GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Phaeobacter inhibens BS107

Pathways are sorted by name. Sort by completeness instead.

Pathway Steps
acetate ybhL, acs
D-alanine Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
alanine alsT
arabinose araE, xacB, xacC, xacD, xacE, xacF
arginine artJ, artM, artP, artQ, rocF, ocd, put1, putA
asparagine ans, bztA, bztB, bztC, bztD
aspartate bztA, bztB, bztC, bztD
cellobiose bgl, aglE', aglF', aglG', aglK', glk
citrate tctA, tctB, tctC, acn, icd
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
deoxyinosine nupA, nupB, nupC', bmpA, deoD, deoB, deoC, adh, acs
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
deoxyribose deoP, deoK, deoC, adh, acs
ethanol etoh-dh-nad, adh, acs
fructose frcA, frcB, frcC, scrK
fucose fucP, fucU, fucI, fucK, fucA, tpi, aldA
fumarate dctM, dctP, dctQ
galactose galP, galdh, galactonolactonase, dgoD, dgoK, dgoA
galacturonate exuT, uxaC, uxaB, uxaA, kdgK, eda
gluconate gntT, gntK, edd, eda
glucose aglE', aglF', aglG', aglK', glk
glucose-6-P uhpT
glucosamine nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
glucuronate exuT, udh, gci, garL, garR, garK
glutamate bztA, bztB, bztC, gltL, gdhA
glycerol glpS, glpT, glpP, glpQ, glpV, glpK, glpD, tpi
histidine hutV, hutW, hutX, hutH, hutU, hutI, hutF, hutG'
isoleucine Bap2, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
4-hydroxybenzoate pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
D-lactate PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, glcD, glcE, glcF
L-lactate lctP, L-LDH
lactose lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
leucine leuT, 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 aglE, aglF, aglG, aglK, susB, glk
mannitol mtlE, mtlF, mtlG, mtlK, mt2d, scrK
mannose frcA, frcB, frcC, man-isomerase, scrK
myoinositol PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
NAG SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
2-oxoglutarate dctP, dctQ, dctM
phenylacetate paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
phenylalanine aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
proline ectP, put1, putA
propionate putP, prpE, pccA, pccB, epi, mcm-large, mcm-small
putrescine potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
pyruvate SLC5A8
rhamnose rhaT, LRA1, LRA2, LRA3, LRA4, aldA
ribose frcA, frcB, frcC, rbsK
D-serine cycA, dsdA
serine snatA, sdaB
sorbitol mtlE, mtlF, mtlG, mtlK, sdh, scrK
succinate dctQ, dctM, dctP
sucrose aglE, aglF, aglG, aglK, ams, scrK, glk
threonine snatA, tdh, kbl, gcvP, gcvT, gcvH, lpd
thymidine nupG, deoA, deoB, deoC, adh, acs
trehalose treF, aglE', aglF', aglG', aglK', glk
tryptophan aroP, tnaA
tyrosine aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
valine Bap2, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
xylitol PLT5, xdhA, xylB
xylose xylF, xylG, xylH, xylA, xylB

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 May 21 2021. The underlying query database was built on May 21 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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