Align glucose transporter, ATPase component (characterized)
to candidate WP_006747565.1 THITH_RS08160 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF3641 (260 letters) >NCBI__GCF_000227685.2:WP_006747565.1 Length = 306 Score = 102 bits (255), Expect = 7e-27 Identities = 70/223 (31%), Positives = 118/223 (52%), Gaps = 12/223 (5%) Query: 16 VEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIRVN 75 VE++ ++ +G + A++ V+ L GEVVGLLGHNGAGK+T +K++ G + AGEI V Sbjct: 7 VELRGVTRRYGRLAALEGVNWSLREGEVVGLLGHNGAGKTTAMKLILGVAEPSAGEILVY 66 Query: 76 GDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAMEAECRK 135 G P +H++ + L +N+ + GRE++ F + A A+C Sbjct: 67 G-----RPPIGRHAHSLRR--RLGYLPENVSFYPQM-TGREVLRYFARLKGEA-PAQCDA 117 Query: 136 IMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQMVAEL 195 ++ R+ N V S G RQ + +A+A+ ++L+ DEPT L P T+ Sbjct: 118 LLERVGLN-AAAKRRVGTYSKGMRQRLGLAQALLGTPRLLLFDEPTVGLDPIATRDFYRT 176 Query: 196 IQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLV--GTVD 236 + L+ QG I L H + + DRA++++ G+L+ GT++ Sbjct: 177 VDDLRRQGTTIVLCSHVLPGIEPHIDRAAILREGRLLAYGTIE 219 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: 147 Number of extensions: 6 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 260 Length of database: 306 Length adjustment: 26 Effective length of query: 234 Effective length of database: 280 Effective search space: 65520 Effective search space used: 65520 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 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