catabolism of small carbon sources in Halopiger salifodinae KCY07-B2

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Halopiger salifodinae KCY07-B2

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
fructose	fruII-A, fruII-B, fruII-C, 1pfk, fba, tpi
ethanol	etoh-dh-nad, adh, acs
L-lactate	lctP, lctO, acs
glutamate	gltP, gdhA
aspartate	glt
fumarate	sdcL
L-malate	sdlC
succinate	sdc
propionate	lctP, prpE, pccA, pccB, epi, mcm-large, mcm-small
citrate	citM, acn, icd
glucose	gtsA, gtsB, gtsC, gtsD, glk
cellobiose	bgl, gtsA, gtsB, gtsC, gtsD, glk
maltose	susB, gtsA, gtsB, gtsC, gtsD, glk
asparagine	ans, glt
D-lactate	lctP, D-LDH
pyruvate	MCT4
2-oxoglutarate	Psest_0084, Psest_0085
sucrose	ams, fruII-A, fruII-B, fruII-C, 1pfk, fba, tpi
threonine	tdcC, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
thymidine	nupG, deoA, deoB, deoC, adh, acs
arabinose	xacG, xacH, xacI, xacJ, xacK, xacB, xacC, xacD, xacE, xacF
deoxyinosine	nupC, deoD, deoB, deoC, adh, acs
xylose	xylT, xdh, xylC, xad, kdaD, dopDH
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
trehalose	treF, gtsA, gtsB, gtsC, gtsD, glk
deoxyribose	deoP, deoK, deoC, adh, acs
acetate	actP, acs
serine	serP, sdaB
tryptophan	aroP, tnaA
glucuronate	exuT, uxaC, uxuB, uxuA, kdgK, eda
gluconate	gntT, gntK, gnd
sorbitol	SOT, sdh, scrK
arginine	rocE, adiA, speB, patA, patD, gabT, gabD
glycerol	glpF, glpK, glpD, tpi
alanine	cycA
glucose-6-P	uhpT
galactose	galP, galK, galT, galE, pgmA
xylitol	fruI, x5p-reductase
mannose	TT_C0211, TT_C0327, TT_C0326, TT_C0328, man-isomerase, scrK
galacturonate	exuT, uxaC, uxaB, uxaA, kdgK, eda
putrescine	puuP, patA, patD, gabT, gabD
D-alanine	cycA, dadA
glucosamine	gamP, nagB
mannitol	mtlA, mtlD
ribose	rbsU, rbsK
D-serine	cycA, dsdA
proline	putP, put1, putA
lysine	lysP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
NAG	nagEcba, nagA, nagB
lactose	lacP, lacZ, galK, galT, galE, pgmA, glk
4-hydroxybenzoate	pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
rhamnose	rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
leucine	leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
myoinositol	iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
fucose	fucP, fucU, fucI, fucK, fucA, tpi, aldA
tyrosine	aroP, HPD, hmgA, maiA, fahA, aacS, atoB
histidine	permease, hutH, hutU, hutI, hutG
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
phenylalanine	aroP, ARO8, PPDCalpha, PPDCbeta, pfor, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
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