GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Sedimenticola selenatireducens DSM 17993

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
D-lactate PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, glcD, glcE, glcF
proline proV, proW, proX, put1, putA
ethanol etoh-dh-nad, adh, ackA, pta
fumarate dctM, dctP, dctQ
L-malate dctM, dctP, dctQ
2-oxoglutarate dctP, dctQ, dctM
pyruvate dctM, dctP, dctQ
succinate dctQ, dctM, dctP
aspartate dauA
phenylalanine livF, livG, livH, livM, livJ, ARO8, ARO10, pad-dh, paaK, padB, padC, padD, padG, padI, padE, padF, padH, boxA, boxB, boxC, boxD, paaF, paaH, paaJ2
leucine livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
threonine braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
D-alanine AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
arginine artJ, artM, artP, artQ, rocF, ocd, put1, putA
glutamate braC, braD, braE, braF, braG, gdhA
serine braC, braD, braE, braF, braG, sdaB
alanine braC, braD, braE, braF, braG
phenylacetate paaT, paaK, padB, padC, padD, padG, padI, padE, padF, padH, boxA, boxB, boxC, boxD, paaF, paaH, paaJ2
isoleucine livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
4-hydroxybenzoate pcaK, hcl, hcrA, hcrB, hcrC, boxA, boxB, boxC, boxD, paaF, paaH, paaJ2
valine livF, livG, livJ, livH, livM, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
propionate putP, prpE, pccA, pccB, epi, mcm-large, mcm-small
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
glycerol glpF, glpK, glpD, tpi
L-lactate lctP, lutA, lutB, lutC
acetate actP, ackA, pta
citrate SLC13A5, acn, icd
lysine argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
sucrose sut, SUS, scrK, galU, pgmA
asparagine ans, dauA
fructose Slc2a5, scrK
glucose MFS-glucose, glk
mannose STP6, mannokinase, manA
sorbitol SOT, sdh, scrK
tyrosine Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
cellobiose cdt, cbp, pgmA, glk
trehalose TRET1, PsTP, pgmA, glk
glucose-6-P uhpT
deoxyribose deoP, deoK, deoC, adh, ackA, pta
maltose malEIICBA, malA, glk
mannitol PLT5, mt2d, scrK
deoxyinosine nupC, deoD, deoB, deoC, adh, ackA, pta
thymidine nupG, deoA, deoB, deoC, adh, ackA, pta
galactose galP, galK, galT, galE, pgmA
glucosamine gamP, nagB
ribose rbsU, rbsK
D-serine cycA, dsdA
tryptophan aroP, tnaA
xylitol fruI, x5p-reductase
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
lactose lacP, lacZ, galK, galT, galE, pgmA, glk
gluconate gntT, gntK, gnd
NAG nagEcba, nagA, nagB
xylose xylT, xylA, xylB
histidine braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
putrescine puuP, patA, patD, gabT, gabD
glucuronate exuT, udh, gci, garL, garR, garK
arabinose araE, araA, araB, araD
fucose fucP, fucU, fucI, fucK, fucA, tpi, aldA
galacturonate exuT, udh, gli, gci, kdgD, dopDH
rhamnose rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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