Protein WP_068461307.1 in Hyphomicrobium sulfonivorans WDL6

GapMind for catabolism of small carbon sources

Protein WP_068461307.1 in Hyphomicrobium sulfonivorans WDL6

Annotation: NCBI__GCF_001541235.1:WP_068461307.1

Length: 508 amino acids

Source: GCF_001541235.1 in NCBI

Candidate for 49 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	hi	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)	53%	100%	534.3	phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39)	53%	508.4
2'-deoxyinosine catabolism	adh	hi	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)	53%	100%	534.3	phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39)	53%	508.4
2-deoxy-D-ribose catabolism	adh	hi	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)	53%	100%	534.3	phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39)	53%	508.4
ethanol catabolism	adh	hi	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)	53%	100%	534.3	phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39)	53%	508.4
L-threonine catabolism	adh	hi	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)	53%	100%	534.3	phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39)	53%	508.4
thymidine catabolism	adh	hi	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)	53%	100%	534.3	phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39)	53%	508.4
L-tryptophan catabolism	adh	hi	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)	53%	100%	534.3	phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39)	53%	508.4
L-phenylalanine catabolism	pad-dh	med	phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)	53%	99%	508.4	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-fucose catabolism	aldA	med	NAD(P)⁺ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)	48%	96%	444.9	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-rhamnose catabolism	aldA	med	NAD(P)⁺ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)	48%	96%	444.9	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-threonine catabolism	aldA	med	NAD(P)⁺ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)	48%	96%	444.9	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
4-hydroxybenzoate catabolism	praB	med	2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)	44%	97%	398.7	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-tryptophan catabolism	praB	med	2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)	44%	97%	398.7	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-arginine catabolism	kauB	med	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)	45%	96%	391.7	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-arginine catabolism	puuC	med	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)	45%	96%	391.7	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-citrulline catabolism	puuC	med	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)	45%	96%	391.7	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
putrescine catabolism	puuC	med	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)	45%	96%	391.7	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-arginine catabolism	gabD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	42%	97%	364	phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39)	53%	508.4
L-arginine catabolism	patD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	42%	97%	364	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-citrulline catabolism	gabD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	42%	97%	364	phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39)	53%	508.4
L-citrulline catabolism	patD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	42%	97%	364	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
putrescine catabolism	gabD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	42%	97%	364	phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39)	53%	508.4
putrescine catabolism	patD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	42%	97%	364	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-tryptophan catabolism	nbaE	lo	2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)	38%	97%	338.6	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-lysine catabolism	patD	lo	aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)	37%	99%	320.1	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-arginine catabolism	davD	lo	Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)	38%	96%	309.7	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-citrulline catabolism	davD	lo	Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)	38%	96%	309.7	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-lysine catabolism	davD	lo	Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)	38%	96%	309.7	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-proline catabolism	davD	lo	Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)	38%	96%	309.7	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
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%	98%	295.8	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
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%	98%	295.8	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
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%	98%	295.8	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
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%	98%	295.8	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-arabinose catabolism	aldA	lo	lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)	35%	98%	283.5	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
D-xylose catabolism	aldA	lo	lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)	35%	98%	283.5	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-arginine catabolism	putA	lo	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)	32%	94%	240.4	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-arginine catabolism	rocA	lo	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)	32%	94%	240.4	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-citrulline catabolism	putA	lo	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)	32%	94%	240.4	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-citrulline catabolism	rocA	lo	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)	32%	94%	240.4	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-proline catabolism	putA	lo	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)	32%	94%	240.4	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-valine catabolism	mmsA	lo	Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)	31%	95%	238.8	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-isoleucine catabolism	iolA	lo	methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)	32%	97%	236.9	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
myo-inositol catabolism	mmsA	lo	methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)	32%	97%	236.9	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
propionate catabolism	iolA	lo	methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)	32%	97%	236.9	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-threonine catabolism	iolA	lo	methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)	32%	97%	236.9	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-valine catabolism	iolA	lo	methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)	32%	97%	236.9	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-lysine catabolism	amaB	lo	L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)	32%	93%	191	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-arginine catabolism	astD	lo	N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)	32%	92%	188.7	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3
L-citrulline catabolism	astD	lo	N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)	32%	92%	188.7	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	53%	534.3

Sequence Analysis Tools

View WP_068461307.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MNPRIDIQSIKPLLGDKVRQWLATPRPMLIDGKWTPAQSGKFFPVYDPATGEKIADVAEG
DAADIDLAVRAARKAFESGPWPSMTPSERGRIIHKLGDLVLEHADELATLESIDNGKPKH
VARAADVTLSADMFHYMSGWTTKIEGKTISISALAAPPGTQFFSATRPEPVGVVGQIIPW
NFPLLMAAWKLGPALATGCTIVLKVAEETPLSALRLGELILEAGIPPGVVNIVPGFGETA
GAALAAHPDVDKIAFTGSTDVGRLIVKAAAGNLKKVSLELGGKSPNIILADADLDLAIPG
ATAAIFFNHGQCCNAGSRLFVHRSIFDRVVEGIAAEASKIKLGHGLDATTEMGPLISEVQ
YNRVTGLLASGLQQGAKAVCGGAGFGGSGYFVPPTIFTNTDPSMRVVAEEIFGPVLVATP
FDEADCSLVAEANNSIYGLAAGIWSTNTAKAQMLANRLRAGTVWMNCYHVFDAALPFGGY
KQSGWGREMGQAVLSNYLETKAITTRLG

This GapMind analysis is from Apr 09 2024. 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:

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 2024 update 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