GapMind for catabolism of small carbon sources

 

Protein Dsui_0105 in Dechlorosoma suillum PS

Annotation: FitnessBrowser__PS:Dsui_0105

Length: 476 amino acids

Source: PS in FitnessBrowser

Candidate for 51 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) 41% 99% 350.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
2'-deoxyinosine catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 41% 99% 350.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
2-deoxy-D-ribose catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 41% 99% 350.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
ethanol catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 41% 99% 350.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-threonine catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 41% 99% 350.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
thymidine catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 41% 99% 350.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-tryptophan catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 41% 99% 350.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-arginine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 42% 95% 339.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-citrulline catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 42% 95% 339.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
putrescine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 42% 95% 339.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-arginine catabolism gabD med succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16) (characterized) 42% 97% 326.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-citrulline catabolism gabD med succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16) (characterized) 42% 97% 326.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
putrescine catabolism gabD med succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16) (characterized) 42% 97% 326.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-arginine catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 40% 96% 317 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-citrulline catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 40% 96% 317 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-lysine catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 40% 96% 317 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-proline catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 40% 96% 317 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 39% 99% 315.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 39% 99% 315.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 39% 99% 315.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 39% 99% 315.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 39% 99% 315.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-arginine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 96% 310.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-citrulline catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 96% 310.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
putrescine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 96% 310.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 39% 98% 302.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 39% 98% 302.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-arabinose catabolism xacF lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 99% 297.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
D-galacturonate catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 99% 297.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
D-glucuronate catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 99% 297.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 38% 96% 297.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
D-xylose catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 99% 297.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-arginine catabolism kauB lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 38% 96% 291.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-tryptophan catabolism nbaE lo aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 37% 95% 284.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
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) 35% 96% 241.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 92% 224.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 92% 224.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 92% 224.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 92% 224.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 92% 224.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 93% 222.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 93% 222.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 93% 222.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 93% 222.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 93% 222.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) 34% 98% 204.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) 34% 98% 204.1 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-lysine catabolism amaB lo Δ1-piperideine-6-carboxylate dehydrogenase (characterized) 36% 77% 192.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
4-hydroxybenzoate catabolism boxD lo 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase; EC 1.2.1.77 (characterized) 31% 92% 134 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
phenylacetate catabolism boxD lo 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase; EC 1.2.1.77 (characterized) 31% 92% 134 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0
L-phenylalanine catabolism boxD lo 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase; EC 1.2.1.77 (characterized) 31% 92% 134 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 48% 431.0

Sequence Analysis Tools

View Dsui_0105 at FitnessBrowser

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

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Sequence

MQQHSRFYIGGQWVAPDGNAFIDVENPATETVIARVPEGTATDADRAARAAAAAFPAWAA
LSGAERGAFLQKIADGLKARQDELGRLIASEVGMPVKLATRVQAGNPIFTFAACARIAAE
GFAEERIGQSLVLKVPTGPVACITPWNFPLHQIAAKVGAALAAGCTVVLKPSEVAPLNAF
LLAEVIEAAGLPAGVFNLVTGYGPVVGEALAAHPALAAVSFTGSTAAGKRVAAVAAATVK
RVSLELGGKSASVVLPDADLAAAVKGTVAGCFLNSGQACSALTRLLVPQERYAEAAALAV
QAAAAYTLGDPLAEGSRLGPLVSGLQRQRVRAMIEQAVADGAELLCGGSAAPEGLPTGYY
VRPTVFGRVRPDAALAREEVFGPVLAILTYRDEAEAEAIANGTDYGLAAAVWSAEEARAL
AFARRLRAGQVDINGAFFNLLAPFGGFKQSGYGRELGRHGVEDFLETQSIQLPQRQ

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