catabolism of small carbon sources in Rubrivirga marina SAORIC-28

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Rubrivirga marina SAORIC-28

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
arabinose	BT0355, araA, araB, araD
glycerol	glpF, glpK, glpD, tpi
cellobiose	bgl, MFS-glucose, glk
maltose	susB, MFS-glucose, glk
trehalose	treF, MFS-glucose, glk
asparagine	ans, glt
fructose	glcP, scrK
glucose	MFS-glucose, glk
glutamate	gltP, gdhA
alanine	alsT
aspartate	glt
fumarate	sdcL
L-malate	sdlC
succinate	sdc
deoxyinosine	nupC, deoD, deoB, deoC, adh, ackA, pta
thymidine	nupC, deoA, deoB, deoC, adh, ackA, pta
histidine	Ga0059261_1577, hutH, hutU, hutI, hutG
gluconate	gntT, gntK, gnd
proline	CCNA_00435, put1, putA
sucrose	ams, MFS-glucose, glk
ethanol	etoh-dh-nad, adh, ackA, pta
L-lactate	Shew_2731, Shew_2732, L-LDH
mannose	gluP, mannokinase, manA
pyruvate	yjcH, actP
threonine	tdcC, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
galactose	HP1174, galK, galT, galE, pgmA
galacturonate	exuT, uxaC, uxaB, uxaA, kdgK, eda
propionate	putP, prpE, pccA, pccB, epi, mcmA
lactose	lacP, lacZ, galK, galT, galE, pgmA, glk
acetate	actP, ackA, pta
citrate	SLC13A5, acn, icd
xylose	xylT, xylA, xylB
glucuronate	dctP, dctQ, dctM, uxaC, uxuB, uxuA, kdgK, eda
glucosamine	gamP, nagB
serine	serP, sdaB
deoxyribose	deoP, deoK, deoC, adh, ackA, pta
sorbitol	SOT, sdh, scrK
tyrosine	aroP, HPD, hmgA, maiA, fahA, aacS, atoB
glucose-6-P	uhpT
2-oxoglutarate	kgtP
isoleucine	Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
leucine	leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
arginine	rocE, rocF, rocD, PRO3, put1, putA
mannitol	PLT5, mt2d, scrK
NAG	nagEcba, nagA, nagB
xylitol	PLT5, xdhA, xylB
phenylalanine	aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
D-alanine	cycA, dadA
D-lactate	lctP, D-LDH
ribose	rbsU, rbsK
D-serine	cycA, dsdA
tryptophan	aroP, tnaA
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
putrescine	puuP, patA, patD, gabT, gabD
lysine	lysP, lat, amaB, lysN, hglS, ydiJ
valine	Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcmA
rhamnose	rhaT, LRA1, LRA2, LRA3, LRA4, aldA
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
fucose	fucP, fucU, fucI, fucK, fucA, tpi, aldA
4-hydroxybenzoate	pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
myoinositol	iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
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.

Downloads

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

Related tools

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