Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (uncharacterized)
to candidate BWI76_RS00545 BWI76_RS00545 putative class-II ketose-bisphosphate aldolase
Query= curated2:Q5WKY5 (293 letters) >FitnessBrowser__Koxy:BWI76_RS00545 Length = 280 Score = 187 bits (474), Expect = 3e-52 Identities = 103/259 (39%), Positives = 149/259 (57%), Gaps = 7/259 (2%) Query: 19 AIGQFNINGLQWAKAILAGAESQQSPVIAAASDRLIDYLGGFQTVVAMMGALTDELGITV 78 AIG FN++ ++ A A+ SP++ S +YLG V A+ E V Sbjct: 20 AIGSFNLHCIEMLPAFFKAAQQSHSPLMIQISTGTAEYLGYRLLVDAVRSLAESE---NV 76 Query: 79 PVVLHLDHGLSIERCKKAVDAGFSSVMFDGSHYPINENIDMTKEVVAYAHAHNVSVEGEV 138 P LHLDH I + A+DAGF+SVM+DGSH + ENI T+ VV A N++VEGE+ Sbjct: 77 PTCLHLDHCSDISAIETAMDAGFTSVMYDGSHLDLEENIGNTRIVVEMARPRNITVEGEL 136 Query: 139 GTVGGMEDGLMA---EIKYADVEECQRFVCETNVDALAAALGSVHGKYKGEPKLGFNEMA 195 G +GG EDG +I + VE+ +RFV ET VD LA ++G+VHG Y G+ ++ + Sbjct: 137 GAIGGSEDGKAVAAEDICFTTVEDAKRFVEETRVDMLAVSVGTVHGLYTGKAQIQHQRLK 196 Query: 196 AISASTNVPLVLHGASGIPDEQLQRAIKLGHAKININTECMIAWSDACRTTFAEQETAFE 255 ISA+T VPLVLHG +G+ DE +++A+ G K+N+ TE + W D C+TTF + + Sbjct: 197 EISAATGVPLVLHGGTGVSDEDMRQAVTEGINKVNVGTEMNVQWVDRCKTTFEKGKVNDS 256 Query: 256 PR-LLLQEGLAMVQATVEK 273 R L+ A+ +EK Sbjct: 257 VRKFLIPANNAVTHVLIEK 275 Lambda K H 0.317 0.132 0.378 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: 197 Number of extensions: 7 Number of successful extensions: 4 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: 293 Length of database: 280 Length adjustment: 26 Effective length of query: 267 Effective length of database: 254 Effective search space: 67818 Effective search space used: 67818 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