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 Ac3H11_3372 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (EC 4.1.2.n4)
Query= SwissProt::P23522 (256 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3372 Length = 277 Score = 217 bits (552), Expect = 2e-61 Identities = 116/258 (44%), Positives = 162/258 (62%), Gaps = 10/258 (3%) Query: 8 NKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMALKG 67 N FK ALA + QIG W L++ + E+L G+DWL++DGEHAPND+ + + QL A+ Sbjct: 6 NSFKQALAQGEAQIGLWLGLADAYTAEILAGTGYDWLLVDGEHAPNDLRSILHQLQAIAS 65 Query: 68 SASA---------PVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPE 118 ++SA V RVP + +IK+ LDIG L+P V+T E+A+ V +TRY PE Sbjct: 66 ASSALPPGARASHAVARVPVGDTALIKQYLDIGAQTLLVPMVDTPEQAQQLVRATRYAPE 125 Query: 119 GIRGV-SVSHRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGP 177 G+RG+ S R++ + Y ++N+ I +LVQ E+ + + ++DAIAAT GVDG+F+GP Sbjct: 126 GVRGMGSALARSSRWQAYPRYVHEANQQICLLVQAETVEAMAHLDAIAATPGVDGVFIGP 185 Query: 178 SDLAAALGHLGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVG 237 +DL+A++GH GN HPDVQ AI R GK GILA EA AR++L GA FVAVG Sbjct: 186 ADLSASMGHPGNPGHPDVQAAIHDGIARILRAGKAPGILATNEAQARQWLAAGALFVAVG 245 Query: 238 SDLGVFRSATQKLADTFK 255 D + SA Q L F+ Sbjct: 246 VDTMLLTSAAQNLLARFR 263 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: 224 Number of extensions: 7 Number of successful extensions: 3 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: 277 Length adjustment: 25 Effective length of query: 231 Effective length of database: 252 Effective search space: 58212 Effective search space used: 58212 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