GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Marinomonas arctica 328

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
myoinositol PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
rhamnose rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
arginine artJ, artM, artP, artQ, astA, astB, astC, astD, astE
histidine hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutF, hutG'
arabinose gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
glycerol glpS, glpT, glpP, glpQ, glpV, glpK, glpD, tpi
threonine sstT, tdh, kbl, gcvP, gcvT, gcvH, lpd
cellobiose bgl, gtsA, gtsB, gtsC, gtsD, glk
maltose aglE, aglF, aglG, aglK, susB, glk
trehalose treF, gtsA, gtsB, gtsC, gtsD, glk
citrate tctA, tctB, tctC, acn, icd
glucose gtsA, gtsB, gtsC, gtsD, glk
mannose frcA, frcB, frcC, man-isomerase, scrK
xylose xylF, xylG, xylH, xylA, xylB
ethanol etoh-dh-nad, adh, ackA, pta
fructose frcA, frcB, frcC, scrK
ribose frcA, frcB, frcC, rbsK
proline putP, put1, putA
asparagine ans, glt
glutamate gltP, gdhA
pyruvate yjcH, actP
serine sstT, sdaB
alanine alsT
aspartate glt
fumarate SLC26dg
galactose ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
sucrose aglE, aglF, aglG, aglK, ams, scrK, glk
propionate putP, prpE, prpC, prpD, acn, prpB
sorbitol mtlE, mtlF, mtlG, mtlK, sdh, scrK
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, aruF, aruG, astC, astD, astE
gluconate gntT, gntK, edd, eda
D-alanine Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
mannitol mtlE, mtlF, mtlG, mtlK, mt2d, scrK
2-oxoglutarate Psest_0084, Psest_0085
L-lactate Shew_2731, Shew_2732, L-LDH
phenylalanine livF, livG, livH, livM, livJ, ARO8, ARO10, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
phenylacetate paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
isoleucine livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
4-hydroxybenzoate pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
putrescine potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
glucuronate dctP, dctQ, dctM, udh, uxuL, gudD, kdgD, dopDH
lactose lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
lysine argT, hisM, hisQ, hisP, alr, amaD, dpkA, amaA, amaB, lysN, hglS, ydiJ
galacturonate exuT, udh, uxuL, garD, kdgD, dopDH
NAG SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
valine livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, prpC, prpD, acn, prpB
glucosamine nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
deoxyribose deoP, deoK, deoC, adh, ackA, pta
acetate actP, ackA, pta
L-malate dctM, dctP, dctQ
succinate dctQ, dctM, dctP
leucine livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
D-lactate lctP, D-LDH
D-serine cycA, dsdA
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
fucose fucP, fucU, fucI, fucK, fucA, tpi, aldA
glucose-6-P uhpT
xylitol PLT5, xdhA, xylB
thymidine nupG, deoA, deoB, deoC, adh, ackA, pta
tyrosine aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
tryptophan aroP, tnaA
deoxyinosine nupA, nupB, nupC', bmpA, deoD, deoB, deoC, adh, ackA, pta

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