GapMind for catabolism of small carbon sources


catabolism of small carbon sources in Dechlorosoma suillum PS

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
isoleucine livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
leucine livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
glutamate gltI, gltJ, gltK, gltL, aspA
aspartate aatJ, aatQ, aatM, aatP
ethanol etoh-dh-nad, adh, acs
fumarate dctM, dctP, dctQ
L-malate dctM, dctP, dctQ
pyruvate dctM, dctP, dctQ
succinate dctQ, dctM, dctP
acetate actP, acs
propionate mctC, prpE, pccA, pccB, epi, mcm-large, mcm-small
threonine phtA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
serine Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
alanine TRIC
valine livF, livG, livJ, livH, livM, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
asparagine ans, aatJ, aatQ, aatM, aatP
proline HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
D-lactate lctP, glcD, glcE, glcF
citrate SLC13A5, acn, icd
L-lactate lctP, lctO, acs
tyrosine Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
D-alanine cycA, dadA
2-oxoglutarate dctP, dctQ, dctM
fructose fruII-ABC, 1pfk, fba, tpi
glucose ptsG-crr
glucose-6-P uhpT
phenylalanine livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
sucrose sut, SUS, scrK, galU, pgmA
mannose manP, manA
sorbitol SOT, sdh, scrK
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
cellobiose cdt, cbp, pgmA, glk
trehalose TRET1, PsTP, pgmA, glk
lysine lysP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
deoxyribose deoP, deoK, deoC, adh, acs
glucosamine gamP, nagB
maltose susB, ptsG-crr
mannitol mtlA, mtlD
ribose rbsU, rbsK
D-serine cycA, dsdA
tryptophan aroP, tnaA
xylitol fruI, x5p-reductase
deoxyinosine nupC, deoD, deoB, deoC, adh, acs
thymidine nupG, deoA, deoB, deoC, adh, acs
glycerol glpF, glpK, glpD, tpi
galactose galP, galK, galT, galE, pgmA
putrescine puuP, patA, patD, gabT, gabD
glucuronate exuT, udh, gci, garL, garR, garK
gluconate gntT, gntK, gnd
NAG nagEcba, nagA, nagB
xylose xylT, xylA, xylB
arginine rocE, rocF, rocD, rocA
fucose fucP, fucU, fucI, fucK, fucA, tpi, aldA
lactose lacP, lacZ, galK, galT, galE, pgmA, glk
arabinose araE, araA, araB, araD
rhamnose rhaT, LRA1, LRA2, LRA3, LRA4, aldA
histidine PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
phenylacetate ppa, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
4-hydroxybenzoate pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
galacturonate exuT, udh, gli, gci, kdgD, dopDH
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.



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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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