GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Azospirillum humicireducens SgZ-5

Pathways are sorted by name. Sort by completeness instead.

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

Links

Downloads

Related tools

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