Protein WP_066605139.1 in Sphingobium czechense LL01

GapMind for catabolism of small carbon sources

Protein WP_066605139.1 in Sphingobium czechense LL01

Annotation: NCBI__GCF_001046645.1:WP_066605139.1

Length: 477 amino acids

Source: GCF_001046645.1 in NCBI

Candidate for 32 steps in catabolism of small carbon sources

Pathway	Step	Score	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
L-phenylalanine catabolism	pad-dh	med	phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)	53%	96%	492.3	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-arginine catabolism	kauB	med	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)	48%	95%	413.3	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-arginine catabolism	puuC	med	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)	48%	95%	413.3	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-citrulline catabolism	puuC	med	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)	48%	95%	413.3	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
putrescine catabolism	puuC	med	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)	48%	95%	413.3	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-arginine catabolism	gabD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	45%	96%	412.1	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-arginine catabolism	patD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	45%	96%	412.1	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-citrulline catabolism	gabD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	45%	96%	412.1	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-citrulline catabolism	patD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	45%	96%	412.1	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
putrescine catabolism	gabD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	45%	96%	412.1	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
putrescine catabolism	patD	med	4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)	45%	96%	412.1	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-fucose catabolism	aldA	med	NAD(P)⁺ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)	44%	94%	397.5	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-rhamnose catabolism	aldA	med	NAD(P)⁺ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)	44%	94%	397.5	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-threonine catabolism	aldA	med	NAD(P)⁺ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)	44%	94%	397.5	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
4-hydroxybenzoate catabolism	praB	med	2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)	41%	97%	370.5	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-tryptophan catabolism	praB	med	2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)	41%	97%	370.5	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-lysine catabolism	patD	med	aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)	42%	98%	367.1	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-tryptophan catabolism	nbaE	med	2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)	41%	92%	351.3	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-valine catabolism	mmsA	lo	Malonate-semialdehyde dehydrogenase 1; MSA dehydrogenase 1; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase 1; MMSA dehydrogenase 1; MSDH 1; EC 1.2.1.27 (uncharacterized)	35%	97%	263.5	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-isoleucine catabolism	iolA	lo	methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)	33%	96%	253.4	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
myo-inositol catabolism	mmsA	lo	methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)	33%	96%	253.4	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
propionate catabolism	iolA	lo	methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)	33%	96%	253.4	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-threonine catabolism	iolA	lo	methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)	33%	96%	253.4	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-valine catabolism	iolA	lo	methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)	33%	96%	253.4	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-arginine catabolism	putA	lo	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)	32%	91%	249.2	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-arginine catabolism	rocA	lo	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)	32%	91%	249.2	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-citrulline catabolism	putA	lo	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)	32%	91%	249.2	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-citrulline catabolism	rocA	lo	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)	32%	91%	249.2	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-proline catabolism	putA	lo	L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)	32%	91%	249.2	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-lysine catabolism	amaB	lo	aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)	32%	87%	226.9	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-arginine catabolism	astD	lo	Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)	33%	92%	198.7	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5
L-citrulline catabolism	astD	lo	Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)	33%	92%	198.7	cumic aldehyde dehydrogenase (EC 1.2.1.29)	63%	627.5

Sequence Analysis Tools

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MLIGGAWEDAGDGRTIAVEDPATGQAFATVPAGTAADVDRAVTKARAAFESAAWSRMRPL
DRGKIIEAIARKIEDNAQELALLESYDNGKAVHHALAVDVPAAVDIFRYMAGWASKIYGQ
VNPISGDGRQYHSYSVREPIGVVGQIVPWNYPLAMAAWKIASALAAGCTIVLKPSEVTPL
TALRLAELALEAGLPEGVLNIVTGYGHEAGQALVEHPGIDKIAFTGSTRVGKQIVQTCAK
DLKRVTLELGGKSPSLIFADADLDKAAIGAALAIFFNSGQVCLAASRLYVERSVFDKVVD
GVAQVAKTFKLGHGRDPDTMLGPLVSKVQQGRVLDYIEQGKASGADLVTGGGTGDREGYF
VEPTIFANPDVDASIVREEIFGPVLVATPFDDVEEVVRQANDTRYGLAANIWTRDLSRAH
LTARKLQAGTVWINTHGMNDPSAPFGGVKESGWGREVGEEGVLHYTETKTVTALLDD

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