GapMind for catabolism of small carbon sources

 

Protein WP_099618369.1 in Marinobacter guineae M3B

Annotation: NCBI__GCF_002744735.1:WP_099618369.1

Length: 488 amino acids

Source: GCF_002744735.1 in NCBI

Candidate for 29 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 60% 98% 589.3 Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 59% 568.9
L-citrulline catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 60% 98% 589.3 Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 59% 568.9
L-lysine catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 60% 98% 589.3 Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 59% 568.9
L-proline catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 60% 98% 589.3 Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 59% 568.9
L-arginine catabolism gabD hi succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 60% 99% 585.5
L-citrulline catabolism gabD hi succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 60% 99% 585.5
putrescine catabolism gabD hi succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 60% 99% 585.5
4-hydroxybenzoate catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 57% 90% 542 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 57% 90% 542 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 57% 90% 542 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3
ethanol catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 57% 90% 542 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3
L-threonine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 57% 90% 542 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3
thymidine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 57% 90% 542 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3
L-tryptophan catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 57% 90% 542 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3
L-arabinose catabolism xacF med 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) 41% 99% 354 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3
D-galacturonate catabolism dopDH med 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) 41% 99% 354 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3
D-glucuronate catabolism dopDH med 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) 41% 99% 354 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3
D-xylose catabolism dopDH med 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) 41% 99% 354 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 38% 96% 331.3 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 38% 96% 331.3 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized) 33% 95% 236.9 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3
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) 33% 88% 235 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3
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) 33% 88% 235 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3
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) 33% 88% 235 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3
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) 33% 88% 235 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3
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) 33% 88% 235 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3
L-lysine catabolism amaB lo Δ1-piperideine-6-carboxylate dehydrogenase (characterized) 34% 78% 225.3 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 36% 93% 224.9 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 36% 93% 224.9 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 60% 589.3

Sequence Analysis Tools

View WP_099618369.1 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

MSPLDTPLLTSVLNDEVPALIGQHWCQREERFEVTNPATGEILARVAECNADDTRAAVAA
AELSGQSWKRVPAKQRAGILRRWFELVTAHTDELARLMTLEQGKPLAEARGEVTYGASFI
EFFGEEAKRMAGETLPGQGPDKRILVMREPVGVVAAITPWNFPMAMITRKCAPAIAAGCT
VVIKPAEATPLTALALARLALEAGVPKGVINVVTASEPVAVGEVLSTDPRVRKLSFTGST
AVGKKLLAQCASTVKKTAMELGGNAPFIVFDDADLDAAVDGAIASKFRNAGQTCVCTNRF
LVQDGVYDAFLEKLTTRVAELKVGNGLEDGIAVGPLINRSAIDKVQRHVDDAVAKGARVT
GGGQPHELGPNFFTPTVLADVTPDMAVATEETFGPLAPVFRFHTAEEAIAMANDTPSGLA
AYLYATDYRRIWHTLEGLEYGMVGVNEGLISSELAPFGGVKESGLGREGSHHGLDEFTEL
KYVCLGGL

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