Protein N515DRAFT_2873 in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Protein N515DRAFT_2873 in Dyella japonica UNC79MFTsu3.2

Annotation: FitnessBrowser__Dyella79:N515DRAFT_2873

Length: 247 amino acids

Source: Dyella79 in FitnessBrowser

Candidate for 18 steps in catabolism of small carbon sources

Pathway	Step	Score	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
D-sorbitol (glucitol) catabolism	sdh	med	L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)	42%	92%	156.4	Acetoacetyl-CoA reductase; EC 1.1.1.36	49%	223.0
4-hydroxybenzoate catabolism	badH	lo	BadH (characterized)	39%	98%	167.9	Acetoacetyl-CoA reductase; EC 1.1.1.36	49%	223.0
phenylacetate catabolism	badH	lo	BadH (characterized)	39%	98%	167.9	Acetoacetyl-CoA reductase; EC 1.1.1.36	49%	223.0
L-phenylalanine catabolism	badH	lo	BadH (characterized)	39%	98%	167.9	Acetoacetyl-CoA reductase; EC 1.1.1.36	49%	223.0
L-rhamnose catabolism	LRA5	lo	2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized)	37%	94%	147.5	Acetoacetyl-CoA reductase; EC 1.1.1.36	49%	223.0
L-fucose catabolism	fucDH	lo	2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)	34%	79%	130.2	Acetoacetyl-CoA reductase; EC 1.1.1.36	49%	223.0
D-mannitol catabolism	mt2d	lo	NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Alt a 8; EC 1.1.1.138 (characterized)	33%	92%	120.9	Acetoacetyl-CoA reductase; EC 1.1.1.36	49%	223.0
L-isoleucine catabolism	ivdG	lo	3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)	33%	97%	119.8	Acetoacetyl-CoA reductase; EC 1.1.1.36	49%	223.0
4-hydroxybenzoate catabolism	fadB	lo	3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized)	34%	89%	115.9	Acetoacetyl-CoA reductase; EC 1.1.1.36	49%	223.0
4-hydroxybenzoate catabolism	paaH	lo	3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized)	34%	89%	115.9	Acetoacetyl-CoA reductase; EC 1.1.1.36	49%	223.0
L-arginine catabolism	fadB	lo	3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized)	34%	89%	115.9	Acetoacetyl-CoA reductase; EC 1.1.1.36	49%	223.0
L-citrulline catabolism	fadB	lo	3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized)	34%	89%	115.9	Acetoacetyl-CoA reductase; EC 1.1.1.36	49%	223.0
L-lysine catabolism	fadB	lo	3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized)	34%	89%	115.9	Acetoacetyl-CoA reductase; EC 1.1.1.36	49%	223.0
phenylacetate catabolism	fadB	lo	3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized)	34%	89%	115.9	Acetoacetyl-CoA reductase; EC 1.1.1.36	49%	223.0
phenylacetate catabolism	paaH	lo	3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized)	34%	89%	115.9	Acetoacetyl-CoA reductase; EC 1.1.1.36	49%	223.0
L-phenylalanine catabolism	fadB	lo	3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized)	34%	89%	115.9	Acetoacetyl-CoA reductase; EC 1.1.1.36	49%	223.0
L-phenylalanine catabolism	paaH	lo	3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized)	34%	89%	115.9	Acetoacetyl-CoA reductase; EC 1.1.1.36	49%	223.0
L-proline catabolism	fadB	lo	3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized)	34%	89%	115.9	Acetoacetyl-CoA reductase; EC 1.1.1.36	49%	223.0

Sequence Analysis Tools

View N515DRAFT_2873 at FitnessBrowser

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MTRIAIVTGGIGGLGTEICRQLALAGRQVIAADLPARADRVAAFQAELADLDGAVRFEPV
DVSDFASCSELIARVEAAHGRVDVLVNAAGITRDTTLRKMDPQHWQELMRVNLDGVFNMC
RHVVEGMSARGFGRIVNLSSVNGQTGQFGQTNYAAAKAGVHGFGMALARETARKGVTVNT
VSPGYCDTPLVARVPAEIRAQILEDIPVGRLGSPADIARAVCFLAADDAGYITGANLPVN
GGYFMSF

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

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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