GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Oceanisphaera arctica V1-41

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
phenylalanine livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
threonine sstT, tdh, kbl, gcvP, gcvT, gcvH, lpd
fructose fruA, fruI, 1pfk, fba, tpi
L-lactate lctP, lutA, lutB, lutC
proline putP, put1, putA
asparagine ans, glt
glutamate gltS, gdhA
D-lactate lctP, D-LDH
2-oxoglutarate Psest_0084, Psest_0085
alanine alsT
aspartate glt
fumarate sdcL
L-malate sdlC
succinate sdc
leucine livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
arginine artJ, artM, artP, artQ, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
putrescine potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
deoxyinosine nupC, deoD, deoB, deoC, adh, ackA, pta
thymidine nupC, deoA, deoB, deoC, adh, ackA, pta
histidine aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
citrate tctA, tctB, tctC, acn, icd
ethanol etoh-dh-nad, adh, ackA, pta
D-alanine Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
serine sstT, sdaB
ribose rbsA, rbsB, rbsC, rbsK
mannose manP, manA
isoleucine livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
phenylacetate paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
valine brnQ, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, prpC, prpD, acn, prpB
tyrosine aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
glucuronate dctP, dctQ, dctM, uxaC, uxuB, uxuA, kdgK, eda
propionate lctP, prpE, prpC, prpD, acn, prpB
sucrose ams, fruA, fruI, 1pfk, fba, tpi
deoxyribose deoP, deoK, deoC, adh, ackA, pta
glycerol glpF, glpK, glpD, tpi
NAG nagP, nagK, nagA, nagB
tryptophan tnaT, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, catI, catJ, pcaF
lysine argT, hisM, hisQ, hisP, cadA, patA, patD, davT, davD, glaH, lhgD
acetate actP, ackA, pta
glucosamine nagX, nagP, nagK, nagA, nagB
glucose ptsG, crr
D-serine cycA, dsdA
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
glucose-6-P uhpT
pyruvate SLC5A8
galacturonate exuT, uxaC, uxaB, uxaA, kdgK, eda
cellobiose bgl, ptsG, crr
maltose susB, ptsG, crr
trehalose treF, ptsG, crr
galactose galP, galK, galT, galE, pgmA
mannitol mtlA, mtlD
sorbitol mtlA, srlD
xylitol fruI, x5p-reductase
gluconate gntT, gntK, edd, eda
xylose xylT, xylA, xylB
myoinositol iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
lactose lacP, lacZ, galK, galT, galE, pgmA, glk
arabinose araE, araA, araB, araD
4-hydroxybenzoate pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
fucose fucP, fucU, fucI, fucK, fucA, tpi, aldA
rhamnose rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA

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