Protein WP_052367856.1 in Algiphilus aromaticivorans DG1253

GapMind for catabolism of small carbon sources

Protein WP_052367856.1 in Algiphilus aromaticivorans DG1253

Annotation: NCBI__GCF_000733765.1:WP_052367856.1

Length: 539 amino acids

Source: GCF_000733765.1 in NCBI

Candidate for 24 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	Aldehyde dehydrogenase 22A1; Novel aldehyde dehydrogenase family 22 member A1; EC 1.2.1.3 (characterized)	42%	87%	401.4	succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24)	40%	363.2
2'-deoxyinosine catabolism	adh	hi	Aldehyde dehydrogenase 22A1; Novel aldehyde dehydrogenase family 22 member A1; EC 1.2.1.3 (characterized)	42%	87%	401.4	succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24)	40%	363.2
2-deoxy-D-ribose catabolism	adh	hi	Aldehyde dehydrogenase 22A1; Novel aldehyde dehydrogenase family 22 member A1; EC 1.2.1.3 (characterized)	42%	87%	401.4	succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24)	40%	363.2
ethanol catabolism	adh	hi	Aldehyde dehydrogenase 22A1; Novel aldehyde dehydrogenase family 22 member A1; EC 1.2.1.3 (characterized)	42%	87%	401.4	succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24)	40%	363.2
L-threonine catabolism	adh	hi	Aldehyde dehydrogenase 22A1; Novel aldehyde dehydrogenase family 22 member A1; EC 1.2.1.3 (characterized)	42%	87%	401.4	succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24)	40%	363.2
thymidine catabolism	adh	hi	Aldehyde dehydrogenase 22A1; Novel aldehyde dehydrogenase family 22 member A1; EC 1.2.1.3 (characterized)	42%	87%	401.4	succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24)	40%	363.2
L-tryptophan catabolism	adh	hi	Aldehyde dehydrogenase 22A1; Novel aldehyde dehydrogenase family 22 member A1; EC 1.2.1.3 (characterized)	42%	87%	401.4	succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24)	40%	363.2
L-arginine catabolism	gabD	hi	succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized)	41%	81%	364.4	Putative aldehyde dehydrogenase-like protein C21C3; EC 1.2.1.-	37%	343.2
L-citrulline catabolism	gabD	hi	succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized)	41%	81%	364.4	Putative aldehyde dehydrogenase-like protein C21C3; EC 1.2.1.-	37%	343.2
putrescine catabolism	gabD	hi	succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized)	41%	81%	364.4	Putative aldehyde dehydrogenase-like protein C21C3; EC 1.2.1.-	37%	343.2
L-arginine catabolism	patD	lo	aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)	33%	95%	235.3	Aldehyde dehydrogenase 22A1; Novel aldehyde dehydrogenase family 22 member A1; EC 1.2.1.3	42%	401.4
L-citrulline catabolism	patD	lo	aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)	33%	95%	235.3	Aldehyde dehydrogenase 22A1; Novel aldehyde dehydrogenase family 22 member A1; EC 1.2.1.3	42%	401.4
putrescine catabolism	patD	lo	aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)	33%	95%	235.3	Aldehyde dehydrogenase 22A1; Novel aldehyde dehydrogenase family 22 member A1; EC 1.2.1.3	42%	401.4
L-arginine catabolism	kauB	lo	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)	33%	92%	213	Aldehyde dehydrogenase 22A1; Novel aldehyde dehydrogenase family 22 member A1; EC 1.2.1.3	42%	401.4
L-arginine catabolism	puuC	lo	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)	33%	92%	213	Aldehyde dehydrogenase 22A1; Novel aldehyde dehydrogenase family 22 member A1; EC 1.2.1.3	42%	401.4
L-citrulline catabolism	puuC	lo	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)	33%	92%	213	Aldehyde dehydrogenase 22A1; Novel aldehyde dehydrogenase family 22 member A1; EC 1.2.1.3	42%	401.4
putrescine catabolism	puuC	lo	4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)	33%	92%	213	Aldehyde dehydrogenase 22A1; Novel aldehyde dehydrogenase family 22 member A1; EC 1.2.1.3	42%	401.4
L-arginine catabolism	astD	lo	N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)	32%	88%	198	Aldehyde dehydrogenase 22A1; Novel aldehyde dehydrogenase family 22 member A1; EC 1.2.1.3	42%	401.4
L-citrulline catabolism	astD	lo	N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)	32%	88%	198	Aldehyde dehydrogenase 22A1; Novel aldehyde dehydrogenase family 22 member A1; EC 1.2.1.3	42%	401.4
L-arginine catabolism	putA	lo	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)	30%	89%	184.1	Aldehyde dehydrogenase 22A1; Novel aldehyde dehydrogenase family 22 member A1; EC 1.2.1.3	42%	401.4
L-arginine catabolism	rocA	lo	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)	30%	89%	184.1	Aldehyde dehydrogenase 22A1; Novel aldehyde dehydrogenase family 22 member A1; EC 1.2.1.3	42%	401.4
L-citrulline catabolism	putA	lo	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)	30%	89%	184.1	Aldehyde dehydrogenase 22A1; Novel aldehyde dehydrogenase family 22 member A1; EC 1.2.1.3	42%	401.4
L-citrulline catabolism	rocA	lo	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)	30%	89%	184.1	Aldehyde dehydrogenase 22A1; Novel aldehyde dehydrogenase family 22 member A1; EC 1.2.1.3	42%	401.4
L-proline catabolism	putA	lo	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)	30%	89%	184.1	Aldehyde dehydrogenase 22A1; Novel aldehyde dehydrogenase family 22 member A1; EC 1.2.1.3	42%	401.4

Sequence Analysis Tools

View WP_052367856.1 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

MSVEAQARAPETPLRQVTEIDCRNPATGETLGTLPAATPAEVQEAVERARAAQKQWAQSS
FRQRRAVLRRMLQSILDDVDELCAAVVADSGKTWENALLGEVMPVCNKIRWIIRYGEKHL
RSESVPSGLLKHKKGRIEYRPLGVVACIVPWNYPFQNIFGSLVAPLMAGNAVVLKASEAV
AWSTQRFRRVFEEALVAEGFPAETVQIINGYGETGAALVRSRVQKILFIGSVGNGRKIIE
GSAEHLTPVVMELGGKDPMIICDDAHLEQAVHSALSGCFINLGQNCIASERLIVQAGIFD
RFVEEVTRIAGDMRQGVPEQPGTLDVGAMTTPQQVRIVDELVRDALASGARALVGGRLPE
GASGSFYPPTVLVDVTPEMRIAREEVFGPVMLIMRAADDAEAVRIANAIDFGLQSSVFSR
DRKRAERIAAELEAGATCINDFGLCYLNQDLPFGGVKYSGFGRMNGRDGLRAYTNPKAVL
SDRFPVAVPQRLYPVGAGDYAKARNGIRLLFATGWRQRFKSLLSLMRGNRASGATQSTR

This GapMind analysis is from Apr 09 2024. 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 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