GapMind for catabolism of small carbon sources

 

Protein Ga0059261_1680 in Sphingomonas koreensis DSMZ 15582

Annotation: Ga0059261_1680 NAD-dependent aldehyde dehydrogenases

Length: 469 amino acids

Source: Korea in FitnessBrowser

Candidate for 49 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-phenylalanine catabolism pad-dh hi phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 58% 99% 556.2 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 50% 450.7
4-hydroxybenzoate catabolism adh lo Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized) 37% 98% 325.1 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
2'-deoxyinosine catabolism adh lo Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized) 37% 98% 325.1 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
2-deoxy-D-ribose catabolism adh lo Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized) 37% 98% 325.1 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
ethanol catabolism adh lo Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized) 37% 98% 325.1 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-threonine catabolism adh lo Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized) 37% 98% 325.1 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
thymidine catabolism adh lo Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized) 37% 98% 325.1 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-tryptophan catabolism adh lo Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized) 37% 98% 325.1 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-arginine catabolism gabD lo succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16) (characterized) 39% 93% 304.7 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-citrulline catabolism gabD lo succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16) (characterized) 39% 93% 304.7 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
putrescine catabolism gabD lo succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16) (characterized) 39% 93% 304.7 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 36% 96% 300.1 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 36% 96% 300.1 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 36% 96% 300.1 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 36% 99% 297.4 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 95% 288.9 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 95% 288.9 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 95% 288.9 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 95% 288.9 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-arginine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 37% 95% 283.5 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-citrulline catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 37% 95% 283.5 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
putrescine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 37% 95% 283.5 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 35% 97% 282.7 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 35% 97% 282.7 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-fucose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 35% 92% 278.9 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-rhamnose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 35% 92% 278.9 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-threonine catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 35% 92% 278.9 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 33% 98% 264.6 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 33% 98% 264.6 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 33% 98% 264.6 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 33% 98% 264.6 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 35% 96% 261.5 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-tryptophan catabolism nbaE lo 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 33% 95% 260.4 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 34% 94% 248.1 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 34% 94% 248.1 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 92% 236.5 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 92% 236.5 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 92% 236.5 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 92% 236.5 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 92% 236.5 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized) 32% 95% 232.6 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 92% 225.3 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 92% 225.3 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 92% 225.3 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 92% 225.3 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 31% 92% 225.3 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 35% 91% 224.6 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 35% 91% 224.6 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2
L-lysine catabolism amaB lo Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale) 33% 93% 218.8 phenylacetaldehyde dehydrogenase (EC 1.2.1.39) 58% 556.2

Sequence Analysis Tools

View Ga0059261_1680 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

VTGVRLIVDGKPLAMAETFPVIDPATGRPFADAPLASTADLDAAVAAARRAFPGWAATPI
EDRAAAILAIADSIEAAKDELARLLSAEQGKPVPNAVGEIMGALAWARATAGLRPAVDVL
KDDDSVRVEVHRKPLGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMKPSSFTPLAALRM
VEIANAHLPPGVLNSVTGEVEIGRAIASHPGIDKIVFTGSTPTGRSIMADGAANLKRLTL
ELGGNDAAIVLPDADVDKVAAKIFAKAFGNSGQICAAVKRVYVHESIHDALAEKLAEMAR
TAVVGPGSDAASQFGPVQNRKQFDLVRALADDARAHGGRFLAGGEAREGDGYFFPLSVVV
DVTDGMRIVDEEQFGPILPVIRYSDPEDALARANANENGLGGSVWSADPAAALAFAQRLE
AGTVWVNDHASISPDVPFGGAKQSGVGTEFGLYGLEEYMQLQTVRVAKN

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, 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