GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_0379 in Dyella japonica UNC79MFTsu3.2

Annotation: FitnessBrowser__Dyella79:N515DRAFT_0379

Length: 476 amino acids

Source: Dyella79 in FitnessBrowser

Candidate for 35 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-fucose catabolism aldA med Lactaldehyde dehydrogenase; EC 1.2.1.22 (uncharacterized) 36% 97% 297.4 phosphonoformaldehyde dehydrogenase 37% 273.5
L-rhamnose catabolism aldA med Lactaldehyde dehydrogenase; EC 1.2.1.22 (uncharacterized) 36% 97% 297.4 phosphonoformaldehyde dehydrogenase 37% 273.5
L-threonine catabolism aldA med Lactaldehyde dehydrogenase; EC 1.2.1.22 (uncharacterized) 36% 97% 297.4 phosphonoformaldehyde dehydrogenase 37% 273.5
L-arginine catabolism gabD lo succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 36% 94% 269.6 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
L-citrulline catabolism gabD lo succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 36% 94% 269.6 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
putrescine catabolism gabD lo succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 36% 94% 269.6 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 34% 87% 234.6 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 34% 87% 234.6 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 34% 87% 234.6 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
4-hydroxybenzoate catabolism adh lo Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized) 34% 85% 233.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
2'-deoxyinosine catabolism adh lo Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized) 34% 85% 233.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
2-deoxy-D-ribose catabolism adh lo Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized) 34% 85% 233.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
ethanol catabolism adh lo Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized) 34% 85% 233.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
L-threonine catabolism adh lo Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized) 34% 85% 233.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
thymidine catabolism adh lo Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized) 34% 85% 233.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
L-tryptophan catabolism adh lo Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized) 34% 85% 233.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized) 32% 91% 224.9 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 35% 96% 223.8 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 34% 91% 221.5 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 34% 91% 221.5 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
L-tryptophan catabolism nbaE lo 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 31% 94% 221.1 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
L-arabinose catabolism xacF lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 34% 93% 216.9 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
D-galacturonate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 34% 93% 216.9 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
D-glucuronate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 34% 93% 216.9 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
D-xylose catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 34% 93% 216.9 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 92% 205.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 92% 205.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 92% 205.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 32% 92% 205.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 30% 92% 189.1 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 30% 92% 189.1 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 30% 92% 189.1 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 30% 92% 189.1 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 30% 92% 189.1 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2
L-valine catabolism mmsA lo malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 30% 92% 189.1 lactaldehyde dehydrogenase (EC 1.2.1.22) 38% 276.2

Sequence Analysis Tools

View N515DRAFT_0379 at FitnessBrowser

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MLEKKYPYYLANKAQTSKAWMDVLDKYSGKVATRVAVPDAKATEQAIAAAVKAAEPMRQF
KPWERQAVLQHCVQRFTERRDELAYALCVEAGKPIKDSAGEVTRLIETFGIAAEEAVRTN
GETINLEIAKRLNGYHGYTRRVPLGPVSFITPFNFPLNLVAHKVAPAIAAGCPFVLKPAE
RTPIGALIIGEVLAETDLPKGAFSILNLDGKHASPLVEDPRFKLLSFTGSQIGWDLKTRA
GHKKVTLELGGNAACIVDADQLPRLDHVIERLVFGAFYQSGQSCISVQRIYAHESLYDEL
KKRLVAAVKGLKAGDPKKKETFLGPMIDEAAAERLHGWIEEARKGGGKVLCGGKRKGPML
EATLMENVRGDAKVNRQEVFGPFALLAPFKSLDEAIAMTNDSDYGLQAGIFTDSLANAMR
AWNELEQGGVIVNDVPSFRVDNMPYGGVKLSGAGREGVRYAIEDMTEIRLMVMRES

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 (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:

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. 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