Align glucose transporter, ATPase component (characterized)
to candidate 5210659 Shew_3087 lipid ABC transporter ATPase/inner membrane protein (RefSeq)
Query= reanno::Phaeo:GFF3641 (260 letters) >FitnessBrowser__PV4:5210659 Length = 620 Score = 89.7 bits (221), Expect = 1e-22 Identities = 66/216 (30%), Positives = 107/216 (49%), Gaps = 20/216 (9%) Query: 27 GIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIRVNGDKVEITNPRD 86 G++ + +S+ + PGE V L+G +GAGKSTL ++L Y +D+G I ++G + P+D Sbjct: 391 GVEVIRGLSLHIAPGERVALVGASGAGKSTLFELLQRFYVLDSGVIALDGIDIASLRPQD 450 Query: 87 ARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAMEAECRKIMNRLNPNFQK 146 R +++ A ++ N+ GR D S E + + R + Sbjct: 451 LRQQYALVPQESVIFATSV--LENVRYGRP--------DASLEEVQAACVAARADEFIAD 500 Query: 147 FSEPVSA--------LSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQMVAELIQQ 198 FSE LSGGQ+Q +AIARA+ + +L++DE T+AL Q V + + Sbjct: 501 FSEGYQTYLGERGVRLSGGQKQRIAIARAILADRPVLLLDEATSALDAVSEQKVKQALDV 560 Query: 199 LKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVGT 234 L QG +I H + V+ DR VM G+L+ + Sbjct: 561 L-MQGRTTLIIAHRLATVLN-ADRILVMDKGELIAS 594 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: 288 Number of extensions: 17 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: 620 Length adjustment: 31 Effective length of query: 229 Effective length of database: 589 Effective search space: 134881 Effective search space used: 134881 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: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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