAVMDDGKVVEQGTV 225 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: 174 Number of extensions: 8 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: 260 Length of database: 344 Length adjustment: 27 Effective length of query: 233 Effective length of database: 317 Effective search space: 73861 Effective search space used: 73861 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: 48 (23.1 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