GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Methylobacterium sp. 4-46 Apr-46

Pathways are sorted by name. Sort by completeness instead.

Pathway Steps
acetate actP, acs
D-alanine AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
alanine braC, braD, braE, braF, braG
arabinose araE, xacB, xacC, xacD, xacE, xacF
arginine braC, braD, braE, braF, braG, rocF, ocd, put1, putA
asparagine ans, aatJ, aatQ, aatM, aatP
aspartate aatJ, aatQ, aatM, aatP
cellobiose cdt, cbp, pgmA, glk
citrate citA, acn, icd
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
deoxyinosine nupC, deoD, deoB, deoC, adh, acs
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
deoxyribose drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
ethanol etoh-dh-nad, adh, acs
fructose Slc2a5, scrK
fucose fucP, fucU, fucI, fucK, fucA, tpi, aldA
fumarate dctM, dctP, dctQ
galactose galP, galdh, galactonolactonase, dgoD, dgoK, dgoA
galacturonate exuT, udh, uxuL, garD, kdgD, dopDH
gluconate gntT, gntK, edd, eda
glucose ptsG-crr
glucose-6-P uhpT
glucosamine gamP, nagB
glucuronate exuT, udh, uxuL, gudD, garL, garR, garK
glutamate braC, braD, braE, braF, braG, gdhA
glycerol glpS, glpT, glpP, glpQ, glpV, glpK, glpD, tpi
histidine braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
isoleucine livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA
4-hydroxybenzoate pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
D-lactate lctP, glcD, glcE, glcF
L-lactate lctP, L-LDH
lactose lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
leucine livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
lysine argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
L-malate dctM, dctP, dctQ
maltose susB, ptsG-crr
mannitol PLT5, mt2d, scrK
mannose STP6, mannokinase, manA
myoinositol iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
NAG nagEcba, nagA, nagB
2-oxoglutarate kgtP
phenylacetate ppa, 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, atoA, atoD, atoB
proline AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
propionate lctP, prpE, pccA, pccB, epi, mcmA
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 dctQ, dctM, dctP
sucrose sacP, scrB, scrK
threonine braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
thymidine nupC, deoA, deoB, deoC, adh, acs
trehalose treF, ptsG-crr
tryptophan aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
tyrosine Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
valine livF, livG, livJ, livH, livM, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcmA
xylitol fruI, x5p-reductase
xylose xylT, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB

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