GapMind for catabolism of small carbon sources

 

Protein WP_108402515.1 in Limnohabitans curvus MWH-C5

Annotation: NCBI__GCF_003063475.1:WP_108402515.1

Length: 492 amino acids

Source: GCF_003063475.1 in NCBI

Candidate for 44 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism gabD med succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 60% 99% 598.6 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 60% 589.0
L-citrulline catabolism gabD med succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 60% 99% 598.6 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 60% 589.0
putrescine catabolism gabD med succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 60% 99% 598.6 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 60% 589.0
L-arginine catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 59% 99% 582 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 60% 589.0
L-citrulline catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 59% 99% 582 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 60% 589.0
L-lysine catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 59% 99% 582 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 60% 589.0
L-proline catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 59% 99% 582 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 60% 589.0
4-hydroxybenzoate catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 93% 545.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 93% 545.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 93% 545.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
ethanol catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 93% 545.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-threonine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 93% 545.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
thymidine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 93% 545.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-tryptophan catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 93% 545.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
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) 38% 98% 335.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
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) 38% 98% 335.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
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) 38% 98% 335.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
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) 38% 98% 335.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 37% 97% 325.9 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 37% 97% 325.9 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-phenylalanine catabolism pad-dh lo Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized) 37% 97% 307.4 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-tryptophan catabolism nbaE lo 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 35% 99% 306.6 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 99% 305.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 99% 305.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 99% 305.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 99% 305.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 35% 97% 293.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 35% 97% 293.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 35% 97% 293.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 35% 97% 293.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 35% 97% 293.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 35% 95% 276.9 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 35% 95% 276.9 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 35% 95% 276.9 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 35% 95% 276.9 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 31% 96% 229.6 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 31% 96% 229.6 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 31% 96% 229.6 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 31% 96% 229.6 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 31% 96% 229.6 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-valine catabolism mmsA lo malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 93% 226.5 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-lysine catabolism amaB lo Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale) 31% 88% 214.9 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 31% 94% 196.4 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 31% 94% 196.4 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 60% 598.6

Sequence Analysis Tools

View WP_108402515.1 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

MDMKTAPLSLLNDPTLLKTDALINGHWVKGASRFDVHDPATGKKLADVANLGPADASAAI
DAANAAWPAWRNKTGKERSIILRKWFDLLMAHQEDLGRIMTAEQGKPFAEAKGEVVYGAS
FVEWFAEEAKRVNGETLPQFDNNRRLMVLKQPIGVCAAITPWNFPLAMITRKVAPALAAG
CPVVIKPAELPPLTALAAAELAIRAGIPDGVLNILTADSDNSIAIGKVFCSSDIVRHISF
TGSTEVGRILMAQSAPSIKKLALELGGNAPFIVFDDADIDSAVEGAMASKYRNAGQTCVC
ANRIYVQDAVYDEFVQKFAAKVKALKVGNGFEDGVTQGPLIEDAAVDKVERHVQDALHKG
GKLITGGHKLTGQFFEPTVIADARADMLCAREETFGPFAPVFRFHKDQEAIDAANNTEFG
LASYFYSRDIGRIYRVSEALEYGMVGINVGIIASEHVPFGGVKQSGLGREGSSHGMDEYV
EMKYLCLGDITK

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