GapMind for catabolism of small carbon sources

 

Protein WP_011373513.1 in Sulfurimonas denitrificans DSM 1251

Annotation: NCBI__GCF_000012965.1:WP_011373513.1

Length: 471 amino acids

Source: GCF_000012965.1 in NCBI

Candidate for 47 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-fucose catabolism aldA med Lactaldehyde dehydrogenase; EC 1.2.1.22 (uncharacterized) 40% 96% 337.4 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 34% 278.5
L-rhamnose catabolism aldA med Lactaldehyde dehydrogenase; EC 1.2.1.22 (uncharacterized) 40% 96% 337.4 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 34% 278.5
L-threonine catabolism aldA med Lactaldehyde dehydrogenase; EC 1.2.1.22 (uncharacterized) 40% 96% 337.4 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 34% 278.5
L-arginine catabolism gabD lo succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) (characterized) 34% 97% 261.9 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-citrulline catabolism gabD lo succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) (characterized) 34% 97% 261.9 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
putrescine catabolism gabD lo succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) (characterized) 34% 97% 261.9 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 33% 94% 254.6 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 33% 94% 254.6 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 33% 94% 254.6 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 33% 94% 254.6 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
4-hydroxybenzoate catabolism adh lo 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; EC 1.2.1.47; EC 1.2.1.3 (characterized) 32% 92% 247.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
2'-deoxyinosine catabolism adh lo 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; EC 1.2.1.47; EC 1.2.1.3 (characterized) 32% 92% 247.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
2-deoxy-D-ribose catabolism adh lo 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; EC 1.2.1.47; EC 1.2.1.3 (characterized) 32% 92% 247.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
ethanol catabolism adh lo 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; EC 1.2.1.47; EC 1.2.1.3 (characterized) 32% 92% 247.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-threonine catabolism adh lo 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; EC 1.2.1.47; EC 1.2.1.3 (characterized) 32% 92% 247.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
thymidine catabolism adh lo 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; EC 1.2.1.47; EC 1.2.1.3 (characterized) 32% 92% 247.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-tryptophan catabolism adh lo 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; EC 1.2.1.47; EC 1.2.1.3 (characterized) 32% 92% 247.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 33% 94% 237.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 33% 94% 237.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-arginine catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 32% 96% 233 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-citrulline catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 32% 96% 233 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
putrescine catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 32% 96% 233 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-arabinose catabolism xacF lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 32% 96% 232.6 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
D-galacturonate catabolism dopDH lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 32% 96% 232.6 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
D-glucuronate catabolism dopDH lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 32% 96% 232.6 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
D-xylose catabolism dopDH lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 32% 96% 232.6 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 34% 97% 232.3 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
4-hydroxybenzoate catabolism praB lo 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 31% 92% 230.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-tryptophan catabolism nbaE lo 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 31% 92% 230.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-tryptophan catabolism praB lo 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 31% 92% 230.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 31% 97% 205.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 30% 92% 198.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-arginine catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 30% 89% 198.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 30% 92% 198.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-arginine catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 30% 89% 198.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-citrulline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 30% 89% 198.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 30% 92% 198.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-citrulline catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 30% 89% 198.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-proline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 30% 89% 198.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 30% 92% 198.7 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-valine catabolism mmsA lo Malonate-semialdehyde dehydrogenase 1; MSA dehydrogenase 1; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase 1; MMSA dehydrogenase 1; MSDH 1; EC 1.2.1.27 (uncharacterized) 30% 92% 196.1 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 89% 193 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 89% 193 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 89% 193 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 89% 193 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 89% 193 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7
L-lysine catabolism amaB lo Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale) 31% 86% 167.9 lactaldehyde dehydrogenase (EC 1.2.1.22) 39% 309.7

Sequence Analysis Tools

View WP_011373513.1 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

MVANIYFGSSEQSRESVGKRVNPYNGEVASEFVTCNADDAKKALNIALLASKEASKTTIA
QRCSWLLDVASKLAQNKEDIAKTITDEVGKPITYSRIEVERCIETVTLAAETMRTMHGET
VNTDAFASGKKTISFFSRVPCGVVVAITPFNFPLNLIAHKIAPALVAGNAVILKPTPEAP
LTAYKFAKLFIESEFAIKDALSVVYGDADVGGTLVTSEIPRVISFTGSVGVGEIITKSAG
IKKVSLELGGNAATFIDKSANLDLAAQRCAIGAFVNSGQVCISLQRIYVHKDIYSEFALK
IAEATKKLVVGSPYEEDTFMGPLVNDEAAKRAMEWVQSAIKEGATPILEPRVEGRVFYPC
VMADVKEDMAIVCQEVFAPIVSLIEVKDFDEALPMMNNSPYGLQFSIFTNDLNLTKRAIN
ELDAGGIVINDMPTLRFDIQPYGGVKLSGVGREGPRFAIEEMSEIKSVIIC

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