GapMind for catabolism of small carbon sources


catabolism of small carbon sources in Bacteroides fluxus YIT 12057

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
galacturonate exuT, uxaC, uxaB, uxaA, kdgK, eda
xylose xylT, xylA, xylB
asparagine yhiT, ans
threonine snatA, tdh, kbl, gcvP, gcvT, gcvH, lpd
cellobiose bgl, MFS-glucose, glk
maltose malI, susB, glk
fructose BT1758, scrK
glucose MFS-glucose, glk
serine snatA, sdaB
alanine snatA
aspartate dauA
fumarate sdcL
L-malate sdlC
succinate sdc
fucose fucP, fucU, fucI, fucK, fucA, tpi, fucO
rhamnose rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
deoxyinosine nupG, deoD, deoB, deoC, adh, ackA, pta
lactose lacP, lacZ, galK, galT, galE, pgmA, glk
NAG nagP, nagK, nagA, nagB
galactose HP1174, galK, galT, galE, pgmA
glucosamine nagX, nagP, nagK, nagA, nagB
glucuronate exuT, uxaC, uxuB, uxuA, kdgK, eda
acetate actP, ackA, pta
citrate SLC13A5, acn, icd
propionate putP, prpE, pccA, pccB, epi, mcm-large, mcm-small
ethanol etoh-dh-nad, adh, ackA, pta
histidine permease, hutH, hutU, hutI, hutG
glutamate gltS, gdhA
D-lactate lctP, D-LDH
tryptophan aroP, tnaA
mannose STP6, mannokinase, manA
sucrose ams, MFS-glucose, glk
trehalose treF, MFS-glucose, glk
thymidine nupG, deoA, deoB, deoC, adh, ackA, pta
L-lactate lctP, lctO, ackA, pta
glucose-6-P uhpT
2-oxoglutarate kgtP
pyruvate SLC5A8
deoxyribose deoP, deoK, deoC, adh, ackA, pta
gluconate gntT, gntK, gnd
mannitol PLT5, mt2d, scrK
sorbitol SOT, sdh, scrK
xylitol PLT5, xdhA, xylB
D-alanine cycA, dadA
ribose rbsU, rbsK
D-serine cycA, dsdA
proline N515DRAFT_2924, put1, putA
isoleucine Bap2, vorA*, vorB, vorC, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
glycerol glpF, glpK, glpD, tpi
valine Bap2, vorA*, vorB, vorC, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
arginine rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
putrescine potA, potB, potC, potD, patA, patD, gabT, gabD
arabinose araE, araA, araB, araD
leucine leuT, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
lysine lysP, lat, amaB, lysN, hglS, ydiJ
myoinositol iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
tyrosine aroP, HPD, hmgA, maiA, fahA, aacS, atoB
4-hydroxybenzoate pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
phenylalanine aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
phenylacetate paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2

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