Protein WP_017549818.1 in Salinicoccus carnicancri Crm

GapMind for catabolism of small carbon sources

Protein WP_017549818.1 in Salinicoccus carnicancri Crm

Annotation: NCBI__GCF_000330705.1:WP_017549818.1

Length: 496 amino acids

Source: GCF_000330705.1 in NCBI

Candidate for 46 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)	58%	99%	583.2	aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5)	52%	486.9
2'-deoxyinosine catabolism	adh	hi	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)	58%	99%	583.2	aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5)	52%	486.9
2-deoxy-D-ribose catabolism	adh	hi	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)	58%	99%	583.2	aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5)	52%	486.9
ethanol catabolism	adh	hi	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)	58%	99%	583.2	aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5)	52%	486.9
L-threonine catabolism	adh	hi	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)	58%	99%	583.2	aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5)	52%	486.9
thymidine catabolism	adh	hi	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)	58%	99%	583.2	aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5)	52%	486.9
L-tryptophan catabolism	adh	hi	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)	58%	99%	583.2	aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5)	52%	486.9
L-phenylalanine catabolism	pad-dh	med	aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)	50%	92%	478	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-fucose catabolism	aldA	med	NAD(P)⁺ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)	51%	96%	470.7	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-rhamnose catabolism	aldA	med	NAD(P)⁺ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)	51%	96%	470.7	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-threonine catabolism	aldA	med	NAD(P)⁺ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)	51%	96%	470.7	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
4-hydroxybenzoate catabolism	praB	med	2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)	42%	97%	387.1	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-tryptophan catabolism	praB	med	2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)	42%	97%	387.1	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-arginine catabolism	gabD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	41%	96%	380.9	aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5)	52%	486.9
L-arginine catabolism	patD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	41%	96%	380.9	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-arginine catabolism	puuC	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	41%	96%	380.9	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-citrulline catabolism	gabD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	41%	96%	380.9	aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5)	52%	486.9
L-citrulline catabolism	patD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	41%	96%	380.9	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-citrulline catabolism	puuC	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	41%	96%	380.9	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
putrescine catabolism	gabD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	41%	96%	380.9	aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5)	52%	486.9
putrescine catabolism	patD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	41%	96%	380.9	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
putrescine catabolism	puuC	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	41%	96%	380.9	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-arginine catabolism	kauB	med	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)	41%	98%	373.6	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-tryptophan catabolism	nbaE	med	aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)	42%	95%	347.1	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-arabinose catabolism	xacF	med	Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized)	41%	98%	341.3	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
D-galacturonate catabolism	dopDH	med	Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized)	41%	98%	341.3	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
D-glucuronate catabolism	dopDH	med	Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized)	41%	98%	341.3	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
D-xylose catabolism	dopDH	med	Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized)	41%	98%	341.3	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-lysine catabolism	patD	lo	aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)	40%	99%	350.9	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-arginine catabolism	davD	lo	Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)	39%	96%	338.2	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-citrulline catabolism	davD	lo	Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)	39%	96%	338.2	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-lysine catabolism	davD	lo	Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)	39%	96%	338.2	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-proline catabolism	davD	lo	Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)	39%	96%	338.2	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-arabinose catabolism	aldA	lo	lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)	36%	98%	300.4	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
D-xylose catabolism	aldA	lo	lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)	36%	98%	300.4	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-valine catabolism	mmsA	lo	Malonate-semialdehyde dehydrogenase; MSA dehydrogenase; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase; MMSA dehydrogenase; MSDH; EC 1.2.1.27 (uncharacterized)	35%	96%	290.4	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-isoleucine catabolism	iolA	lo	methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)	35%	96%	290	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
myo-inositol catabolism	mmsA	lo	methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)	35%	96%	290	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
propionate catabolism	iolA	lo	methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)	35%	96%	290	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-threonine catabolism	iolA	lo	methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)	35%	96%	290	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-valine catabolism	iolA	lo	methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)	35%	96%	290	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-arginine catabolism	putA	lo	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)	35%	94%	258.5	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-arginine catabolism	rocA	lo	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)	35%	94%	258.5	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-citrulline catabolism	putA	lo	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)	35%	94%	258.5	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-citrulline catabolism	rocA	lo	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)	35%	94%	258.5	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2
L-proline catabolism	putA	lo	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)	35%	94%	258.5	Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3	58%	583.2

Sequence Analysis Tools

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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

MMAIMVLKQRVNEFLDGEKGLYIDGGYVQAHGGKMFDVLNPATEEVIAQVSEADESDIDN
AVQAARKAFDAGEWTKMEPAERSRLIYKFADLLEEHREELAQLEALDNGKAYQQALEDDV
DGTVQHFRYYAGWATKISGKTPNVSPDYVTYTVHEPVGVVGQIIPWNYPLAMAGWKLGAA
LAAGCTIVIKPASETPLSLLYAAKLFKEAGFPDGVVNVVPGAGSVAGNALVTHPGVDKVA
FTGSTRTGGSIMKKAADDIKSVTLELGGKSPAIVLEDADLDTALDGIFDGTMYNTGQNCS
ATTRIYVHRNLYEKVLDALKDKAEKAVVGPGLDEATDMGPLVSEKQLDTVLGYIEKGKEE
GARLITGGSRKGDKGYFVEPTIFADVEDDMTIAREEIFGPVMSVFVFDEVDEVISRANDS
EYGLAASVWTENIKKGHYIAGKLESGTVWVNDFGLELETMPFGGYKKSGIGREMGGDYGI
SNYVEVKSVFVNIKQD

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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