Align glucose transporter, ATPase component (characterized)
to candidate SM_b20904 SM_b20904 sugar uptake ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF3641 (260 letters) >FitnessBrowser__Smeli:SM_b20904 Length = 261 Score = 357 bits (915), Expect = e-103 Identities = 178/246 (72%), Positives = 209/246 (84%) Query: 13 TPLVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEI 72 TPLVEMK+ISISFGGI AVD SVDLYPGEVV LLGHNGAGKSTLIK+LSGAY+ DAGEI Sbjct: 6 TPLVEMKNISISFGGIHAVDDASVDLYPGEVVALLGHNGAGKSTLIKILSGAYKRDAGEI 65 Query: 73 RVNGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAMEAE 132 +NG+ EI NPRDA+ + IETIYQTLA+ADN+DAA+NL+LGREL TP+G +DD AMEA+ Sbjct: 66 LINGEPAEINNPRDAKKYGIETIYQTLAVADNVDAAANLYLGRELRTPWGTLDDVAMEAK 125 Query: 133 CRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQMV 192 R++M RLNPNFQ+F EPV ALSGGQRQSVAIARA+ F+A+ILIMDEPTAALGP ET V Sbjct: 126 AREVMGRLNPNFQRFKEPVKALSGGQRQSVAIARAILFDARILIMDEPTAALGPQETAQV 185 Query: 193 AELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVGTVDIDDVTDDDLLSMIILG 252 ELI+QLK +GIGIFLI HD++ V +L DR SVMKNGQ+VG +DVT D++L MII+G Sbjct: 186 GELIKQLKREGIGIFLISHDIHDVFDLADRVSVMKNGQVVGHARTEDVTKDEVLGMIIMG 245 Query: 253 KRPGEA 258 K P +A Sbjct: 246 KVPPKA 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: 252 Number of extensions: 8 Number of successful extensions: 1 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: 261 Length adjustment: 25 Effective length of query: 235 Effective length of database: 236 Effective search space: 55460 Effective search space used: 55460 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