GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Pseudomonas fluorescens GW456-L13

Pathways are sorted by name. Sort by completeness instead.

Pathway Steps
acetate actP, ackA, pta
D-alanine Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
alanine braC, braD, braE, braF, braG
arabinose araF, araG, araH, xacB, xacC, xacD, xacE, xacF
arginine artJ, artM, artP, artQ, arcA, arcB, arcC, aruF, aruG, astC, astD, astE
asparagine ans, aatJ, aatQ, aatM, aatP
aspartate aatJ, aatQ, aatM, aatP
cellobiose bgl, gtsA, gtsB, gtsC, gtsD, glk
citrate citM, acn, icd
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
deoxyinosine nupC, deoD, deoB, deoC, adh, ackA, pta
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
deoxyribose deoP, deoK, deoC, adh, ackA, pta
ethanol etoh-dh-nad, adh, ackA, pta
fructose fruA, fruI, 1pfk, fba, tpi
fucose HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
fumarate dctA
galactose PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galdh, galactonolactonase, dgoD, dgoK, dgoA
galacturonate PS417_04205, udh, uxuL, garD, kdgD, dopDH
gluconate gntT, gntK, edd, eda
glucose gtsA, gtsB, gtsC, gtsD, glk
glucose-6-P uhpT
glucosamine gamP, nagB
glucuronate exuT, uxaC, uxuB, uxuA, kdgK, eda
glutamate gltI, gltJ, gltK, gltL, gdhA
glycerol glpS, glpT, glpP, glpQ, glpV, glpK, glpD, tpi
histidine hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutF, hutG'
isoleucine livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
4-hydroxybenzoate pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
D-lactate lctP, D-LDH
L-lactate lctP, lutA, lutB, lutC
lactose lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
leucine livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
lysine argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
L-malate dctA
maltose susB, gtsA, gtsB, gtsC, gtsD, glk
mannitol mtlE, mtlF, mtlG, mtlK, mt2d, scrK
mannose mtlG, mtlF, mtlE, mtlK, man-isomerase, scrK
myoinositol iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
NAG nagF, nagEcb, 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, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
proline putP, put1, putA
propionate putP, prpE, prpC, acnD, prpF, acn, prpB
putrescine potA, potB, potC, potD, patA, patD, gabT, gabD
pyruvate yjcH, actP
rhamnose rhaT, LRA1, LRA2, LRA3, LRA4, aldA
ribose rbsA, rbsB, rbsC, rbsK
D-serine dsdX, dsdA
serine braC, braD, braE, braF, braG, sdaB
sorbitol mtlE, mtlF, mtlG, mtlK, sdh, scrK
succinate dctA
sucrose ams, gtsA, gtsB, gtsC, gtsD, glk
threonine braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
thymidine nupG, deoA, deoB, deoC, adh, ackA, pta
trehalose treF, gtsA, gtsB, gtsC, gtsD, glk
tryptophan aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, catI, catJ, pcaF
tyrosine aroP, HPD, hmgA, maiA, fahA, aacS, atoB
valine livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, prpC, acnD, prpF, acn, prpB
xylitol PLT5, xdhA, xylB
xylose gtsA, gtsB, gtsC, gtsD, 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 May 21 2021. The underlying query database was built on May 21 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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