GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Aquimarina macrocephali JAMB N27

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
galactose HP1174, galK, galT, galE, pgmA
asparagine ans, glt
glutamate gltP, aspA
alanine alsT
aspartate glt
fumarate sdcL
L-malate sdlC
succinate sdc
pyruvate dctM, dctP, dctQ
phenylalanine aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
threonine tdcC, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
phenylacetate paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
leucine brnQ, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
deoxyinosine nupC, deoD, deoB, deoC, adh, ackA, pta
isoleucine brnQ, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
arginine rocE, rocF, rocD, PRO3, put1, putA
propionate putP, prpE, pccA, pccB, epi, mcm-large, mcm-small
tyrosine aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
L-lactate Shew_2731, Shew_2732, lctO, ackA, pta
histidine permease, hutH, hutU, hutI, hutF, hutG'
lactose lacP, lacZ, galK, galT, galE, pgmA, glk
ethanol etoh-dh-nad, adh, ackA, pta
maltose malI, malP, pgmB, glk
deoxyribose deoP, deoK, deoC, adh, ackA, pta
acetate actP, ackA, pta
cellobiose bgl, MFS-glucose, glk
citrate SLC13A5, acn, icd
proline proY, put1, putA
trehalose treF, MFS-glucose, glk
thymidine nupC, deoA, deoB, deoC, adh, ackA, pta
glycerol glpF, glpK, glpD, tpi
glucose MFS-glucose, glk
glucosamine gamP, nagB
D-lactate lctP, D-LDH
serine serP, sdaB
citrulline PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, rocD, PRO3, put1, putA
valine brnQ, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
fructose fruII-ABC, 1pfk, fba, tpi
glucose-6-P uhpT
2-oxoglutarate kgtP
mannose manP, manA
D-serine cycA, dsdA
tryptophan aroP, tnaA
NAG nagEcba, nagA, nagB
sucrose ams, MFS-glucose, glk
D-alanine cycA, dadA
mannitol mtlA, mtlD
ribose rbsU, rbsK
sorbitol mtlA, srlD
xylitol fruI, x5p-reductase
xylose Echvi_1871, xylA, xylB
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
4-hydroxybenzoate pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
gluconate gntT, gntK, gnd
arabinose Echvi_1880, araA, araB, araD
lysine lysP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
glucuronate exuT, udh, gci, kdgD, dopDH
putrescine puuP, patA, patD, gabT, gabD
rhamnose rhaT, LRA1, LRA2, LRA3, LRA4, aldA
galacturonate exuT, udh, gli, gci, kdgD, dopDH
fucose fucP, fucU, fucI, fucK, fucA, tpi, aldA
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 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