GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Paraburkholderia atlantica CCGE1002

Pathways are sorted by name. Sort by completeness instead.

Pathway Steps
acetate deh, acs
D-alanine mctP, dadA
alanine cycA
arabinose araF, araG, araH, xacB, xacC, xacD, xacE, xacF
arginine artJ, artM, artP, artQ, astA, astB, astC, astD, astE
asparagine ans, aatJ, aatQ, aatM, aatP
aspartate aatJ, aatQ, aatM, aatP
cellobiose bgl, gtsA, gtsB, gtsC, gtsD, glk
citrate citA, acn, icd
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
deoxyinosine nupC, deoD, deoB, deoC, adh, acs
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
deoxyribose drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
ethanol etoh-dh-nad, adh, acs
fructose frcA, frcB, frcC, scrK
fucose HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
fumarate dctA
galactose ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
galacturonate exuT, 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, udh, uxuL, gudD, garL, garR, garK
glutamate gltI, gltJ, gltK, gltL, gdhA
glycerol glpF, glpK, glpD, tpi
histidine PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
isoleucine livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
4-hydroxybenzoate pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
D-lactate mctP, glcD, glcE, glcF
L-lactate mctP, lldE, lldF, lldG
lactose lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
leucine livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
lysine argT, hisM, hisQ, hisP, cadA, patA, patD, 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 frcA, frcB, frcC, man-isomerase, scrK
myoinositol PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
NAG nagF, nagEcb, nagA, nagB
2-oxoglutarate kgtP
phenylacetate H281DRAFT_04042, 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 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
propionate mctP, prpE, prpC, acnD, prpF, acn, prpB
putrescine potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
pyruvate yjcH, actP
rhamnose rhaP, rhaQ, rhaS, rhaT', LRA1, LRA2, LRA3, LRA5, LRA6
ribose rbsA, rbsB, rbsC, rbsK
D-serine cycA, dsdA
serine Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
sorbitol mtlE, mtlF, mtlG, mtlK, sdh, scrK
succinate dctA
sucrose ams, gtsA, gtsB, gtsC, gtsD, glk
threonine snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
thymidine nupG, deoA, deoB, deoC, adh, acs
trehalose treF, gtsA, gtsB, gtsC, gtsD, glk
tryptophan aroP, tnaA
tyrosine Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
valine livF, livG, livJ, livH, livM, ofo, acdH, ech, bch, mmsB, mmsA, prpC, acnD, prpF, acn, prpB
xylitol HSERO_RS17000, HSERO_RS17005, HSERO_RS17010, HSERO_RS17020, xdhA, xylB
xylose xylF, xylG, xylH, xdh, xylC, xad, kdaD, dopDH

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 Apr 09 2024. 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