Align 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16; EC 4.1.2.55) (characterized)
to candidate Synpcc7942_0017 Synpcc7942_0017 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase
Query= metacyc::MONOMER-4906 (205 letters) >FitnessBrowser__SynE:Synpcc7942_0017 Length = 187 Score = 94.7 bits (234), Expect = 9e-25 Identities = 58/178 (32%), Positives = 100/178 (56%), Gaps = 6/178 (3%) Query: 11 KIVAVLRANSVEEAKEKALAVFEGGVHLIEITFTVPDADTVIKELSFLKEK--GAIIGAG 68 +IVAVLR+ + + A G+ +E+T+T +D + LS L++K GAG Sbjct: 13 RIVAVLRSPDLTQGFAMAETAIARGLRWLEVTWT---SDRPAELLSQLRDKYPDCCWGAG 69 Query: 69 TVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLGHTIL 128 ++ S+ +A+ +GA+F VSP L + + + + + ++PG +TPTE++ A G ++ Sbjct: 70 SLLSLTDLEEAIAAGAQFGVSPILSLPLLERAQARDLPFLPGALTPTEIMTAHAAGAAVV 129 Query: 129 KLFPGEVV-GPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSALVKGT 185 KLFP GP +V++++ P + K GG++ D V + AG +AVG+GS L T Sbjct: 130 KLFPASSAGGPAYVRSLQQPLNHPKLFACGGIHPDAVQSYLDAGAIAVGLGSQLFAKT 187 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: 91 Number of extensions: 6 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: 205 Length of database: 187 Length adjustment: 20 Effective length of query: 185 Effective length of database: 167 Effective search space: 30895 Effective search space used: 30895 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 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