GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Azospirillum humicireducens SgZ-5

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
isoleucine livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
leucine livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
4-hydroxybenzoate pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
glycerol glpS, glpT, glpP, glpQ, glpV, glpK, glpD, tpi
proline AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
D-alanine AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
cellobiose bgl, mglA, mglB, mglC, glk
fructose fruA, fruI, 1pfk, fba, tpi
xylose xylF, xylG, xylH, xylA, xylB
citrate citW, citD, citE, citF
glucose mglA, mglB, mglC, glk
L-lactate lctP, lutA, lutB, lutC
NAG nagF, nagEcb, nagA, nagB
ethanol etoh-dh-nad, adh, acs
acetate actP, acs
asparagine ans, glt
D-lactate lctP, D-LDH
2-oxoglutarate Psest_0084, Psest_0085
pyruvate yjcH, actP
serine sdaC, sdaB
aspartate glt
fumarate dctA
L-malate dctA
succinate dctA
phenylalanine livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
valine livF, livG, livJ, livH, livM, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
phenylacetate ppa, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
threonine braC, braD, braE, braF, braG, tdcB, tdcE, pccA, pccB, epi, mcm-large, mcm-small
histidine braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
arginine braC, braD, braE, braF, braG, rocF, ocd, put1, putA
galactose ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
putrescine potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
propionate lctP, prpE, pccA, pccB, epi, mcm-large, mcm-small
arabinose gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
gluconate gntA, gntB, gntC, gntK, edd, eda
sucrose ams, fruA, fruI, 1pfk, fba, tpi
maltose susB, mglA, mglB, mglC, glk
trehalose treF, mglA, mglB, mglC, glk
glucuronate exuT, uxaC, uxuB, uxuA, kdgK, eda
glutamate braC, braD, braE, braF, braG, gdhA
ribose rbsA, rbsB, rbsC, rbsK
alanine braC, braD, braE, braF, braG
glucosamine gamP, nagB
mannose manP, manA
tryptophan aroP, kynA, kynB, kyn, andAa, andAb, andAc, andAd, catA, catB, catC, pcaD, catI, catJ, pcaF
deoxyinosine H281DRAFT_01115, H281DRAFT_01114, H281DRAFT_01113, H281DRAFT_01112, deoD, deoB, deoC, adh, acs
tyrosine Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
lysine bgtB, hisP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
deoxyribose deoP, deoK, deoC, adh, acs
lactose lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
galacturonate exuT, uxaC, uxaB, uxaA, kdgK, eda
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
thymidine nupG, deoA, deoB, deoC, adh, acs
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
rhamnose rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
mannitol PLT5, mt2d, scrK
sorbitol SOT, sdh, scrK
glucose-6-P uhpT
D-serine cycA, dsdA
xylitol PLT5, xdhA, xylB
fucose HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
myoinositol iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda

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