Protein WP_073038418.1 in Desulfacinum infernum DSM 9756

GapMind for catabolism of small carbon sources

Protein WP_073038418.1 in Desulfacinum infernum DSM 9756

Annotation: NCBI__GCF_900129305.1:WP_073038418.1

Length: 260 amino acids

Source: GCF_900129305.1 in NCBI

Candidate for 29 steps in catabolism of small carbon sources

Pathway	Step	Score	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
L-leucine catabolism	liuC	med	methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)	52%	76%	247.3	crotonase (EC 4.2.1.150)	49%	238.0
4-hydroxybenzoate catabolism	ech	med	crotonase (EC 4.2.1.150) (characterized)	49%	100%	238	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
L-arginine catabolism	ech	med	crotonase (EC 4.2.1.150) (characterized)	49%	100%	238	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
L-citrulline catabolism	ech	med	crotonase (EC 4.2.1.150) (characterized)	49%	100%	238	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
L-lysine catabolism	ech	med	crotonase (EC 4.2.1.150) (characterized)	49%	100%	238	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
phenylacetate catabolism	ech	med	crotonase (EC 4.2.1.150) (characterized)	49%	100%	238	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
L-phenylalanine catabolism	ech	med	crotonase (EC 4.2.1.150) (characterized)	49%	100%	238	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
L-proline catabolism	ech	med	crotonase (EC 4.2.1.150) (characterized)	49%	100%	238	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
L-valine catabolism	ech	med	crotonase (EC 4.2.1.150) (characterized)	49%	100%	238	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
L-isoleucine catabolism	hpcD	med	3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)	45%	100%	216.5	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
propionate catabolism	hpcD	med	3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)	45%	100%	216.5	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
L-threonine catabolism	hpcD	med	3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)	45%	100%	216.5	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
L-valine catabolism	hpcD	med	3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)	45%	100%	216.5	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
L-isoleucine catabolism	ech	med	Enoyl-CoA isomerase/hydratase fer4; Fe-regulated protein 4; Ferrichrome A biosynthesis protein fer4; EC 4.2.1.17 (characterized)	43%	92%	203	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
4-hydroxybenzoate catabolism	paaF	med	enoyl-CoA hydratase (EC 4.2.1.17) (characterized)	41%	100%	187.2	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
phenylacetate catabolism	paaF	med	enoyl-CoA hydratase (EC 4.2.1.17) (characterized)	41%	100%	187.2	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
L-phenylalanine catabolism	paaF	med	enoyl-CoA hydratase (EC 4.2.1.17) (characterized)	41%	100%	187.2	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
4-hydroxybenzoate catabolism	badK	lo	BadK (characterized)	39%	100%	176.4	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
phenylacetate catabolism	badK	lo	BadK (characterized)	39%	100%	176.4	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
L-phenylalanine catabolism	badK	lo	BadK (characterized)	39%	100%	176.4	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
phenylacetate catabolism	paaG	lo	2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)	36%	100%	154.8	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
L-phenylalanine catabolism	paaG	lo	2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)	36%	100%	154.8	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
4-hydroxybenzoate catabolism	dch	lo	cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)	37%	100%	145.2	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
phenylacetate catabolism	dch	lo	cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)	37%	100%	145.2	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
L-phenylalanine catabolism	dch	lo	cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)	37%	100%	145.2	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
4-hydroxybenzoate catabolism	badI	lo	BadI (characterized)	34%	97%	131.3	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
phenylacetate catabolism	badI	lo	BadI (characterized)	34%	97%	131.3	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
L-phenylalanine catabolism	badI	lo	BadI (characterized)	34%	97%	131.3	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3
L-valine catabolism	bch	lo	3-hydroxyisobutyryl-CoA hydrolase, mitochondrial; 3-hydroxyisobutyryl-coenzyme A hydrolase; HIB-CoA hydrolase; HIBYL-CoA-H; EC 3.1.2.4 (characterized)	31%	56%	105.1	methylglutaconyl-CoA hydratase (EC 4.2.1.18)	52%	247.3

Sequence Analysis Tools

View WP_073038418.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MEQQVVLEERQGQVAILTLNRPEVMNSLNFAMLRGLHEKVESLRFDNDVRVIIITGAGPK
AFCAGADLKERATLNDQQVKEFILTIRNLFTNIEYLPKPVIAAVNGIALGGGTELALACD
IRIASTTATMGLTETRLAIIPGAGGTQRLPRLVGRGKAKELIFTGRRVGAEEALSIGLVN
QVAEPEKLLDACLEMAGMICETGPIAIQQAKYAINYGLETDLHTGLAIESNAYWITIPTE
DRLEGLAAFREKRKPVYKGK

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources