GapMind for catabolism of small carbon sources


catabolism of small carbon sources in Sphingomonas indica Dd16

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
ethanol etoh-dh-nad, adh, acs
acetate deh, acs
aspartate glt
fumarate dctA
L-malate dctA
2-oxoglutarate kgtP
succinate dctA
threonine snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
histidine Ga0059261_1577, hutH, hutU, hutI, hutG
proline CCNA_00435, put1, putA
asparagine ans, glt
glutamate gltP, gdhA
serine snatA, sdaB
alanine snatA
isoleucine Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
valine Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
phenylalanine aroP, ARO8, iorAB, 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
leucine leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
tyrosine aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
propionate putP, prpE, pccA, pccB, epi, mcm-large, mcm-small
glycerol glpF, glpK, glpD, tpi
arginine rocE, rocF, rocD, PRO3, put1, putA
citrate SLC13A5, acn, icd
mannose manP, manA
glucose ptsG-crr
glucose-6-P uhpT
pyruvate SLC5A8
L-lactate lctP, L-LDH
trehalose treF, ptsG-crr
lactose lacP, lacZ, galK, galT, galE, pgmA, glk
cellobiose cdt, cbp, pgmA, glk
fructose fruII-ABC, 1pfk, fba, tpi
mannitol PLT5, mt1d, mak, manA
lysine lysP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
deoxyribose deoP, deoK, deoC, adh, acs
galactose galP, galK, galT, galE, pgmA
sucrose sut, SUS, scrK, galU, pgmA
D-alanine cycA, dadA
glucosamine gamP, nagB
D-lactate lctP, D-LDH
maltose susB, ptsG-crr
ribose rbsU, rbsK
D-serine cycA, dsdA
sorbitol mtlA, srlD
tryptophan aroP, tnaA
xylitol fruI, x5p-reductase
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
deoxyinosine nupC, deoD, deoB, deoC, adh, acs
thymidine nupG, deoA, deoB, deoC, adh, acs
gluconate gntT, gntK, gnd
NAG nagEcba, nagA, nagB
xylose xylT, xylA, xylB
putrescine puuP, patA, patD, gabT, gabD
glucuronate exuT, udh, gci, kdgD, dopDH
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
arabinose araE, araA, araB, araD
galacturonate exuT, udh, gli, gci, kdgD, dopDH
fucose fucP, fucU, fucI, fucK, fucA, tpi, aldA
rhamnose rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
4-hydroxybenzoate pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
myoinositol iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi

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