GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Roseicitreum antarcticum ZS2-28

Pathways are sorted by name. Sort by completeness instead.

Pathway Steps
acetate ybhL, acs
D-alanine Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
alanine alsT
arabinose gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
arginine artJ, artM, artP, artQ, arcA, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
asparagine ans, bztA, bztB, bztC, bztD
aspartate bztA, bztB, bztC, bztD
cellobiose bgl, gtsA, gtsB, gtsC, gtsD, glk
citrate SLC13A5, acn, icd
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
deoxyinosine H281DRAFT_01115, H281DRAFT_01114, H281DRAFT_01113, H281DRAFT_01112, deoD, deoB, deoC, adh, acs
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
deoxyribose deoP, deoK, deoC, adh, acs
ethanol etoh-dh-nad, adh, acs
fructose frcA, frcB, frcC, scrK
fucose fucP, fucU, fucI, fucK, fucA, tpi, aldA
fumarate Dshi_1194, Dshi_1195
galactose ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
galacturonate exuT, uxaC, uxaB, uxaA, kdgK, eda
gluconate gntT, gntK, edd, eda
glucose gtsA, gtsB, gtsC, gtsD, glk
glucose-6-P uhpT
glucosamine gamP, nagB
glucuronate dctP, dctQ, dctM, uxaC, uxuB, uxuA, kdgK, eda
glutamate bztA, bztB, bztC, gltL, gdhA
glycerol glpS, glpT, glpP, glpQ, glpV, glpK, glpD, tpi
histidine hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutF, hutG'
isoleucine natA, natB, natC, natD, natE, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
4-hydroxybenzoate pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
D-lactate lctP, glcD, glcE, glcF
L-lactate Shew_2731, Shew_2732, L-LDH
lactose lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
leucine aapJ, aapQ, aapM, aapP, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
lysine argT, hisM, hisQ, hisP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
L-malate Dshi_1194, Dshi_1195
maltose aglE, aglF, aglG, aglK, susB, glk
mannitol PLT5, mt2d, scrK
mannose frcA, frcB, frcC, man-isomerase, scrK
myoinositol iatP, iatA, ibpA, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
NAG nagEcba, nagA, nagB
2-oxoglutarate Psest_0084, Psest_0085
phenylacetate paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
phenylalanine livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
proline ectP, put1, putA
propionate putP, prpE, pccA, pccB, epi, mcm-large, mcm-small
putrescine potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
pyruvate yjcH, actP
rhamnose rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
ribose frcA, frcB, frcC, rbsK
D-serine cycA, dsdA
serine snatA, sdaB
sorbitol SOT, sdh, scrK
succinate Dshi_1194, Dshi_1195
sucrose aglE, aglF, aglG, aglK, ams, scrK, glk
threonine snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
thymidine nupG, deoA, deoB, deoC, adh, acs
trehalose treF, gtsA, gtsB, gtsC, gtsD, glk
tryptophan aroP, tnaA
tyrosine aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
valine natA, natB, natC, natD, natE, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
xylitol PLT5, xdhA, xylB
xylose xylF, xylG, xylH, xylA, xylB

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 Dec 12 2024. 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