Align glucose transporter, ATPase component (characterized)
to candidate WP_026126106.1 CDO52_RS22210 ATP-binding cassette domain-containing protein
Query= reanno::Phaeo:GFF3641 (260 letters) >NCBI__GCF_002263495.1:WP_026126106.1 Length = 270 Score = 192 bits (489), Expect = 5e-54 Identities = 107/239 (44%), Positives = 152/239 (63%), Gaps = 9/239 (3%) Query: 13 TPLVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEI 72 TPL+E + +G + A+D ++LYPGE++ ++G NGAGKSTLIK LSGA D GEI Sbjct: 13 TPLLEAHGLVKRYGRVTALDGTDLELYPGEILAVIGDNGAGKSTLIKCLSGAVVPDEGEI 72 Query: 73 RVNGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTP------FGLVDD 126 R++G V + P ARS IET++QTLA++ +LD ASNLFLGREL P F +D Sbjct: 73 RLDGGPVRLDTPLAARSAGIETVHQTLAVSPSLDIASNLFLGRELRKPGVVGAVFRTLDH 132 Query: 127 SAMEAECRKIMNRLN-PNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALG 185 M E + ++ L Q + V LSGGQRQ+VA+ARA F ++++IMDEPTAALG Sbjct: 133 KRMREEALRHLDALGVMTIQNPGQAVETLSGGQRQAVAVARAAAFGSRVVIMDEPTAALG 192 Query: 186 PHETQMVAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVGTVDID--DVTD 242 E+ V +LI +++ G+ + +I H++ V E+ DR + + G+ V TV D D+TD Sbjct: 193 VRESHAVLDLILRVRESGLAVIVISHNMPHVFEIADRIHIQRLGRRVATVTPDECDMTD 251 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: 184 Number of extensions: 5 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: 270 Length adjustment: 25 Effective length of query: 235 Effective length of database: 245 Effective search space: 57575 Effective search space used: 57575 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