GapMind for catabolism of small carbon sources

 

Protein WP_047093279.1 in Erythrobacter marinus HWDM-33

Annotation: NCBI__GCF_001013305.1:WP_047093279.1

Length: 472 amino acids

Source: GCF_001013305.1 in NCBI

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism astD hi Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 48% 94% 431.4 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 32% 219.2
L-arginine catabolism astD hi astD: succinylglutamate-semialdehyde dehydrogenase (EC 1.2.1.71) (TIGR03240) 95% 599.7 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 32% 219.2
L-citrulline catabolism astD hi Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 48% 94% 431.4 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 32% 219.2
L-citrulline catabolism astD hi astD: succinylglutamate-semialdehyde dehydrogenase (EC 1.2.1.71) (TIGR03240) 95% 599.7 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 32% 219.2
4-hydroxybenzoate catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 48% 94% 429.9 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 48% 431.4
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 48% 94% 429.9 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 48% 431.4
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 48% 94% 429.9 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 48% 431.4
ethanol catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 48% 94% 429.9 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 48% 431.4
L-threonine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 48% 94% 429.9 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 48% 431.4
thymidine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 48% 94% 429.9 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 48% 431.4
L-tryptophan catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 48% 94% 429.9 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 48% 431.4
L-lysine catabolism amaB lo L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale) 33% 86% 200.7 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 48% 431.4
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 31% 85% 177.6 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 48% 431.4
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 31% 85% 177.6 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 48% 431.4
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 31% 85% 177.6 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 48% 431.4
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 87% 176.8 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 48% 431.4
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 87% 176.8 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 48% 431.4
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 87% 176.8 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 48% 431.4
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 87% 176.8 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 48% 431.4
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 87% 176.8 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 48% 431.4

Sequence Analysis Tools

View WP_047093279.1 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

MGTPQELVSFEPATGKELWRGAHGNVDAIVARARRAWPKWAALPLANRIELMRRFVNEVR
KDHDEFSELISRETGKPLWEARTEVEAVMAKIEISIRAYGERTGQRKLDSALQGIAALRH
KPHGVMAVLGPYNFPAHLPNGHMIPALIAGNAVILKPSEKTPAVGAKLVELLNRCGIPEG
VVQLLIGGPDEGKALVAHDDVNGVLFTGSAQVGIAINRKLATDPGKILALEMGGNNPMIV
WDTPKIADAAALIVQSAFTTAGQRCTAARRLIVKASMYDEVVAETKKLADRAIVGGPFDE
PAPFMGPVIDNATADQLTESFVYLLSNGGKAIKHMRRLQDDLPFVSPAIIDTTAMSDRPD
VELFGPLLQVIKVDDFDEAIAEANNTRFGLSASLVGGTPQQYNRFWANIRAGIVNWNRPT
NGASSAAPFGGVGYSGNHRPAAFYAADYCAYPVTSTEMEQPRASVGVGFKES

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