GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Hafnia paralvei ATCC 29927

Pathways are sorted by name. Sort by completeness instead.

Pathway Steps
acetate actP, ackA, pta
D-alanine cycA, dadA
alanine cycA
arabinose araF, araG, araH, araA, araB, araD
arginine artJ, artM, artP, artQ, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD
asparagine ans, aatJ, aatQ, aatM, aatP
aspartate aatJ, aatQ, aatM, aatP
cellobiose bgl, mglA, mglB, mglC, glk
citrate citA, citD, citE, citF
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
deoxyinosine nupC, deoD, deoB, deoC, ald-dh-CoA
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
deoxyribose deoP, deoK, deoC, ald-dh-CoA
ethanol etoh-dh-nad, ald-dh-CoA
fructose fruA, fruB, 1pfk, fba, tpi
fucose fucP, fucU, fucI, fucK, fucA, tpi, fucO
fumarate dctA
galactose mglA, mglB, mglC, galK, galT, galE, pgmA
galacturonate exuT, uxaC, uxaB, uxaA, kdgK, eda
gluconate gntT, gntK, edd, eda
glucose mglA, mglB, mglC, glk
glucose-6-P uhpT
glucosamine manX, manY, manZ, nagB
glucuronate exuT, uxaC, uxuB, uxuA, kdgK, eda
glutamate gltI, gltJ, gltK, gltL, aspA
glycerol glpF, glpK, glpA, glpB, glpC, glpD, tpi
histidine hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
isoleucine livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
4-hydroxybenzoate pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
D-lactate lctP, D-LDH
L-lactate lctP, L-LDH
lactose lacY, lacZ, galK, galT, galE, pgmA, glk
leucine livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
lysine lysP, cadA, patA, patD, davT, davD, glaH, lhgD
L-malate dctA
maltose malE, malF, malG, malK, susB, glk
mannitol mtlA, mtlD
mannose manX, manY, manZ, manA
myoinositol iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
NAG nagEcba, nagA, nagB
2-oxoglutarate kgtP
phenylacetate ppa, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
phenylalanine livF, livG, livH, livM, livJ, ARO8, ARO10, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
proline proV, proW, proX, put1, putA
propionate putP, prpE, prpC, prpD, acn, prpB
putrescine potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
pyruvate yjcH, actP
rhamnose rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
ribose rbsA, rbsB, rbsC, rbsK
D-serine cycA, dsdA
serine dlsT, sdaB
sorbitol mtlA, srlD
succinate dctA
sucrose ams, fruA, fruB, 1pfk, fba, tpi
threonine tdcC, tdh, kbl, gcvP, gcvT, gcvH, lpd
thymidine nupC, deoA, deoB, deoC, ald-dh-CoA
trehalose treEIIA, treB, treC, glk
tryptophan aroP, tnaA
tyrosine aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
valine brnQ, ofo, acdH, ech, bch, mmsB, mmsA, prpC, prpD, acn, prpB
xylitol fruI, x5p-reductase
xylose xylT, 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 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