Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (uncharacterized)
to candidate Echvi_0155 Echvi_0155 ketose-bisphosphate aldolases
Query= curated2:Q5WKY5 (293 letters) >FitnessBrowser__Cola:Echvi_0155 Length = 274 Score = 160 bits (406), Expect = 2e-44 Identities = 91/211 (43%), Positives = 127/211 (60%), Gaps = 4/211 (1%) Query: 24 NINGLQWAKAILAGAESQQSPVIAAASDRLIDYLGGFQTVVAMMGALTDELGITVPVVLH 83 N L+ + +L A + PVI + IDY+G T VAM A E G V +H Sbjct: 21 NFYNLETLQGVLKAASAMDEPVILQLTKSSIDYMG-LNTAVAMGRAALKEYG--VEGWIH 77 Query: 84 LDHGLSIERCKKAVDAGFSSVMFDGSHYPINENIDMTKEVVAYAHAHNVSVEGEVGTVGG 143 LDHG S+E + +DAGF SVM DGS P EN+ +T+EVV AH + +VE E+G V Sbjct: 78 LDHGGSVELAQACLDAGFDSVMIDGSELPFEENVKITQEVVRRAHKYGANVEAELGYVAK 137 Query: 144 MEDGLMAEIKYADVEECQRFVCETNVDALAAALGSVHGKYKGEPKLGFNEMAAISASTNV 203 + + + EE + FV +T VDALA ++G+ HG YK EPKL F+ ++ I+A+T Sbjct: 138 LGQSHEHQ-GFTTAEEAKTFVEQTGVDALAISIGTAHGFYKQEPKLQFDLLSEIAAATEA 196 Query: 204 PLVLHGASGIPDEQLQRAIKLGHAKININTE 234 LVLHG+SG+P+EQL++AI G K+N+ TE Sbjct: 197 TLVLHGSSGVPEEQLRKAISGGICKVNLATE 227 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: 186 Number of extensions: 12 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: 274 Length adjustment: 26 Effective length of query: 267 Effective length of database: 248 Effective search space: 66216 Effective search space used: 66216 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