GapMind for catabolism of small carbon sources

 

Protein WP_092057747.1 in Desulfuromonas acetexigens

Annotation: NCBI__GCF_900111775.1:WP_092057747.1

Length: 472 amino acids

Source: GCF_900111775.1 in NCBI

Candidate for 49 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 48% 99% 424.5 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
2'-deoxyinosine catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 48% 99% 424.5 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
2-deoxy-D-ribose catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 48% 99% 424.5 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
ethanol catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 48% 99% 424.5 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-threonine catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 48% 99% 424.5 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
thymidine catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 48% 99% 424.5 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-tryptophan catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 48% 99% 424.5 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-arginine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 42% 95% 351.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-citrulline catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 42% 95% 351.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
putrescine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 42% 95% 351.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-arginine catabolism gabD med succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16) (characterized) 40% 96% 311.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-citrulline catabolism gabD med succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16) (characterized) 40% 96% 311.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
putrescine catabolism gabD med succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16) (characterized) 40% 96% 311.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized) 38% 96% 327 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-arginine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 95% 320.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-citrulline catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 95% 320.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
putrescine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 95% 320.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 38% 98% 320.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 38% 98% 320.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 38% 98% 320.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 38% 98% 320.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 38% 98% 320.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 95% 314.3 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 37% 98% 309.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 37% 98% 309.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-tryptophan catabolism nbaE lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 37% 97% 308.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 99% 301.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 99% 301.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 99% 301.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 99% 301.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-arabinose catabolism xacF lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 36% 97% 288.5 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
D-galacturonate catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 36% 97% 288.5 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
D-glucuronate catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 36% 97% 288.5 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
D-xylose catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 36% 97% 288.5 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 36% 99% 280.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-valine catabolism mmsA lo Malonate-semialdehyde dehydrogenase 1; MSA dehydrogenase 1; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase 1; MMSA dehydrogenase 1; MSDH 1; EC 1.2.1.27 (uncharacterized) 36% 93% 261.5 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 92% 246.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 92% 246.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 92% 246.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 92% 246.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 92% 246.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 95% 243.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 95% 243.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 95% 243.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 95% 243.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 95% 243.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) 35% 92% 213 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) 35% 92% 213 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5
L-lysine catabolism amaB lo Δ1-piperideine-6-carboxylate dehydrogenase (characterized) 33% 87% 194.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 54% 513.5

Sequence Analysis Tools

View WP_092057747.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MRDYQKFYIDGRWVESRGRETIEVVNPASEQVMARIPAGVGEDAEAAIAAARRAFDGWAA
TPVAQRQALLEKLRHGLSERAEELAEVITDEVGMPLKMTQRVQVGLPIAVLESTIKLLDD
FSFEETVGNSLVLREAVGVVACITPWNYPLHQIVAKLAPALAAGCTVILKPSEVAPCNAF
ILAELIDAAGFPPGVFNLICGTGPVVGEVLAAHPEVDMVSFTGSTRAGKRVSELAAATVK
RLALELGGKSAAVVLDDADLATAIKGTLNACFLNSGQTCSAHTRLLVPESRYDEAARLAT
EGARGFTVGDPKGGQAKLGPLVSAVQRERVREYIQKGLAEGAELLCGGAEAPEGLATGYY
VQPTVFGRVTPTMTIAREEIFGPVLSILTYRDEAEAIRIANDSPYGLAGAVWSADGERAQ
RVARRLRTGQVDINGGRFNLLAPFGGYKQSGHGREFGTFGLEEFLEIKSLQL

This GapMind analysis is from Sep 24 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