GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Magnetospirillum magneticum AMB-1

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
L-lactate lctP, lutA, lutB, lutC
fumarate dctM, dctP, dctQ
L-malate dctM, dctP, dctQ
pyruvate dctM, dctP, dctQ
succinate dctQ, dctM, dctP
acetate actP, acs
D-lactate lctP, D-LDH
2-oxoglutarate Psest_0084, Psest_0085
aspartate dauA
phenylalanine livF, livG, livH, livM, livJ, ARO8, iorA, iorB, padB, padC, padD, padG, padI, padE, padF, padH, bcrA, bcrB, bcrC, bcrD, dch, had, oah, pimB, gcdH, ech, fadB, atoB
phenylacetate ppa, paaK, padB, padC, padD, padG, padI, padE, padF, padH, bcrA, bcrB, bcrC, bcrD, dch, had, oah, pimB, gcdH, ech, fadB, atoB
4-hydroxybenzoate pcaK, hcl, hcrA, hcrB, hcrC, bcrA, bcrB, bcrC, bcrD, dch, had, oah, pimB, gcdH, ech, fadB, atoB
proline AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
threonine braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
D-alanine AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
putrescine potA, potB, potC, potD, patA, patD, gabT, gabD
glutamate braC, braD, braE, braF, braG, gdhA
propionate lctP, prpE, pccA, pccB, epi, mcm-large, mcm-small
cellobiose bgl, SemiSWEET, glk
glucose SemiSWEET, glk
alanine braC, braD, braE, braF, braG
leucine livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
isoleucine livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
valine livF, livG, livJ, livH, livM, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
arginine braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
citrate SLC13A5, acn, icd
ethanol etoh-dh-nad, adh, acs
glucosamine SLC2A2, glc-kinase, nagB
sucrose sut, SUS, scrK, galU, pgmA
asparagine ans, dauA
fructose Slc2a5, scrK
maltose susB, SemiSWEET, glk
mannose STP6, mannokinase, manA
trehalose treF, SemiSWEET, glk
serine braC, braD, braE, braF, braG, sdaB
glucose-6-P uhpT
deoxyribose deoP, deoK, deoC, adh, acs
ribose rbsU, rbsK
deoxyinosine nupC, deoD, deoB, deoC, adh, acs
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
mannitol PLT5, mt2d, scrK
NAG nagEcba, nagA, nagB
sorbitol SOT, sdh, scrK
lysine lysP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
lactose lacP, lacZ, galK, galT, galE, pgmA, glk
galactose galP, galK, galT, galE, pgmA
D-serine cycA, dsdA
tryptophan aroP, tnaA
xylitol fruI, x5p-reductase
thymidine nupC, deoA, deoB, deoC, adh, acs
glycerol glpF, glpK, glpD, tpi
histidine braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
gluconate gntT, gntK, gnd
xylose xylT, xylA, xylB
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
glucuronate exuT, udh, gci, garL, garR, garK
rhamnose rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
tyrosine Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, aacS, atoB
arabinose araE, araA, araB, araD
fucose fucP, fucU, fucI, fucK, fucA, tpi, aldA
galacturonate exuT, udh, gli, gci, kdgD, dopDH
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.

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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