GapMind for catabolism of small carbon sources

 

Protein WP_055437407.1 in Lacinutrix algicola AKS293

Annotation: NCBI__GCF_001418085.1:WP_055437407.1

Length: 500 amino acids

Source: GCF_001418085.1 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
4-hydroxybenzoate catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 63% 97% 645.2 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
2'-deoxyinosine catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 63% 97% 645.2 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
2-deoxy-D-ribose catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 63% 97% 645.2 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
ethanol catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 63% 97% 645.2 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-threonine catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 63% 97% 645.2 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
thymidine catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 63% 97% 645.2 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-tryptophan catabolism adh med Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 63% 97% 645.2 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 99% 371.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 99% 371.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 99% 371.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 99% 371.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 43% 92% 366.3 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 42% 97% 360.5 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 42% 97% 360.5 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 42% 97% 360.5 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-arginine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 97% 355.5 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-citrulline catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 97% 355.5 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
putrescine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 97% 355.5 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 39% 97% 344.4 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 39% 97% 344.4 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-arginine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 95% 334.3 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-citrulline catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 95% 334.3 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
putrescine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 95% 334.3 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-tryptophan catabolism nbaE lo 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 35% 100% 323.6 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 97% 305.1 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 97% 305.1 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 97% 305.1 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 97% 305.1 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-arabinose catabolism xacF lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 99% 280 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
D-galacturonate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 99% 280 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
D-glucuronate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 99% 280 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
D-xylose catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 37% 99% 280 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 93% 216.1 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 93% 216.1 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 93% 216.1 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 93% 216.1 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 93% 216.1 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-isoleucine catabolism iolA 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) 31% 93% 201.1 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
myo-inositol 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) 31% 93% 201.1 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
propionate catabolism iolA 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) 31% 93% 201.1 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-threonine catabolism iolA 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) 31% 93% 201.1 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-valine catabolism iolA 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) 31% 93% 201.1 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
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) 31% 93% 201.1 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 94% 190.3 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 94% 190.3 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5
L-lysine catabolism amaB lo Δ1-piperideine-6-carboxylate dehydrogenase (characterized) 31% 79% 183.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 70% 726.5

Sequence Analysis Tools

View WP_055437407.1 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

MANVTKPEFKEKYGNFIGGKFVDPVKGQYFDNVSPVDGKVFTQAARSTQEDIDLALDAAH
EAFPAWSTSSATERSNMLLKIAQVMEDNFEYLATLETIDNGKPIRESRAADIPYCIDHFR
YFAGVIRADEGSISEHDKDTVSIVLHEPVGVVGEIIPWNFPMLMLAWKIAPALAAGCTAV
VKPAEQTPTSVIMLMELIGDILPAGVLNIVTGFGAEAGAALATSKRIAKLSFTGSTETGR
KVLHNAAENIIPVTMELGGKSPNVFFPSVADHDDDFFSKAIEGALMFSLNQGEICTAPSR
ILVHEDIADLFIEKMKVRLKAIKTGNPLDPETMIGSQVSKPQYDKILDYIKIGKDEGAEV
VAGGDAGNYEGELSEGYYIQPTVLKGNNKMRIFQEEIFGPVVALTTFSSTEEAIAIANDT
PYGLGAGVWSRDAHELYQVPRAIQAGRVWVNQYHTYPAHAPFGGVKESGFGRENHKMALD
HYRVVKNMLISYDKKPMGFF

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