GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Marinobacter adhaerens HP15

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 alsT
arabinose araE, araA, araB, araD
arginine artJ, artM, artP, artQ, astA, astB, astC, astD, astE
asparagine ans, glt
aspartate glt
cellobiose bgl, gtsA, gtsB, gtsC, gtsD, glk
citrate tctA, tctB, tctC, acn, icd
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
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 fucP, fucU, fucI, fucK, fucA, tpi, aldA
fumarate Dshi_1194, Dshi_1195
galactose PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galK, galT, galE, pgmA
galacturonate exuT, uxaC, uxaB, uxaA, kdgK, eda
gluconate gntT, gntK, edd, eda
glucose gtsA, gtsB, gtsC, gtsD, glk
glucose-6-P uhpT
glucosamine SLC2A2, glc-kinase, nagB
glucuronate exuT, udh, gci, kdgD, dopDH
glutamate gltP, gdhA
glycerol glpS, glpT, glpP, glpQ, glpV, glpK, glpD, tpi
histidine PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
isoleucine livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
4-hydroxybenzoate pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
D-lactate lctP, glcD, glcE, glcF
L-lactate Shew_2731, Shew_2732, lutA, lutB, lutC
lactose lacA', lacC', lacB', klh, gtsA, gtsB, gtsC, gtsD, 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 Dshi_1194, Dshi_1195
maltose susB, gtsA, gtsB, gtsC, gtsD, glk
mannitol mtlA, mtlD
mannose manP, manA
myoinositol iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
NAG nagEcba, nagA, nagB
2-oxoglutarate Psest_0084, Psest_0085
phenylacetate paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
phenylalanine livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
proline putP, put1, putA
propionate putP, prpE, prpC, acnD, prpF, acn, prpB
putrescine potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
pyruvate yjcH, actP
rhamnose rhaT, LRA1, LRA2, LRA3, LRA4, aldA
ribose rbsU, rbsK
D-serine cycA, dsdA
serine braC, braD, braE, braF, braG, sdaB
sorbitol mtlA, srlD
succinate Dshi_1194, Dshi_1195
sucrose ams, gtsA, gtsB, gtsC, gtsD, glk
threonine braC, braD, braE, braF, braG, tdcB, tdcE, prpC, acnD, prpF, acn, prpB
thymidine nupG, deoA, deoB, deoC, adh, ackA, pta
trehalose treF, gtsA, gtsB, gtsC, gtsD, glk
tryptophan aroP, kynA, kynB, kyn, antA, antB, antC, xylE, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
tyrosine Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, 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 fruI, x5p-reductase
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.

Links

Downloads

Related tools

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