GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Cobetia crustatorum JO1

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
isoleucine livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
leucine livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
phenylalanine livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
arginine artJ, artM, artP, artQ, aruH, aruI, kauB, gbuA, gabT, gabD
putrescine potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
glycerol glpS, glpT, glpP, glpQ, glpV, glpK, glpD, tpi
propionate lctP, prpE, prpC, acnD, prpF, acn, prpB
sorbitol mtlE, mtlF, mtlG, mtlK, sdh, scrK
citrate tctA, tctB, tctC, acn, icd
fructose fruA, fruI, 1pfk, fba, tpi
ethanol etoh-dh-nad, adh, acs
maltose susB, MFS-glucose, glk
proline putP, put1, putA
asparagine ans, glt
glucose MFS-glucose, glk
glutamate gltS, gdhA
L-lactate lctP, L-LDH
alanine alsT
aspartate glt
fumarate sdcL
L-malate sdlC
succinate sdc
sucrose thuE, thuF, thuG, thuK, ams, scrK, glk
gluconate gntA, gntB, gntC, gntK, edd, eda
serine braC, braD, braE, braF, braG, sdaB
trehalose thuE, thuF, thuG, thuK, treF, glk
D-alanine Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
mannitol mtlE, mtlF, mtlG, mtlK, mt2d, scrK
2-oxoglutarate dctP, dctQ, dctM
pyruvate dctM, dctP, dctQ
galactose sglS, galdh, galactonolactonase, dgoD, dgoK*, dgoA
D-lactate lctP, D-LDH
glucose-6-P uhpT
ribose rbsA, rbsB, rbsC, rbsK
valine livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, prpC, acnD, prpF, acn, prpB
threonine braC, braD, braE, braF, braG, tdcB, tdcE, prpC, acnD, prpF, acn, prpB
tyrosine aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
xylose xylT, xdh, xylC, xad, kdaD, dopDH
lactose lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK*, dgoA, glk
deoxyinosine nupC, deoD, deoB, deoC, adh, acs
thymidine nupC, deoA, deoB, deoC, adh, acs
cellobiose bgl, MFS-glucose, glk
mannose STP6, man-isomerase, scrK
NAG nagEcba, nagA, nagB
arabinose Echvi_1880, xacB, xacC, xacD, xacE, xacF
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
acetate actP, acs
glucosamine gamP, nagB
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
4-hydroxybenzoate pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
deoxyribose deoP, deoK, deoC, adh, acs
xylitol fruI, x5p-reductase
glucuronate exuT, uxaC, uxuB, uxuA, kdgK, eda
lysine argT, hisM, hisQ, hisP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
D-serine cycA, dsdA
tryptophan aroP, tnaA
rhamnose Echvi_1617, LRA1, LRA2, LRA3, LRA4, aldA
galacturonate exuT, uxaC, uxaB, uxaA, kdgK, eda
histidine PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
fucose fucP, fucU, fucI, fucK, fucA, tpi, aldA
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.

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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:

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:

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:

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:

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