GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Halomonas smyrnensis AAD6

Pathways are sorted by name. Sort by completeness instead.

Pathway Steps
acetate actP, 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, astA, astB, astC, astD, astE
asparagine ans, glt
aspartate glt
cellobiose bgl, SSS-glucose, glk
citrate tctA, tctB, tctC, acn, icd
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
deoxyinosine nupC, 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 fruA, fruI, 1pfk, fba, tpi
fucose fucP, fucU, fucI, fucK, fucA, tpi, aldA
fumarate Dshi_1194, Dshi_1195
galactose sglS, galdh, galactonolactonase, dgoD, dgoK, dgoA
galacturonate exuT, uxaC, uxaB, uxaA, kdgK, eda
gluconate gntA, gntB, gntC, gntK, edd, eda
glucose SSS-glucose, glk
glucose-6-P uhpT
glucosamine gdh, AO353_21715, AO353_21720, AO353_21725, AO353_21710, glucosaminate-lyase, kdgK, kdgA
glucuronate exuT, uxaC, uxuB, uxuA, kdgK, eda
glutamate gltP, gdhA
glycerol glpF, glpK, glpD, tpi
histidine hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
isoleucine Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
4-hydroxybenzoate pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
D-lactate lctP, glcD, glcE, glcF
L-lactate lctP, lctO, acs
lactose lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
leucine aapJ, aapQ, aapM, aapP, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
lysine argT, hisM, hisQ, hisP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
L-malate Dshi_1194, Dshi_1195
maltose thuE, thuF, thuG, thuK, susB, glk
mannitol mtlE, mtlF, mtlG, mtlK, mt2d, scrK
mannose STP6, man-isomerase, scrK
myoinositol PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
NAG nagEcba, nagA, nagB
2-oxoglutarate Psest_0084, Psest_0085
phenylacetate paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
phenylalanine aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
proline proV, proW, proX, put1, putA
propionate lctP, prpE, prpC, acnD, prpF, acn, prpB
putrescine puuP, patA, patD, gabT, gabD
pyruvate yjcH, actP
rhamnose Echvi_1617, rhaM, rhaA, rhaB, rhaD, tpi, aldA
ribose rbsU, rbsK
D-serine cycA, dsdA
serine sstT, sdaB
sorbitol mtlE, mtlF, mtlG, mtlK, sdh, scrK
succinate Dshi_1194, Dshi_1195
sucrose thuE, thuF, thuG, thuK, ams, scrK, glk
threonine sstT, tdh, kbl, gcvP, gcvT, gcvH, lpd
thymidine nupC, deoA, deoB, deoC, adh, acs
trehalose thuE, thuF, thuG, thuK, treF, glk
tryptophan aroP, tnaA
tyrosine aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
valine Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, prpC, acnD, prpF, acn, prpB
xylitol fruI, x5p-reductase
xylose xylT, 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 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