GapMind for catabolism of small carbon sources

 

Protein WP_026607654.1 in Methylocapsa acidiphila B2

Annotation: NCBI__GCF_000427445.1:WP_026607654.1

Length: 474 amino acids

Source: GCF_000427445.1 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
4-hydroxybenzoate catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 48% 100% 426.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
2'-deoxyinosine catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 48% 100% 426.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
2-deoxy-D-ribose catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 48% 100% 426.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
ethanol catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 48% 100% 426.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-threonine catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 48% 100% 426.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
thymidine catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 48% 100% 426.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-tryptophan catabolism adh med Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized) 48% 100% 426.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-arginine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 42% 94% 329.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-citrulline catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 42% 94% 329.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
putrescine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 42% 94% 329.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-phenylalanine catabolism pad-dh med phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized) 40% 96% 295.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 37% 97% 307.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 37% 97% 307.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-arginine catabolism gabD lo 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 (characterized) 38% 88% 292.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-citrulline catabolism gabD lo 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 (characterized) 38% 88% 292.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
putrescine catabolism gabD lo 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 (characterized) 38% 88% 292.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-arginine catabolism kauB lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 95% 285 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-arginine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 95% 285 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-citrulline catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 95% 285 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
putrescine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 95% 285 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-fucose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 37% 94% 278.5 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-rhamnose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 37% 94% 278.5 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-threonine catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 37% 94% 278.5 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 96% 277.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 96% 277.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 96% 277.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 96% 277.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 36% 97% 266.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 36% 97% 266.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-arabinose catabolism xacF lo 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) 36% 97% 258.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
D-galacturonate catabolism dopDH lo 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) 36% 97% 258.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
D-glucuronate catabolism dopDH lo 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) 36% 97% 258.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
D-xylose catabolism dopDH lo 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) 36% 97% 258.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 34% 99% 230.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 30% 91% 216.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 30% 91% 216.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 30% 91% 216.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 30% 91% 216.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 30% 91% 216.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized) 33% 90% 214.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 96% 209.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 96% 209.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 96% 209.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 96% 209.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 96% 209.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 34% 93% 196.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 34% 93% 196.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 59% 535.8

Sequence Analysis Tools

View WP_026607654.1 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

MRDYLKFFIDGAWVDPIDPRVLDVVNPATEAPVGRISLASAVDVDRAVVAARRAFKTFSR
SSRDERISLLDRVVAEFERRASDLAEAMTEEMGAPAWLARQAQFGAGLAHLKIAREILQR
YSFEEPLDATTRLLKEPIGVCGLITPWNWPLNQICCKLAPALATGCAVVLKPSELAPFSA
YLVAEILQAAGAPAGVFNMVNGDGPVAGAALSGHPLVDMVSFTGSTRAGVEVARNAAPTV
KRVCQELGGKSPFILLEDADFAEAVPWAVAAIMRNSGQSCNAPTRLLAPASRMEEVVRLA
RAAGEAQAPGDPNSNAKLGPVVSDAQWRKVQALIHKGVEEGATLVLGGPGKPEGLERGYY
VRPTIFADVTNDMTIAREEIFGPVLAILSYETESQAIEIANDTVYGLAAYVYGELAHARA
VAAELRAGQVVLNGVPFDFAAPFGGYKQSGNGREWGALAFNEFLEVKAVMGWSP

This GapMind analysis is from Apr 09 2024. 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