catabolism of small carbon sources in Erythrobacter marinus HWDM-33

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Erythrobacter marinus HWDM-33

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
xylose	xylT, xdh, xylC, xad, kdaD, dopDH
ethanol	etoh-dh-nad, adh, acs
proline	putP, put1, putA
acetate	deh, acs
asparagine	agcS, ans
fructose	glcP, scrK
alanine	alsT
fumarate	sdcL
L-malate	sdlC
succinate	sdc
propionate	putP, prpE, pccA, pccB, epi, mcm-large, mcm-small
rhamnose	Echvi_1617, rhaM, rhaA, rhaB, rhaD, tpi, aldA
threonine	snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
cellobiose	bgl, MFS-glucose, glk
glucose	MFS-glucose, glk
glutamate	gltP, gdhA
serine	snatA, sdaB
trehalose	treF, MFS-glucose, glk
aspartate	glt
isoleucine	Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
valine	Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
leucine	leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
phenylalanine	aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
tyrosine	aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
glycerol	glpF, glpK, glpD, tpi
citrate	SLC13A5, acn, icd
sucrose	ams, glcP, scrK
D-lactate	lctP, D-LDH
L-lactate	lctP, L-LDH
maltose	malI, susB, glk
galactose	HP1174, galdh, galactonolactonase, dgoD, dgoK, dgoA
gluconate	gntT, gntK, edd, eda
glucose-6-P	uhpT
2-oxoglutarate	kgtP
pyruvate	SLC5A8
mannose	manP, manA
arginine	rocE, astA, astB, astC, astD, astE
deoxyinosine	nupC, deoD, deoB, deoC, adh, acs
mannitol	PLT5, mt2d, scrK
sorbitol	SOT, sdh, scrK
deoxyribose	deoP, deoK, deoC, adh, acs
D-alanine	cycA, dadA
glucosamine	gamP, nagB
ribose	rbsU, rbsK
D-serine	cycA, dsdA
tryptophan	aroP, tnaA
xylitol	fruI, x5p-reductase
galacturonate	exuT, uxaC, uxaB, uxaA, kdgK, eda
glucuronate	exuT, uxaC, uxuB, uxuA, kdgK, eda
lysine	lysP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
arabinose	araE, xacB, xacC, xacD, xacE, xacF
lactose	lacA', lacC', lacB', klh, MFS-glucose, glk
thymidine	nupG, deoA, deoB, deoC, adh, acs
NAG	nagEcba, nagA, nagB
citrulline	PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, ocd, put1, putA
putrescine	puuP, patA, patD, gabT, gabD
fucose	fucP, fucU, fucI, fucK, fucA, tpi, aldA
histidine	Ga0059261_1577, hutH, hutU, hutI, hutG
4-hydroxybenzoate	pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
myoinositol	iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
phenylacetate	paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

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