Align 5-keto-4-deoxy-D-glucarate aldolase; KDGluc aldolase; KDGlucA; 2-dehydro-3-deoxy-D-glucarate aldolase; 2-keto-3-deoxy-D-glucarate aldolase; 5-dehydro-4-deoxy-D-glucarate aldolase; Alpha-keto-beta-deoxy-D-glucarate aldolase; EC 4.1.2.20 (characterized)
to candidate PfGW456L13_3931 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (EC 4.1.2.n4)
Query= SwissProt::P23522 (256 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3931 Length = 266 Score = 224 bits (572), Expect = 1e-63 Identities = 110/238 (46%), Positives = 152/238 (63%), Gaps = 1/238 (0%) Query: 8 NKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMALKG 67 N FKAAL + Q G W+ + + E++ G+DW+++DGEHAPN + + QL A+ Sbjct: 6 NAFKAALNSSGTQYGIWAGFATGYAAEIVATTGYDWMLIDGEHAPNTVPGVLAQLQAVAP 65 Query: 68 SASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGVSVS- 126 ++APVVR + +IK+LLDIG +IP VET +A+ V + RYPP GIRGV Sbjct: 66 YSTAPVVRAVNGDANLIKQLLDIGAQTLMIPMVETAAQAQALVRAMRYPPHGIRGVGGGL 125 Query: 127 HRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDLAAALGH 186 RA + V DY +++ + ++VQ+ES+ GV+NV AIAA EGVD +F+GP+DL+ LGH Sbjct: 126 TRATRWDDVPDYLNTAHEQLCLIVQVESRTGVENVAAIAAVEGVDAVFIGPADLSIGLGH 185 Query: 187 LGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDLGVFR 244 GN HP+VQ+ IQ+ N A GK GILAP E DARRY WG F+AV D+ + R Sbjct: 186 AGNPGHPEVQERIQYAVNATLAAGKACGILAPNEEDARRYQRWGCQFIAVAIDISLLR 243 Lambda K H 0.318 0.134 0.392 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: 192 Number of extensions: 3 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: 256 Length of database: 266 Length adjustment: 25 Effective length of query: 231 Effective length of database: 241 Effective search space: 55671 Effective search space used: 55671 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