GapMind for catabolism of small carbon sources

 

Protein WP_036262823.1 in Methylocapsa aurea KYG

Annotation: NCBI__GCF_000746085.1:WP_036262823.1

Length: 506 amino acids

Source: GCF_000746085.1 in NCBI

Candidate for 48 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 hi Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 76% 98% 789.3 NAD+-dependent secondary alcohol dehydrogenase III monomer 74% 764.6
2'-deoxyinosine catabolism adh hi Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 76% 98% 789.3 NAD+-dependent secondary alcohol dehydrogenase III monomer 74% 764.6
2-deoxy-D-ribose catabolism adh hi Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 76% 98% 789.3 NAD+-dependent secondary alcohol dehydrogenase III monomer 74% 764.6
ethanol catabolism adh hi Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 76% 98% 789.3 NAD+-dependent secondary alcohol dehydrogenase III monomer 74% 764.6
L-threonine catabolism adh hi Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 76% 98% 789.3 NAD+-dependent secondary alcohol dehydrogenase III monomer 74% 764.6
thymidine catabolism adh hi Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 76% 98% 789.3 NAD+-dependent secondary alcohol dehydrogenase III monomer 74% 764.6
L-tryptophan catabolism adh hi Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 76% 98% 789.3 NAD+-dependent secondary alcohol dehydrogenase III monomer 74% 764.6
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 45% 94% 392.1 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 45% 94% 392.1 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 45% 94% 392.1 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 45% 94% 392.1 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 45% 92% 390.2 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 41% 97% 368.6 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 41% 97% 368.6 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-tryptophan catabolism nbaE med 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 40% 100% 363.2 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 42% 95% 353.2 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 42% 95% 353.2 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 42% 95% 353.2 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-arginine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 97% 349.7 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-citrulline catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 97% 349.7 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
putrescine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 97% 349.7 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-arginine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 97% 337 NAD+-dependent secondary alcohol dehydrogenase III monomer 74% 764.6
L-citrulline catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 97% 337 NAD+-dependent secondary alcohol dehydrogenase III monomer 74% 764.6
putrescine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 97% 337 NAD+-dependent secondary alcohol dehydrogenase III monomer 74% 764.6
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 37% 99% 310.1 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 38% 98% 290 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 38% 98% 290 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 38% 98% 290 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 38% 98% 290 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 97% 283.5 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 97% 283.5 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 97% 283.5 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 97% 283.5 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 32% 98% 241.1 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 32% 98% 241.1 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 97% 221.5 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 97% 221.5 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 97% 221.5 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 97% 221.5 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 97% 221.5 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 97% 221.5 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-arginine catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 32% 85% 216.1 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-arginine catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 32% 85% 216.1 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-citrulline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 32% 85% 216.1 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-citrulline catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 32% 85% 216.1 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-proline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 32% 85% 216.1 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 92% 186.4 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 92% 186.4 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 76% 789.3

Sequence Analysis Tools

View WP_036262823.1 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

MVDKILADIAHEIAIRPHYDNFIGGKWVPAVKGQTFENISPIDGRVICTVARSSAEDVEL
ALDAAHAARGAWGRTSPAERSLALLRIADRIEQKLDMLAMVETIDNGKPIRETKAADLPL
AVDHFRYFAGCLRAQEGGISEIDHDTVAYHFHEPLGVVAQIIPWNFPLLMAVWKLAPALA
AGNCVILKPAEQTPMSVMVLVDMIGDLLPPGVLNVINGFGVEAGKPLAQNKRIAKVAFTG
ETTTGRLIMQYASENIIPVTLELGGKSPNIFFADVADEDDDFFDKALEGFSMFALNQGEV
CTCPSRALVQEKIYDRFMERAVARVKKIKQGNPLDPATMIGAQASNDQLEKILSYLDIGR
QEGAKVLAGGGRADVGPELAGGFYVQPTILEGHNKMRIFQEEIFGPVLSVTSFKDDEEAL
EIANDTLYGLGAGVWTRNGTRAYRFGRAIEAGRVWTNCYHLYPAHAAFGGYKQSGIGREN
HKMMLDHYQKTKNMLVSYSPKALGFF

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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