Align glucose transporter, ATPase component (characterized)
to candidate Ga0059261_2542 Ga0059261_2542 ABC-type (unclassified) transport system, ATPase component
Query= reanno::Phaeo:GFF3641 (260 letters) >FitnessBrowser__Korea:Ga0059261_2542 Length = 258 Score = 109 bits (272), Expect = 7e-29 Identities = 79/248 (31%), Positives = 129/248 (52%), Gaps = 11/248 (4%) Query: 10 AGATPLVEMKDISISFGGIKAV--DHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQM 67 AG P + +SI+ K V VS+ + GEVVGLLG NGAGK+T + G + Sbjct: 14 AGTPPTSGLAVVSIAKSYDKRVVLSDVSLSVGKGEVVGLLGPNGAGKTTCFYSVMGLVKP 73 Query: 68 DAGEIRVNGDKVEITNPRDARSHNIETIY--QTLALADNLDAASNLFLGRELVTPFGLVD 125 DAG I ++G V+IT R + Y Q ++ L A N+ EL P D Sbjct: 74 DAGRIMLDG--VDITPLPMYRRAILGLGYLPQETSIFRGLTVAKNISAVLELSEP----D 127 Query: 126 DSAMEAECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALG 185 SA A +++ + P ALSGG+R+ IARA+ + I+++DEP A + Sbjct: 128 KSARAARLDQLLEEFGLTRLR-DAPAMALSGGERRRAEIARALAADPSIMLLDEPFAGID 186 Query: 186 PHETQMVAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVGTVDIDDVTDDDL 245 P + +L+++LK + IG+ + DH+V +++ DRAS++ +G+++ +D+ D Sbjct: 187 PISIADIRDLVKELKTRNIGVLITDHNVRETLDIVDRASIIYDGRVLFAGSPEDLVADAN 246 Query: 246 LSMIILGK 253 + + LG+ Sbjct: 247 VRRLYLGE 254 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: 153 Number of extensions: 4 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: 258 Length adjustment: 24 Effective length of query: 236 Effective length of database: 234 Effective search space: 55224 Effective search space used: 55224 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: 47 (22.7 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