Protein NP_662456.1 in Chlorobaculum tepidum TLS

GapMind for catabolism of small carbon sources

Protein NP_662456.1 in Chlorobaculum tepidum TLS

Annotation: NCBI__GCF_000006985.1:NP_662456.1

Length: 457 amino acids

Source: GCF_000006985.1 in NCBI

Candidate for 41 steps in catabolism of small carbon sources

Pathway	Step	Score	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
L-arginine catabolism	gabD	hi	aldehyde dehydrogenase-like protein yneI (characterized)	49%	97%	433	betaine aldehyde dehydrogenase (EC 1.2.1.8)	35%	276.6
L-citrulline catabolism	gabD	hi	aldehyde dehydrogenase-like protein yneI (characterized)	49%	97%	433	betaine aldehyde dehydrogenase (EC 1.2.1.8)	35%	276.6
putrescine catabolism	gabD	hi	aldehyde dehydrogenase-like protein yneI (characterized)	49%	97%	433	betaine aldehyde dehydrogenase (EC 1.2.1.8)	35%	276.6
4-hydroxybenzoate catabolism	adh	med	aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)	47%	97%	410.6	aldehyde dehydrogenase-like protein yneI	49%	433.0
2'-deoxyinosine catabolism	adh	med	aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)	47%	97%	410.6	aldehyde dehydrogenase-like protein yneI	49%	433.0
2-deoxy-D-ribose catabolism	adh	med	aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)	47%	97%	410.6	aldehyde dehydrogenase-like protein yneI	49%	433.0
ethanol catabolism	adh	med	aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)	47%	97%	410.6	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-threonine catabolism	adh	med	aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)	47%	97%	410.6	aldehyde dehydrogenase-like protein yneI	49%	433.0
thymidine catabolism	adh	med	aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)	47%	97%	410.6	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-tryptophan catabolism	adh	med	aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)	47%	97%	410.6	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-arginine catabolism	davD	lo	Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)	33%	93%	258.1	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-citrulline catabolism	davD	lo	Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)	33%	93%	258.1	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-lysine catabolism	davD	lo	Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)	33%	93%	258.1	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-proline catabolism	davD	lo	Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)	33%	93%	258.1	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-fucose catabolism	aldA	lo	NAD⁺-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)	35%	95%	257.7	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-rhamnose catabolism	aldA	lo	NAD⁺-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)	35%	95%	257.7	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-threonine catabolism	aldA	lo	NAD⁺-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)	35%	95%	257.7	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-arginine catabolism	patD	lo	4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)	33%	91%	255.8	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-citrulline catabolism	patD	lo	4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)	33%	91%	255.8	aldehyde dehydrogenase-like protein yneI	49%	433.0
putrescine catabolism	patD	lo	4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)	33%	91%	255.8	aldehyde dehydrogenase-like protein yneI	49%	433.0
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)	34%	94%	255	aldehyde dehydrogenase-like protein yneI	49%	433.0
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)	34%	94%	255	aldehyde dehydrogenase-like protein yneI	49%	433.0
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)	34%	94%	255	aldehyde dehydrogenase-like protein yneI	49%	433.0
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)	34%	94%	255	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-arabinose catabolism	aldA	lo	lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)	33%	95%	243.4	aldehyde dehydrogenase-like protein yneI	49%	433.0
D-xylose catabolism	aldA	lo	lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)	33%	95%	243.4	aldehyde dehydrogenase-like protein yneI	49%	433.0
4-hydroxybenzoate catabolism	praB	lo	2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)	31%	93%	241.5	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-tryptophan catabolism	praB	lo	2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)	31%	93%	241.5	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-phenylalanine catabolism	pad-dh	lo	aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)	32%	87%	240.4	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-lysine catabolism	patD	lo	aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)	32%	94%	237.3	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-arginine catabolism	puuC	lo	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	32%	92%	231.9	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-citrulline catabolism	puuC	lo	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	32%	92%	231.9	aldehyde dehydrogenase-like protein yneI	49%	433.0
putrescine catabolism	puuC	lo	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	32%	92%	231.9	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-arginine catabolism	kauB	lo	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)	31%	92%	217.2	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-isoleucine catabolism	iolA	lo	malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)	31%	92%	198.7	aldehyde dehydrogenase-like protein yneI	49%	433.0
myo-inositol catabolism	mmsA	lo	malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)	31%	92%	198.7	aldehyde dehydrogenase-like protein yneI	49%	433.0
propionate catabolism	iolA	lo	malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)	31%	92%	198.7	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-threonine catabolism	iolA	lo	malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)	31%	92%	198.7	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-valine catabolism	iolA	lo	malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)	31%	92%	198.7	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-valine catabolism	mmsA	lo	Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)	31%	90%	187.2	aldehyde dehydrogenase-like protein yneI	49%	433.0
L-lysine catabolism	amaB	lo	Δ¹-piperideine-6-carboxylate dehydrogenase (characterized)	30%	77%	171.4	aldehyde dehydrogenase-like protein yneI	49%	433.0

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

MIVTINPATGEQLAEYPVMIAGQIDSVLRQADADFRRWRSTSFGERRTCMKRLAELLREQ
AEKHGRIITLEMGKPFSQAVAEVNKCAWVCDYFADHAEEFLQPEQSEIDGAKGIVAFEPL
GVILGVMPWNFPYWQVLRFAAPILMAGNGIVVKHAPNVTGCAIAIEKLFRDAGFPEHLYR
AVHIDLDEVDRLTGFMIDHPVIKAVSVTGSTGAGQAVAAKAGKALKRSVLELGGSDPYIV
LEDADLAQAVDACVAGRLLNAGQSCIAAKRFIVRKEIIGEFTKKIVQRMQTAVMGDPFAK
STEVGPIAREDLRDLVHSQVQRSVEAGAELLWGGHVPNAPGWYYPPTVLSGVKPGMPAYS
EEIFGPVATIIEVADDDEAVAIANDSEFGLGSAVFSQDVERALGIARRLEAGSCFINTMV
KSDPRLPFGGVKQSGYGRELSHHGIREFVNIKTFYLP

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)
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