GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Geotalea uraniireducens Rf4

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
acetate actP, ackA, pta
fumarate dctM, dctP, dctQ
L-malate dctM, dctP, dctQ
succinate dctQ, dctM, dctP
threonine snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
ethanol etoh-dh-nad, adh, ackA, pta
glutamate gltP, aspA
serine snatA, sdaB
alanine TRIC
aspartate glt
pyruvate mctC
isoleucine livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
propionate mctC, prpE, prpC, prpD, acn, prpB
leucine livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
citrate SLC13A5, acn, icd
valine livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, prpC, prpD, acn, prpB
glucose MFS-glucose, glk
proline proY, put1, putA
cellobiose cdt, cbp, pgmA, glk
trehalose TRET1, PsTP, pgmA, glk
glucose-6-P uhpT
2-oxoglutarate kgtP
arginine rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
asparagine ans, glt
L-lactate lctP, L-LDH
maltose malEIICBA, malA, glk
mannose STP6, mannokinase, manA
sucrose ams, MFS-glucose, glk
galactose galP, galK, galT, galE, pgmA
D-alanine cycA, dadA
fructose Slc2a5, scrK
glucosamine gamP, nagB
D-lactate lctP, D-LDH
mannitol mtlA, mtlD
ribose rbsU, rbsK
D-serine cycA, dsdA
sorbitol mtlA, srlD
tryptophan aroP, tnaA
xylitol fruI, x5p-reductase
deoxyribose deoP, deoK, deoC, adh, ackA, pta
deoxyinosine nupC, deoD, deoB, deoC, adh, ackA, pta
thymidine nupG, deoA, deoB, deoC, adh, ackA, pta
lysine lysP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
lactose lacP, lacZ, galK, galT, galE, pgmA, glk
glycerol glpF, glpK, glpD, tpi
NAG nagP, nagK, nagA, nagB
putrescine puuP, patA, patD, gabT, gabD
citrulline PS417_17590, PS417_17595, PS417_17600, PS417_17605, arcB, arcC, rocD, PRO3, put1, putA
gluconate gntT, gntK, gnd
xylose xylT, xylA, xylB
tyrosine aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
glucuronate exuT, udh, gci, kdgD, dopDH
fucose fucP, fucU, fucI, fucK, fucA, tpi, aldA
rhamnose rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
arabinose araE, araA, araB, araD
galacturonate exuT, udh, gli, gci, kdgD, dopDH
histidine permease, hutH, hutU, hutI, hutG
4-hydroxybenzoate pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
phenylalanine aroP, ARO8, iorA, iorB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
phenylacetate ppa, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
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 Apr 09 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