catabolism of small carbon sources in Ardenticatena maritima 110S

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Ardenticatena maritima 110S

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
isoleucine	livF, livG, livJ, livH, livM, ofoA, ofoB, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
threonine	braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
maltose	aglE, aglF, aglG, aglK, susB, glk
trehalose	aglE, aglF, aglG, aglK, treF, glk
sucrose	aglE, aglF, aglG, aglK, ams, scrK, glk
ethanol	etoh-dh-nad, adh, acs
L-lactate	Shew_2731, Shew_2732, L-LDH
pyruvate	dctM, dctP, dctQ
aspartate	natF, bgtB', natH, bgtA
alanine	braC, braD, braE, braF, braG
asparagine	ans, natF, bgtB', natH, bgtA
serine	braC, braD, braE, braF, braG, sdaB
D-lactate	larD, D-LDH
glucose	aglE', aglF', aglG', aglK', glk
cellobiose	bgl, aglE', aglF', aglG', aglK', glk
glutamate	dmeA, gdhA
valine	livF, livG, livJ, livH, livM, ofoA, ofoB, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
phenylalanine	livF, livG, livH, livM, livJ, ARO8, PPDCalpha, PPDCbeta, pfor, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
leucine	livF, livG, livJ, livH, livM, ilvE, ofoA, ofoB, liuA, liuB, liuD, liuC, liuE, aacS, atoB
lactose	lacP, lacZ, galK, galT, galE, pgmA, glk
propionate	putP, prpE, pccA, pccB, epi, mcm-large, mcm-small
deoxyribose	deoP, deoK, deoC, adh, acs
proline	HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
glycerol	glpF, glpK, glpD, tpi
galactose	galP, galK, galT, galE, pgmA
deoxyinosine	nupC, deoD, deoB, deoC, adh, acs
thymidine	nupG, deoA, deoB, deoC, adh, acs
citrate	SLC13A5, acn, icd
xylose	xylT, xylA, xylB
histidine	aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
acetate	actP, acs
fructose	Slc2a5, scrK
ribose	rbsU, rbsK
tryptophan	aroP, tnaA
arginine	rocE, arcA, arcB, arcC, rocD, rocA
NAG	nagEcba, nagA, nagB
sorbitol	SOT, sdh, scrK
xylitol	PLT5, xdhA, xylB
phenylacetate	paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
fumarate	dctA
glucose-6-P	uhpT
L-malate	sdlC
2-oxoglutarate	kgtP
succinate	sdc
glucosamine	gamP, nagB
mannose	manP, manA
D-serine	cycA, dsdA
gluconate	gntT, gntK, gnd
mannitol	PLT5, mt2d, scrK
tyrosine	Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
D-alanine	cycA, dadA
lysine	lysP, lat, amaB, lysN, hglS, ydiJ
putrescine	puuP, patA, patD, gabT, gabD
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
glucuronate	exuT, udh, gci, garL, garR, garK
arabinose	araE, araA, araB, araD
rhamnose	rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
4-hydroxybenzoate	pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
fucose	fucP, fucU, fucI, fucK, fucA, tpi, aldA
galacturonate	exuT, uxaC, uxaB, uxaA, kdgK, eda
myoinositol	iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi

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