GapMind for catabolism of small carbon sources

 

Protein WP_057507768.1 in Stenotrophomonas chelatiphaga DSM 21508

Annotation: NCBI__GCF_001431535.1:WP_057507768.1

Length: 454 amino acids

Source: GCF_001431535.1 in NCBI

Candidate for 46 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 hi aldehyde dehydrogenase-like protein yneI (characterized) 50% 97% 445.3
L-citrulline catabolism gabD hi aldehyde dehydrogenase-like protein yneI (characterized) 50% 97% 445.3
putrescine catabolism gabD hi aldehyde dehydrogenase-like protein yneI (characterized) 50% 97% 445.3
4-hydroxybenzoate catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 47% 97% 424.9 aldehyde dehydrogenase-like protein yneI 50% 445.3
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 47% 97% 424.9 aldehyde dehydrogenase-like protein yneI 50% 445.3
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 47% 97% 424.9 aldehyde dehydrogenase-like protein yneI 50% 445.3
ethanol catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 47% 97% 424.9 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-threonine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 47% 97% 424.9 aldehyde dehydrogenase-like protein yneI 50% 445.3
thymidine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 47% 97% 424.9 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-tryptophan catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 47% 97% 424.9 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 94% 276.2 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 94% 276.2 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 94% 276.2 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 94% 276.2 aldehyde dehydrogenase-like protein yneI 50% 445.3
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 32% 92% 241.1 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 32% 92% 241.1 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 34% 96% 240.7 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 32% 91% 240.4 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 32% 91% 240.4 aldehyde dehydrogenase-like protein yneI 50% 445.3
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 32% 91% 240.4 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-arginine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 32% 92% 239.6 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-citrulline catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 32% 92% 239.6 aldehyde dehydrogenase-like protein yneI 50% 445.3
putrescine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 32% 92% 239.6 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-arabinose catabolism xacF lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 233.4 aldehyde dehydrogenase-like protein yneI 50% 445.3
D-galacturonate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 233.4 aldehyde dehydrogenase-like protein yneI 50% 445.3
D-glucuronate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 233.4 aldehyde dehydrogenase-like protein yneI 50% 445.3
D-xylose catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 233.4 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-tryptophan catabolism nbaE lo 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 31% 94% 232.6 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 32% 95% 230.3 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 32% 95% 230.3 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 32% 95% 230.3 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 32% 95% 230.3 aldehyde dehydrogenase-like protein yneI 50% 445.3
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 32% 95% 230.3 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 30% 91% 205.3 aldehyde dehydrogenase-like protein yneI 50% 445.3
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 30% 91% 205.3 aldehyde dehydrogenase-like protein yneI 50% 445.3
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 30% 91% 205.3 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 30% 91% 205.3 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 30% 91% 205.3 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 30% 88% 204.1 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 30% 84% 182.6 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 30% 84% 182.6 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 30% 84% 182.6 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 30% 84% 182.6 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 30% 84% 182.6 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-arginine catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 30% 90% 164.1 aldehyde dehydrogenase-like protein yneI 50% 445.3
L-citrulline catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 30% 90% 164.1 aldehyde dehydrogenase-like protein yneI 50% 445.3

Sequence Analysis Tools

View WP_057507768.1 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

MTVEIVNPTTGRVDYRHELLDKAGIEQRLQAAAGAFPAWSATSLQERAAVLRAIGAQLRE
RKDDIQGAMTREMGKLKVEALAEVEKCAAACEYYADHAADYLKPQLIDTEAQRSYVRYEP
IGCVFAVMPWNFPIWQVFRFLAPAFMAGNVALLKHASNVPQCADLINEVVRAGGLPDGVF
DVLHIDNDQAADVLRDRRVKAVTLTGSERAGRSIAANAGDQLKKCVMELGGSDAFVVLDD
ADLDKAIDAAVKSRFDNSGQTCIAAKRFIVVEAVADAFTERFVAAAGERRYGDPADARTT
LAPMARADLRDELHKQVQASVAKGARVLAGGEPVDGSHAGYPATVLDQVGPGMPAYDEEL
FGPVAAVIRVKDEAEALKVANDTRFGLGGSVWTTDAARGEAFAQQMECGAAFVNSIVKSD
VRLPFGGSKESGFGRELAEHGIHEFMNIKTIYVA

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