GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Ochrobactrum thiophenivorans DSM 7216

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
fucose SM_b21103, SM_b21104, SM_b21105, SM_b21106, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
arginine braC, braD, braE, braF, braG, rocF, ocd, put1, putA
glutamate braC, braD, braE, braF, braG, gdhA
proline aapJ, aapQ, aapM, aapP, put1, putA
asparagine ans, aapJ, aapQ, aapM, aapP
mannose frcA, frcB, frcC, mannokinase, manA
trehalose treF, mglA, mglB, mglC, glk
xylose xylF, xylG, xylH, xylA, xylB
aspartate aapJ, aapQ, aapM, aapP
fructose frcA, frcB, frcC, scrK
glucose mglA, mglB, mglC, glk
glycerol glpF, glpK, glpD, tpi
ribose frcA, frcB, frcC, rbsK
citrate cimH, acn, icd
ethanol etoh-dh-nad, adh, acs
acetate deh, acs
D-alanine cycA, dadA
alanine cycA
fumarate dctA
L-malate dctA
2-oxoglutarate kgtP
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
myoinositol PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
threonine braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
galactose ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
arabinose gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
lysine argT, hisM, hisQ, hisP, lysDH, amaB, lysN, hglS, ydiJ
putrescine potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
sorbitol mtlE, mtlF, mtlG, mtlK, sdh, scrK
D-lactate larD, glcD, glcE, glcF
mannitol mtlE, mtlF, mtlG, mtlK, mt2d, scrK
serine braC, braD, braE, braF, braG, sdaB
L-lactate larD, L-LDH
D-serine cycA, dsdA
propionate putP, prpE, pccA, pccB, epi, mcm-large, mcm-small
deoxyinosine H281DRAFT_01115, H281DRAFT_01114, H281DRAFT_01113, H281DRAFT_01112, deoD, deoB, deoC, adh, acs
cellobiose bgl, mglA, mglB, mglC, glk
deoxyribose deoP, deoK, deoC, adh, acs
maltose susB, mglA, mglB, mglC, glk
sucrose ams, mglA, mglB, mglC, glk
xylitol PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
citrulline PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, ocd, put1, putA
gluconate gntT, gntK, edd, eda
NAG nagP, nagK, nagA, nagB
lactose lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
glucuronate exuT, uxaC, uxuB, uxuA, kdgK, eda
glucosamine nagX, nagP, nagK, nagA, nagB
glucose-6-P uhpT
pyruvate SLC5A8
tryptophan aroP, tnaA
histidine braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
galacturonate exuT, udh, gli, gci, kdgD, dopDH
thymidine nupG, deoA, deoB, deoC, adh, acs
tyrosine aroP, HPD, hmgA, maiA, fahA, aacS, atoB
phenylalanine livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
rhamnose rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
4-hydroxybenzoate pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
phenylacetate paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2

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 24 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