GapMind for catabolism of small carbon sources

 

Protein Synpcc7942_0684 in Synechococcus elongatus PCC 7942

Annotation: Synpcc7942_0684 3-oxoacyl-[acyl-carrier-protein] reductase

Length: 249 amino acids

Source: SynE in FitnessBrowser

Candidate for 28 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism ivdG med 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale) 41% 99% 176 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
L-rhamnose catabolism LRA1 med NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized) 42% 98% 167.9 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
D-sorbitol (glucitol) catabolism sdh med L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized) 41% 94% 151 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
ethanol catabolism etoh-dh-nad lo alcohol dehydrogenase (EC 1.1.1.1) (characterized) 37% 100% 151 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
L-rhamnose catabolism LRA5 lo 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized) 35% 94% 144.1 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized) 36% 91% 143.7 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
D-galactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 36% 91% 142.9 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
lactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 36% 91% 142.9 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
D-sorbitol (glucitol) catabolism srlD lo sorbitol-6-phosphate dehydrogenase (characterized) 37% 99% 142.1 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
4-hydroxybenzoate catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 38% 53% 138.7 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
4-hydroxybenzoate catabolism paaH lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 38% 53% 138.7 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
L-arginine catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 38% 53% 138.7 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
L-citrulline catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 38% 53% 138.7 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
L-lysine catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 38% 53% 138.7 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
phenylacetate catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 38% 53% 138.7 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
phenylacetate catabolism paaH lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 38% 53% 138.7 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
L-phenylalanine catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 38% 53% 138.7 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
L-phenylalanine catabolism paaH lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 38% 53% 138.7 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
L-proline catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 38% 53% 138.7 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
xylitol catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 33% 97% 132.5 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
D-xylose catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 33% 97% 132.5 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
glycerol catabolism dhaD lo NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized) 31% 95% 128.6 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
D-mannitol catabolism mt2d lo NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized) 33% 98% 122.9 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
2-deoxy-D-ribonate catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate dehydrogenase (characterized) 33% 94% 122.5 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
2-deoxy-D-ribose catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate dehydrogenase (characterized) 33% 94% 122.5 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
L-fucose catabolism fucDH lo Short-chain dehydrogenase/reductase SDR (characterized, see rationale) 33% 97% 122.1 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
D-xylose catabolism DKDP-dehydrog lo SDR family oxidoreductase (characterized, see rationale) 34% 96% 115.5 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2
D-xylose catabolism xdh lo D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized) 30% 93% 104 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) 100% 467.2

Sequence Analysis Tools

View Synpcc7942_0684 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MTALPLTDRIALVTGASRGIGRAIALELAAAGAKVAVNYASSAGAADEVVAAIAAAGGEA
FAVKADVSQESEVEALFAAVIERWGRLDVLVNNAGITRDTLLLRMKRDDWQSVLDLNLGG
VFLCSRAAAKIMLKQRSGRIINIASVVGEMGNPGQANYSAAKAGVIGLTKTVAKELASRG
ITVNAVAPGFIATDMTSELAAEKLLEVIPLGRYGEAAEVAGVVRFLAADPAAAYITGQVI
NIDGGLVMA

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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