GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Pseudomonas fluorescens GW456-L13

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, aacS, atoB
phenylalanine livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
tryptophan aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, catI, catJ, pcaF
lysine argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
phenylacetate ppa, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
threonine braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
arginine artJ, artM, artP, artQ, arcA, arcB, arcC, aruF, aruG, astC, astD, astE
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
4-hydroxybenzoate pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
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
glycerol glpS, glpT, glpP, glpQ, glpV, glpK, glpD, tpi
putrescine potA, potB, potC, potD, patA, patD, gabT, gabD
tyrosine aroP, HPD, hmgA, maiA, fahA, aacS, atoB
cellobiose bgl, gtsA, gtsB, gtsC, gtsD, glk
mannitol mtlE, mtlF, mtlG, mtlK, mt2d, scrK
serine braC, braD, braE, braF, braG, sdaB
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
L-lactate lctP, lutA, lutB, lutC
NAG nagF, nagEcb, nagA, nagB
ribose rbsA, rbsB, rbsC, rbsK
acetate actP, ackA, pta
citrate citM, acn, icd
proline putP, put1, putA
D-lactate lctP, D-LDH
pyruvate yjcH, actP
D-serine dsdX, dsdA
fumarate dctA
L-malate dctA
2-oxoglutarate kgtP
succinate dctA
propionate putP, prpE, prpC, acnD, prpF, acn, prpB
sorbitol mtlE, mtlF, mtlG, mtlK, sdh, scrK
glucosamine gamP, nagB
mannose manP, manA
glucose-6-P uhpT
maltose susB, gtsA, gtsB, gtsC, gtsD, glk
sucrose ams, gtsA, gtsB, gtsC, gtsD, glk
trehalose treF, gtsA, gtsB, gtsC, gtsD, glk
lactose lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
deoxyribose deoP, deoK, deoC, adh, ackA, pta
galacturonate PS417_04205, udh, uxuL, garD, kdgD, dopDH
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
glucuronate exuT, uxaC, uxuB, uxuA, kdgK, eda
xylitol PLT5, xdhA, xylB
xylose gtsA, gtsB, gtsC, gtsD, xylA, xylB
deoxyinosine nupC, deoD, deoB, deoC, adh, ackA, pta
thymidine nupG, deoA, deoB, deoC, adh, ackA, pta
rhamnose rhaT, LRA1, LRA2, LRA3, LRA4, aldA
fucose HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
myoinositol iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda

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 17 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