Align glucose transporter, ATPase component (characterized)
to candidate 7026950 Shewana3_4079 ABC transporter related (RefSeq)
Query= reanno::Phaeo:GFF3641 (260 letters) >FitnessBrowser__ANA3:7026950 Length = 235 Score = 93.6 bits (231), Expect = 3e-24 Identities = 71/215 (33%), Positives = 110/215 (51%), Gaps = 9/215 (4%) Query: 19 KDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIRVNGDK 78 +D+ +SFG S++L G V+ L G NG+GKSTL+K+L+G G+I V+G K Sbjct: 9 RDLEMSFGPRLLFKAHSLELCQGNVIYLQGDNGSGKSTLMKILAGLQPPSKGKIEVSGFK 68 Query: 79 VEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAMEAECRKI-M 137 + R+ ++Q L D NL G PF A + I M Sbjct: 69 KDAWWTRNPLLGKAVYLHQHPYLFDGT-VNYNLTYG----LPFAASKTEAKRRIGQAIEM 123 Query: 138 NRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQMVAELIQ 197 +L Q + S LSGG+RQ +AIARA K+L++DEPT+ + +V ++IQ Sbjct: 124 AQLGSLLQARA---SNLSGGERQRLAIARAWILQPKLLMLDEPTSNMDKDSQALVLQMIQ 180 Query: 198 QLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLV 232 QLK QG G+ L H A+ +C++ +++ Q++ Sbjct: 181 QLKQQGTGMLLSSHQNCALTAICEQQWHIEDQQVI 215 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: 117 Number of extensions: 7 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: 235 Length adjustment: 24 Effective length of query: 236 Effective length of database: 211 Effective search space: 49796 Effective search space used: 49796 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 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