GapMind for catabolism of small carbon sources

 

Protein WP_015447966.1 in Rhodanobacter denitrificans 2APBS1

Annotation: NCBI__GCF_000230695.2:WP_015447966.1

Length: 476 amino acids

Source: GCF_000230695.2 in NCBI

Candidate for 27 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) 38% 97% 304.7 phosphonoformaldehyde dehydrogenase 38% 277.7
L-rhamnose catabolism aldA med Lactaldehyde dehydrogenase; EC 1.2.1.22 (uncharacterized) 38% 97% 304.7 phosphonoformaldehyde dehydrogenase 38% 277.7
L-threonine catabolism aldA med Lactaldehyde dehydrogenase; EC 1.2.1.22 (uncharacterized) 38% 97% 304.7 phosphonoformaldehyde dehydrogenase 38% 277.7
L-arginine catabolism gabD lo succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 37% 95% 275.8 phosphonoformaldehyde dehydrogenase 38% 277.7
L-citrulline catabolism gabD lo succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 37% 95% 275.8 phosphonoformaldehyde dehydrogenase 38% 277.7
putrescine catabolism gabD lo succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 37% 95% 275.8 phosphonoformaldehyde dehydrogenase 38% 277.7
4-hydroxybenzoate catabolism adh lo Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized) 33% 96% 226.9 phosphonoformaldehyde dehydrogenase 38% 277.7
2'-deoxyinosine catabolism adh lo Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized) 33% 96% 226.9 phosphonoformaldehyde dehydrogenase 38% 277.7
2-deoxy-D-ribose catabolism adh lo Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized) 33% 96% 226.9 phosphonoformaldehyde dehydrogenase 38% 277.7
ethanol catabolism adh lo Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized) 33% 96% 226.9 phosphonoformaldehyde dehydrogenase 38% 277.7
L-threonine catabolism adh lo Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized) 33% 96% 226.9 phosphonoformaldehyde dehydrogenase 38% 277.7
thymidine catabolism adh lo Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized) 33% 96% 226.9 phosphonoformaldehyde dehydrogenase 38% 277.7
L-tryptophan catabolism adh lo Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized) 33% 96% 226.9 phosphonoformaldehyde dehydrogenase 38% 277.7
4-hydroxybenzoate catabolism praB lo 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 33% 90% 221.5 phosphonoformaldehyde dehydrogenase 38% 277.7
L-tryptophan catabolism nbaE lo 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 33% 90% 221.5 phosphonoformaldehyde dehydrogenase 38% 277.7
L-tryptophan catabolism praB lo 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 33% 90% 221.5 phosphonoformaldehyde dehydrogenase 38% 277.7
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 35% 96% 219.5 phosphonoformaldehyde dehydrogenase 38% 277.7
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 35% 96% 219.5 phosphonoformaldehyde dehydrogenase 38% 277.7
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 35% 96% 219.5 phosphonoformaldehyde dehydrogenase 38% 277.7
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 35% 96% 219.5 phosphonoformaldehyde dehydrogenase 38% 277.7
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 34% 94% 218.4 phosphonoformaldehyde dehydrogenase 38% 277.7
L-valine catabolism mmsA lo Malonate-semialdehyde dehydrogenase; MSA dehydrogenase; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase; MMSA dehydrogenase; MSDH; EC 1.2.1.27 (uncharacterized) 30% 84% 163.3 phosphonoformaldehyde dehydrogenase 38% 277.7
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 30% 84% 162.2 phosphonoformaldehyde dehydrogenase 38% 277.7
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 30% 84% 162.2 phosphonoformaldehyde dehydrogenase 38% 277.7
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 30% 84% 162.2 phosphonoformaldehyde dehydrogenase 38% 277.7
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 30% 84% 162.2 phosphonoformaldehyde dehydrogenase 38% 277.7
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 30% 84% 162.2 phosphonoformaldehyde dehydrogenase 38% 277.7

Sequence Analysis Tools

View WP_015447966.1 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

MLNKSYPYYLANRPQASKTMLEVRDKYSGRLATRVAVPDAKAVEKAIAAAVNAAKPMREF
KPWARQTVLQYCAARFAERRDELAEALCIEAGKPIKDAAGEVTRLIETFRIAAEEAVRIN
GETINLELASRLDGYHGYTRRVPLGPVSFITPFNFPLNLVAHKVAPAIAAGCPFVLKPSE
KTPIGALIIGEVLAETDLPKGAFSILTLDGAHAAPLVEDPRFKLLSFTGGQVGWALKARA
GHKKVTLELGGNAACIVDADQDGKLDHVVQRLVFGAFYQSGQSCIGVQRIYAHADIYDAL
KRKLVAATKKLKAGDPKDRSVFLGPMIDEAAAERLHGWILEAKQAGGRILCGGKRHGNML
DATLMENVPADAKANRMEAFGPFALLAPFRRFDEAIAMVNDSDYGLQAGIFTDSLAHAMR
AWNELEQGGVIVNDIPSFRVDNMPYGGVKLSGLGREGVRYAIEDMSETRLMVMRES

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