GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Pseudomonas fluorescens FW300-N1B4

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
valine livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, prpC, acnD, prpF, acn, prpB
isoleucine livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
leucine livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
phenylalanine livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
arginine artJ, artM, artP, artQ, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
lysine argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
threonine braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
myoinositol PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
4-hydroxybenzoate pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
putrescine potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
galactose PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galdh, galactonolactonase, dgoD, dgoK, dgoA
histidine hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutF, hutG'
arabinose araF, araG, araH, xacB, xacC, xacD, xacE, xacF
glucosamine gdh, AO353_21715, AO353_21720, AO353_21725, AO353_21710, glucosaminate-lyase, kdgK, kdgA
glycerol glpS, glpT, glpP, glpQ, glpV, glpK, glpD, tpi
tyrosine aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
sucrose thuE, thuF, thuG, thuK, ams, scrK, glk
cellobiose bgl, gtsA, gtsB, gtsC, gtsD, glk
galacturonate exuT, udh, uxuL, garD, kdgD, dopDH
mannitol mtlE, mtlF, mtlG, mtlK, mt2d, scrK
mannose mtlG, mtlF, mtlE, mtlK, man-isomerase, scrK
serine braC, braD, braE, braF, braG, sdaB
sorbitol mtlE, mtlF, mtlG, mtlK, sdh, scrK
D-alanine Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
alanine braC, braD, braE, braF, braG
asparagine ans, aatJ, aatQ, aatM, aatP
fructose fruA, fruI, 1pfk, fba, tpi
glucose gtsA, gtsB, gtsC, gtsD, glk
glutamate gltI, gltJ, gltK, gltL, gdhA
aspartate aatJ, aatQ, aatM, aatP
ethanol etoh-dh-nad, adh, ackA, pta
gluconate gntT, gntK, edd, eda
D-lactate lctP, glcD, glcE, glcF
L-lactate lctP, lutA, lutB, lutC
ribose rbsA, rbsB, rbsC, rbsK
trehalose treEIIA, treB, treC, glk
acetate actP, ackA, pta
citrate citM, acn, icd
proline putP, put1, putA
pyruvate yjcH, actP
fumarate dctA
L-malate dctA
2-oxoglutarate kgtP
succinate dctA
propionate putP, prpE, prpC, acnD, prpF, acn, prpB
maltose susB, gtsA, gtsB, gtsC, gtsD, glk
D-serine cycA, dsdA
glucose-6-P uhpT
glucuronate exuT, udh, uxuL, gudD, kdgD, dopDH
lactose lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
tryptophan aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, catI, catJ, pcaF
deoxyribose deoP, deoK, deoC, adh, ackA, pta
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
xylose gtsA, gtsB, gtsC, gtsD, xylA, xylB
deoxyinosine nupC, deoD, deoB, deoC, adh, ackA, pta
thymidine nupG, deoA, deoB, deoC, adh, ackA, pta
xylitol PLT5, xdhA, xylB
rhamnose rhaT, LRA1, LRA2, LRA3, LRA4, aldA
NAG nagEcba, nagA, nagB
fucose HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
phenylacetate ppa, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2

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 Aug 02 2021. The underlying query database was built on Aug 02 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