GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Alistipes indistinctus YIT 12060

Pathways are sorted by name. Sort by completeness instead.

Pathway Steps
acetate actP, ackA, pta
D-alanine cycA, dadA
alanine cycA
arabinose araE, araA, araB, araD
arginine rocE, rocF, rocD, rocA
asparagine yhiT, ans
aspartate glt
cellobiose bgl, MFS-glucose, glk
citrate SLC13A5, acn, icd
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
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 BT1758, scrK
fucose fucP, fucU, fucI, fucK, fucA, tpi, fucO
fumarate dctA
galactose galP, galK, galT, galE, pgmA
galacturonate exuT, uxaC, uxaB, uxaA, kdgK, eda
gluconate gntT, gntK, gnd
glucose MFS-glucose, glk
glucose-6-P uhpT
glucosamine nagX, nagP, nagK, nagA, nagB
glucuronate exuT, uxaC, uxuB, uxuA, kdgK, eda
glutamate gltS, gdhA
glycerol glpF, glpK, glpD, tpi
histidine permease, hutH, hutU, hutI, hutG
isoleucine Bap2, vorA*, vorB, vorC, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
4-hydroxybenzoate pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
D-lactate lctP, D-LDH
L-lactate lctP, lctO, ackA, pta
lactose lacP, lacZ, galK, galT, galE, pgmA, glk
leucine leuT, ilvE, vorA*, vorB, vorC, liuA, liuB, liuD, liuC, liuE, aacS, atoB
lysine lysP, lat, amaB, lysN, hglS, ydiJ
L-malate sdlC
maltose susB, MFS-glucose, glk
mannitol mtlA, mtlD
mannose STP6, mannokinase, manA
myoinositol iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
NAG nagP, nagK, nagA, nagB
2-oxoglutarate kgtP
phenylacetate paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
phenylalanine aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
proline proY, put1, putA
propionate putP, prpE, pccA, pccB, epi, mcm-large, mcm-small
putrescine puuP, patA, patD, gabT, gabD
pyruvate SLC5A8
rhamnose rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
ribose BT2809, rbsK
D-serine cycA, dsdA
serine serP, sdaB
sorbitol SOT, sdh, scrK
succinate sdc
sucrose ams, BT1758, scrK
threonine tdcC, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
thymidine nupC, deoA, deoB, deoC, adh, ackA, pta
trehalose BT2158, klh, MFS-glucose, glk
tryptophan aroP, tnaA
tyrosine aroP, HPD, hmgA, maiA, fahA, aacS, atoB
valine Bap2, vorA*, vorB, vorC, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
xylitol PLT5, xdhA, xylB
xylose xylT, 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 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