GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Nitriliruptor alkaliphilus DSM 45188

Pathways are sorted by name. Sort by completeness instead.

Pathway Steps
acetate actP, acs
D-alanine cycA, dadA
alanine braC, braD, braE, braF, braG
arabinose gguA, gguB, chvE, araA, araB, araD
arginine rocE, arcA, arcB, arcC, rocD, PRO3, put1, putA
asparagine ans, dauA
aspartate dauA
cellobiose bgl, mglA, mglB, mglC, glk
citrate tctA, tctB, tctC, acn, icd
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
deoxyinosine nupA, nupB, nupC', bmpA, deoD, deoB, deoC, adh, acs
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
deoxyribose deoP, deoK, deoC, adh, acs
ethanol etoh-dh-nad, adh, acs
fructose fruII-ABC*, 1pfk, fba, tpi
fucose fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
fumarate sdcL
galactose gguA, gguB, chvE, galK, galT, galE, pgmA
galacturonate exuT, udh, gli, gci, kdgD, dopDH
gluconate gntT, gntK, edd, eda
glucose mglA, mglB, mglC, glk
glucose-6-P uhpT
glucosamine nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
glucuronate exuT, uxaC, uxuB, uxuA, kdgK, eda
glutamate gltS_Syn, gdhA
glycerol glpF, glpK, glpD, tpi
histidine natA, natB, natC, natD, natE, hutH, hutU, hutI, hutG
isoleucine natA, natB, natC, natD, natE, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
4-hydroxybenzoate pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
D-lactate lctP, D-LDH
L-lactate Shew_2731, Shew_2732, lctO, acs
lactose lacP, lacZ, galK, galT, galE, pgmA, glk
leucine natA, natB, natC, natD, natE, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
lysine lysP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
L-malate sdlC
maltose susB, mglA, mglB, mglC, glk
mannitol PLT5, mt2d, scrK
mannose TM1746, TM1747, TM1748, TM1749, TM1750, mannokinase, manA
myoinositol PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
NAG SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
2-oxoglutarate kgtP
phenylacetate paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
phenylalanine livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
proline putP, put1, putA
propionate putP, prpE, pccA, pccB, epi, mcm-large, mcm-small
putrescine potA, potB, potC, potD, patA, patD, gabT, gabD
pyruvate yjcH, actP
rhamnose rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
ribose rbsU, rbsK
D-serine cycA, dsdA
serine braC, braD, braE, braF, braG, sdaB
sorbitol SOT, sdh, scrK
succinate sdc
sucrose ams, fruII-ABC*, 1pfk, fba, tpi
threonine braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
thymidine nupG, deoA, deoB, deoC, adh, acs
trehalose treF, mglA, mglB, mglC, glk
tryptophan tnaT, tnaA
tyrosine aroP, HPD, hmgA, maiA, fahA, aacS, atoB
valine natA, natB, natC, natD, natE, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
xylitol PLT5, xdhA, xylB
xylose xylF, xylG, xylH, 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 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