GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Sinorhizobium meliloti 1021

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
leucine livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB
arginine braC, braD, braE, braF, braG, arcA, arcB, arcC, ocd, put1, putA
lactose lacE, lacF, lacG, lacK, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
myoinositol PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
deoxyinosine H281DRAFT_01115, H281DRAFT_01114, H281DRAFT_01113, H281DRAFT_01112, deoD, deoB, deoC, adh, ackA, pta
fucose SM_b21103, SM_b21104, SM_b21105, SM_b21106, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
histidine braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
rhamnose rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
xylose xylF, xylG, xylH, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
galactose ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
arabinose gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
glycerol glpS, glpT, glpP, glpQ, glpV, glpK, glpD, tpi
NAG SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB
sucrose thuE, thuF, thuG, thuK, ams, scrK, glk
cellobiose bgl, aglE', aglF', aglG', aglK', glk
gluconate gntA, gntB, gntC, gntK, edd, eda
glucosamine SM_b21216, SM_b21219, SM_b21220, SM_b21221, glc-kinase, nagB
glutamate braC, braD, braE, braF, braG, gdhA
maltose thuE, thuF, thuG, thuK, susB, glk
proline aapJ, aapQ, aapM, aapP, put1, putA
sorbitol mtlE, mtlF, mtlG, mtlK, sdh, scrK
trehalose treF, aglE', aglF', aglG', aglK', glk
asparagine ans, aapJ, aapQ, aapM, aapP
glucose aglE', aglF', aglG', aglK', glk
mannose frcA, frcB, frcC, mannokinase, manA
putrescine potE, patA, patD, gabT, gabD
aspartate aapJ, aapQ, aapM, aapP
ethanol etoh-dh-nad, adh, ackA, pta
fructose frcA, frcB, frcC, scrK
ribose frcA, frcB, frcC, rbsK
acetate deh, ackA, pta
pyruvate dctM, dctP, dctQ
alanine alsT
fumarate dctA
L-malate dctA
succinate dctA
isoleucine livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
valine livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
threonine braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
lysine argT, hisM, hisQ, hisP, lysDH, amaB, lysN, hglS, ydiJ
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
mannitol mtlE, mtlF, mtlG, mtlK, mt2d, scrK
serine braC, braD, braE, braF, braG, sdaB
phenylalanine livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
4-hydroxybenzoate pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
phenylacetate paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
propionate putP, prpE, pccA, pccB, epi, mcm-large, mcm-small
thymidine nupG, deoA, deoB, deoC, adh, ackA, pta
tyrosine aroP, HPD, hmgA, maiA, fahA, aacS, atoB
deoxyribose deoP, deoK, deoC, adh, ackA, pta
glucuronate dctP, dctQ, dctM, udh, uxuL, gudD, kdgD, dopDH
D-alanine AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
D-lactate lctP, glcD, glcE, glcF
citrate tctA, tctB, tctC, acn, icd
xylitol PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
L-lactate lctP, L-LDH
galacturonate exuT, udh, uxuL, garD, kdgD, dopDH
glucose-6-P uhpT
2-oxoglutarate kgtP
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
D-serine cycA, dsdA
tryptophan aroP, tnaA

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