Align 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16; EC 4.1.2.55) (characterized)
to candidate CCNA_01562 CCNA_01562 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxyphosphogluconate aldolase
Query= metacyc::MONOMER-4906 (205 letters) >FitnessBrowser__Caulo:CCNA_01562 Length = 224 Score = 103 bits (258), Expect = 2e-27 Identities = 68/207 (32%), Positives = 108/207 (52%), Gaps = 17/207 (8%) Query: 12 IVAVLRANSVEEAKEKALAVFEGGVHLIEITFTVPDADTVIKELSFL---KEKGAIIGAG 68 ++ V VE K A +GG IE T A V E++ + I+G G Sbjct: 17 VIPVFYHPDVEVCKNVIQACADGGAPCIEFTNRGDFASHVFYEVTRYFAEADPRVIMGVG 76 Query: 69 TVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLGHTIL 128 ++ + +GA+F+V P L+ ++++ C + + Y PG + +E+ A +LG I+ Sbjct: 77 SIVDAPTAGIYIANGAKFVVGPILNADVAKVCNRRKIPYSPGCGSASEISYAEELGCEIV 136 Query: 129 KLFPGEVV-GPQFVKAMKGPFPNVKFVPTGGVNLD--NVCEWFKAGVLAVGVGSALV--- 182 K+FPG V GP FVKA+ GP P + +PTGGV+ D +V +WF AG++A G+GS L+ Sbjct: 137 KVFPGSSVGGPDFVKAVLGPMPWTRIMPTGGVDPDEASVKKWFGAGIVAAGMGSKLITQE 196 Query: 183 -------KGTPDEVREKAKAFVEKIRG 202 G +VRE ++K+RG Sbjct: 197 MLDAKDYAGISKKVRETVD-LIKKVRG 222 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: 147 Number of extensions: 7 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: 224 Length adjustment: 22 Effective length of query: 183 Effective length of database: 202 Effective search space: 36966 Effective search space used: 36966 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