GapMind for catabolism of small carbon sources

 

Protein GFF2584 in Pseudomonas stutzeri RCH2

Annotation: Psest_2634 glycine betaine aldehyde dehydrogenase

Length: 490 amino acids

Source: psRCH2 in FitnessBrowser

Candidate for 32 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 50% 98% 473 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-citrulline catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 50% 98% 473 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
putrescine catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 50% 98% 473 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 42% 92% 377.1 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 41% 97% 374.4 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 41% 97% 374.4 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 96% 365.2 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 96% 365.2 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 96% 365.2 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 96% 363.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 96% 363.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 96% 363.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 96% 363.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 38% 97% 339.7 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 38% 97% 339.7 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 38% 97% 339.7 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 38% 97% 339.7 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 97% 335.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 97% 335.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 97% 335.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 97% 335.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-tryptophan catabolism nbaE lo 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 38% 97% 335.1 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 39% 100% 333.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 35% 95% 253.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 35% 95% 253.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 35% 95% 253.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 35% 95% 253.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 35% 95% 253.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized) 35% 94% 252.7 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 34% 95% 219.2 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 34% 95% 219.2 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4
L-lysine catabolism amaB lo Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized) 31% 85% 202.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 80% 795.4

Sequence Analysis Tools

View GFF2584 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MARFPRQQLYIHGGYVDASSNETFESINPANGEVLAQVAEAGAADLERAVESAEQGQRIW
AALTGIERARIMRRAVDLLRERNDELALLETLDTGKPLSETRSVDIVTGADVLEYYAGLA
PAIEGEQIPLRDSSFVYTRREPLGVVAGIGAWNYPIQIALWKAAPALAAGNAMIFKPSEV
TSLSALKLAEIFSEAGLPDGVFNVLTGSGAGVGALITEHPRIAKVSFTGGVATGKKVMAS
AASSSLKDVTMELGGKSPLIICEDADLDRAADIAVMANFFSSGQVCTNGTRVFVPAGLKA
AFEAKLLERVQRIRLGDPQQEETNFGPLVSFAHMNNVLDYIAKGKAAGARLLCGGERVTE
GEYAKGAFVAPTIFSDCSDDMAIVCEEIFGPVLSLLEYQDEDEVIRRANDTEYGLAAGVV
TADLARAHRIIHRLEAGICWINTWGESPAQMPVGGYKQSGIGRENGIASLAHYTRVKSVQ
VELGEFASVF

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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