GapMind for catabolism of small carbon sources

 

Protein WP_054255979.1 in Acidovorax caeni R-24608

Annotation: NCBI__GCF_001298675.1:WP_054255979.1

Length: 501 amino acids

Source: GCF_001298675.1 in NCBI

Candidate for 23 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-valine catabolism mmsA hi Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized) 82% 99% 842.8 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 60% 614.4
L-valine catabolism mmsA med mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27) (TIGR01722) 100% 733.1 malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) 60% 614.4
L-isoleucine catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 60% 92% 614.4
myo-inositol catabolism mmsA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 60% 92% 614.4
propionate catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 60% 92% 614.4
L-threonine catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 60% 92% 614.4
L-valine catabolism iolA hi malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 60% 92% 614.4
L-arabinose catabolism xacF lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 35% 99% 266.9 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 82% 842.8
D-galacturonate catabolism dopDH lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 35% 99% 266.9 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 82% 842.8
D-glucuronate catabolism dopDH lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 35% 99% 266.9 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 82% 842.8
D-xylose catabolism dopDH lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 35% 99% 266.9 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 82% 842.8
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 98% 248.1 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 82% 842.8
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 98% 248.1 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 82% 842.8
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 98% 248.1 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 82% 842.8
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 32% 97% 220.7 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 82% 842.8
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 32% 97% 220.7 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 82% 842.8
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) 33% 94% 211.5 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 82% 842.8
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) 33% 94% 211.5 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 82% 842.8
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) 33% 94% 211.5 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 82% 842.8
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) 33% 94% 211.5 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 82% 842.8
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) 33% 94% 211.5 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 82% 842.8
L-lysine catabolism amaB lo Δ1-piperideine-6-carboxylate dehydrogenase (characterized) 31% 88% 182.6 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 82% 842.8
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 30% 92% 165.6 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 82% 842.8
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 30% 92% 165.6 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) 82% 842.8

Sequence Analysis Tools

View WP_054255979.1 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

MGATIPTVKLLINGQFVESKTTQWRDVVNPATQEVLARVPFATPDEINAAVANAKEAFKT
WKKTPIGARARIFLKLQQLIRENMKELAAILTAEQGKTLPDAEGDVFRGLEVVEHASAIG
NLQLGELANNVANGVDTYTVLQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSE
QDPLVTMRLCELALEAGVPPGVLNVIHGGEDAVNAICDHPDIKAISFVGSTRVGTHVYNR
ASLNGKRVQCMMGAKNHAVVLPDANKEQTLNAIAGASFGAAGQRCMALPVVMLVGEAQQW
LPDLVAKAKSLKVSGGTEPGTDVGPVISCAALSRIEGLIERGVAEGATLALDGRKPTVPG
YEKGNFVGPTIFSDVKPGMTIYDQEIFGPVLCVVGAETLDEAIEFINANPNGNGTAVFTQ
SGAAARKFQEEIDVGQVGINVPVPVPVPLFSFTGSRASKLGDLGPYGKQVVLFYTQTKTV
TARWFDDSTASHGVNTTISLK

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