GapMind for catabolism of small carbon sources

 

Protein WP_068105561.1 in Nocardioides dokdonensis FR1436

Annotation: NCBI__GCF_001653335.1:WP_068105561.1

Length: 497 amino acids

Source: GCF_001653335.1 in NCBI

Candidate for 28 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 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 (characterized) 49% 99% 451.1 vanillin dehydrogenase (EC 1.2.1.67) 48% 439.9
2'-deoxyinosine catabolism adh hi Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 (characterized) 49% 99% 451.1 vanillin dehydrogenase (EC 1.2.1.67) 48% 439.9
2-deoxy-D-ribose catabolism adh hi Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 (characterized) 49% 99% 451.1 vanillin dehydrogenase (EC 1.2.1.67) 48% 439.9
ethanol catabolism adh hi Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 (characterized) 49% 99% 451.1 vanillin dehydrogenase (EC 1.2.1.67) 48% 439.9
L-threonine catabolism adh hi Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 (characterized) 49% 99% 451.1 vanillin dehydrogenase (EC 1.2.1.67) 48% 439.9
thymidine catabolism adh hi Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 (characterized) 49% 99% 451.1 vanillin dehydrogenase (EC 1.2.1.67) 48% 439.9
L-tryptophan catabolism adh hi Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 (characterized) 49% 99% 451.1 vanillin dehydrogenase (EC 1.2.1.67) 48% 439.9
L-phenylalanine catabolism pad-dh med phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized) 40% 95% 355.5 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 49% 451.1
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 95% 319.3 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 49% 451.1
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 95% 319.3 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 49% 451.1
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 95% 319.3 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 49% 451.1
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 41% 95% 319.3 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 49% 451.1
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 36% 100% 320.5 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 49% 451.1
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 36% 100% 320.5 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 49% 451.1
L-tryptophan catabolism nbaE lo aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 37% 95% 298.5 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 49% 451.1
L-arginine catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 36% 90% 253.4 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 49% 451.1
L-arginine catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 36% 90% 253.4 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 49% 451.1
L-citrulline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 36% 90% 253.4 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 49% 451.1
L-citrulline catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 36% 90% 253.4 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 49% 451.1
L-proline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 36% 90% 253.4 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 49% 451.1
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized) 32% 93% 231.1 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 49% 451.1
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 223.8 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 49% 451.1
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 223.8 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 49% 451.1
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 223.8 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 49% 451.1
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 223.8 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 49% 451.1
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 223.8 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 49% 451.1
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 33% 92% 209.5 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 49% 451.1
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 33% 92% 209.5 Geranial dehydrogenase; GaDH; Geraniol oxidation pathway protein B; EC 1.2.1.86 49% 451.1

Sequence Analysis Tools

View WP_068105561.1 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

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Sequence

MTQTQGQRPIATDALDRDTFYIDGAWAAPATGAVIEVVSPHTEQVVARVPDGSPADIDAA
VAAARRAFDEGPWPRTSPEERIEVLQRFSHLYAARLGDMAELITIEMGSPTSFSNLAQSP
APWMQVEAFIAIARDFPWEAARSGVLGSDVVVRHEPVGVVAAIPPWNVPQFTLISKVVPA
LLAGCTVVAKPAPESPLDAYLLAELLDEAGVPPGVVNIVAGGREVGAHLVAHPGIDKVAF
TGSTAAGRLIGAVCGEQLKRCSLELGGKSAAIVLADADLGPTMEGLRFTALMNSGQACVA
QTRILAPRSRYDEVVDALAETVGSMPVGDPADPATEVGPMVARRQQERVSSYIELGQQEG
ARLVVGGTGMPDGLERGWYVRPTVFADVDNRMRIAQEEIFGPVLSVIAYDDVDDAVRIAN
DSDYGLAGTVWTTDQEAGLDVARRVRTGTYGINTYTMDFAAPFGGFKASGLGREFGPEGL
AQYTETKSIYVPPAPAV

This GapMind analysis is from Apr 09 2024. 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