GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_3729 in Dyella japonica UNC79MFTsu3.2

Annotation: N515DRAFT_3729 aminomuconate-semialdehyde/2-hydroxymuconate-6-semialdehyde dehydrogenase

Length: 483 amino acids

Source: Dyella79 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
4-hydroxybenzoate catabolism adh med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 49% 99% 476.9 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
4-hydroxybenzoate catabolism praB med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 49% 99% 476.9 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
2'-deoxyinosine catabolism adh med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 49% 99% 476.9 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
2-deoxy-D-ribose catabolism adh med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 49% 99% 476.9 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
ethanol catabolism adh med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 49% 99% 476.9 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-threonine catabolism adh med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 49% 99% 476.9 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
thymidine catabolism adh med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 49% 99% 476.9 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-tryptophan catabolism adh med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 49% 99% 476.9 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-tryptophan catabolism nbaE med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 49% 99% 476.9 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-tryptophan catabolism praB med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 49% 99% 476.9 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-arginine catabolism patD med Gamma-aminobutyraldehyde dehydrogenase; ABALDH; EC 1.2.1.19; 1-pyrroline dehydrogenase; 4-aminobutanal dehydrogenase; 5-aminopentanal dehydrogenase; EC 1.2.1.- (uncharacterized) 42% 99% 347.4 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-citrulline catabolism patD med Gamma-aminobutyraldehyde dehydrogenase; ABALDH; EC 1.2.1.19; 1-pyrroline dehydrogenase; 4-aminobutanal dehydrogenase; 5-aminopentanal dehydrogenase; EC 1.2.1.- (uncharacterized) 42% 99% 347.4 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
putrescine catabolism patD med Gamma-aminobutyraldehyde dehydrogenase; ABALDH; EC 1.2.1.19; 1-pyrroline dehydrogenase; 4-aminobutanal dehydrogenase; 5-aminopentanal dehydrogenase; EC 1.2.1.- (uncharacterized) 42% 99% 347.4 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-lysine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 42% 99% 346.3 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-phenylalanine catabolism pad-dh med Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized) 40% 97% 343.2 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-arginine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 41% 96% 332 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-arginine catabolism puuC med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 41% 96% 332 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-citrulline catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 41% 96% 332 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-citrulline catabolism puuC med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 41% 96% 332 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
putrescine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 41% 96% 332 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
putrescine catabolism puuC med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 41% 96% 332 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 93% 328.2 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-arabinose catabolism xacF med 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 42% 95% 304.3 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
D-galacturonate catabolism dopDH med 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 42% 95% 304.3 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
D-glucuronate catabolism dopDH med 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 42% 95% 304.3 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
D-xylose catabolism dopDH med 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 42% 95% 304.3 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 38% 96% 306.6 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 38% 96% 306.6 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 38% 96% 306.6 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 38% 96% 306.6 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-fucose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 37% 95% 300.8 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-rhamnose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 37% 95% 300.8 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-threonine catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 37% 95% 300.8 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 36% 96% 265.8 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 36% 96% 265.8 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 36% 96% 265.8 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 36% 96% 265.8 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 36% 96% 265.8 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 35% 98% 265.4 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 35% 98% 265.4 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized) 34% 94% 254.6 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 91% 241.1 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 91% 241.1 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 91% 241.1 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 91% 241.1 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 91% 241.1 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) 35% 93% 223.4 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) 35% 93% 223.4 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6
L-lysine catabolism amaB lo L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale) 32% 93% 208.8 retinal dehydrogenase (EC 1.2.1.36) 51% 494.6

Sequence Analysis Tools

View N515DRAFT_3729 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

MPSLRLANLIDGRLQAPRQERWLEVFEPATGEVFAHCPESSFADVDAAVAAAVAAAPGWA
ATPSEQRARLLQRLADLIEARLDEFAALESRDSGKPLSLARSLDIPRAVSNLRYFAAAIV
PWSSESHAMELGAINYTLRQPLGVVACISPWNLPLYLFTWKIAPALAAGNAVVAKPSEIT
PCTAALLGELSIEAGFPPGVLNIVQGRGPEVGQALVEHRDVKAVSFTGSTRTGAQIAAAA
APRFKKLSLELGGKNPAIVFADADLSDANLDTIVRSGFANQGEICLCGSRLLVQRSIYDA
FRERYLAKVRALRVGDPREAATDLGALVSREHFDKVTGCIAQARAEGGRVLCGGDALALP
GPLAGGWYVAPTVIEGLGPETATNQQEIFGPVVTLIPFDDEAQALAIANGTGYGLAASLW
TTDLSRAHRFGAQLDFGIVWINCWLLRDLRTPFGGAKQSGVGREGGVEALRFFTEPKNIC
IRY

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