GapMind for catabolism of small carbon sources


catabolism of small carbon sources in Photobacterium jeanii R-40508

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
threonine sstT, tdh, kbl, grdA, grdE, grdB, grdD, grdC, ackA
deoxyinosine nupC, deoD, deoB, deoC, adh, ackA, pta
glycerol glpF, glpK, glpA, glpB, glpC, glpD, tpi
thymidine nupC, deoA, deoB, deoC, adh, ackA, pta
tyrosine tyrP, HPD, hmgA, maiA, fahA, aacS, atoB
propionate lctP, prpE, prpC, prpD, acn, prpB
fructose fruA, fruB, 1pfk, fba, tpi
ethanol etoh-dh-nad, adh, ackA, pta
acetate satP, ackA, pta
proline putP, put1, putA
asparagine ans, glt
glucose ptsG, crr
glutamate gltS, gdhA
D-lactate lctP, D-LDH
serine sdaC, sdaB
alanine alsT
aspartate glt
fumarate sdcL
L-malate sdlC
succinate sdc
arginine artJ, artM, artP, artQ, astA, astB, astC, astD, astE
sucrose ams, fruA, fruB, 1pfk, fba, tpi
L-lactate Shew_2731, Shew_2732, lutA, lutB, lutC
maltose malE, malF, malG, malK, susB, glk
histidine hutV, hutW, hutX, hutH, hutU, hutI, hutG
cellobiose bgl, ptsG, crr
NAG nagEcba, nagA, nagB
trehalose treEIIA, treB, treC, glk
glucosamine gamP, nagB
mannose manP, manA
ribose rbsA, rbsB, rbsC, rbsK
glucose-6-P uhpT
pyruvate yjcH, actP
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
isoleucine brnQ, ofo, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB
phenylalanine aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
valine brnQ, ofo, acdH, ech, bch, mmsB, mmsA, prpC, prpD, acn, prpB
leucine brnQ, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
deoxyribose deoP, deoK, deoC, adh, ackA, pta
putrescine potA, potB, potC, potD, patA, patD, gabT, gabD
galactose galP, galK, galT, galE, pgmA
lactose lacP, lacZ, galK, galT, galE, pgmA, glk
citrate SLC13A5, acn, icd
tryptophan tnaB, tnaA
sorbitol SOT, sdh, scrK
D-alanine Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
2-oxoglutarate kgtP
xylitol fruI, x5p-reductase
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
mannitol PLT5, mt2d, scrK
D-serine cycA, dsdA
gluconate gntT, gntK, edd, eda
glucuronate exuT, udh, gci, garL, garR, garK
galacturonate exuT, uxaC, uxaB, uxaA, kdgK, eda
xylose xylT, xylA, xylB
lysine argT, hisM, hisQ, hisP, lat, amaB, lysN, hglS, ydiJ
arabinose araE, araA, araB, araD
rhamnose rhaT, LRA1, LRA2, LRA3, LRA4, aldA
4-hydroxybenzoate pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
fucose fucP, fucU, fucI, fucK, fucA, tpi, aldA
myoinositol iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
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