Align 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16; EC 4.1.2.55) (characterized)
to candidate WP_152617858.1 BS73_RS13710 2-dehydro-3-deoxyphosphogluconate aldolase
Query= metacyc::MONOMER-4906 (205 letters) >NCBI__GCF_000744815.1:WP_152617858.1 Length = 204 Score = 116 bits (291), Expect = 2e-31 Identities = 62/170 (36%), Positives = 99/170 (58%), Gaps = 1/170 (0%) Query: 13 VAVLRANSVEEAKEKALAVFEGGVHLIEITFTVPDA-DTVIKELSFLKEKGAIIGAGTVT 71 +A+LR E E + ++ G+ L+E+ A + + + E+G ++GAGTVT Sbjct: 1 MAILRGLDRERTVEVSRRAWQAGIRLVEVPVQSEAAVEALAAAVEAGAERGEVVGAGTVT 60 Query: 72 SVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLGHTILKLF 131 +VE+ +A +GA F V+P E+++ G+ ++PGV T +E+ +A LG T LK F Sbjct: 61 TVERVERAAAAGARFTVAPGFCREVAEASLAAGLPHLPGVATASEIQRAQALGLTWLKAF 120 Query: 132 PGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSAL 181 P +G +++AM GPFP +FV TGG++ N E+ AG AV +GSAL Sbjct: 121 PAAELGASWIRAMHGPFPEARFVATGGMSPGNAEEFLSAGAAAVALGSAL 170 Lambda K H 0.318 0.136 0.393 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: 104 Number of extensions: 9 Number of successful extensions: 2 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: 205 Length of database: 204 Length adjustment: 21 Effective length of query: 184 Effective length of database: 183 Effective search space: 33672 Effective search space used: 33672 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 45 (21.9 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