GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Burkholderia phytofirmans PsJN

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
phenylalanine livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
isoleucine livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
leucine livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
phenylacetate ppa, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
tyrosine Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
myoinositol PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
putrescine potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
arginine artJ, artM, artP, artQ, astA, astB, astC, astD, astE
fucose BPHYT_RS34250, BPHYT_RS34245, BPHYT_RS34240, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
galactose ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
histidine BPHYT_RS24000, BPHYT_RS24005, BPHYT_RS24010, BPHYT_RS24015, hutH, hutU, hutI, hutF, hutG'
arabinose araF, araG, araH, xacB, xacC, xacD, xacE, xacF
gluconate gadh1, gadh2, gadh3, kguT, kguK, kguD, edd, eda
glycerol glpS, glpT, glpP, glpQ, glpV, glpK, glpD, tpi
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
glucuronate exuT, udh, uxuL, gudD, garL, garR, garK
proline HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
propionate mctC, prpE, prpC, acnD, prpF, acn, prpB
cellobiose bgl, gtsA, gtsB, gtsC, gtsD, glk
galacturonate exuT, udh, uxuL, garD, kdgD, dopDH
serine Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
sorbitol mtlE, mtlF, mtlG, mtlK, sdh, scrK
trehalose treF, gtsA, gtsB, gtsC, gtsD, glk
asparagine ans, aatJ, aatQ, aatM, aatP
glucose gtsA, gtsB, gtsC, gtsD, glk
glutamate gltI, gltJ, gltK, gltL, gdhA
mannose frcA, frcB, frcC, man-isomerase, scrK
xylose xylF, xylG, xylH, xylA, xylB
aspartate aatJ, aatQ, aatM, aatP
ethanol etoh-dh-nad, adh, ackA, pta
fructose frcA, frcB, frcC, scrK
D-lactate mctP, glcD, glcE, glcF
L-lactate mctP, lldE, lldF, lldG
NAG nagF, nagEcb, nagA, nagB
ribose rbsA, rbsB, rbsC, rbsK
acetate actP, ackA, pta
citrate citA, acn, icd
D-alanine mctP, dadA
fumarate dctA
L-malate dctA
2-oxoglutarate kgtP
pyruvate mctC
succinate dctA
valine livF, livG, livJ, livH, livM, ofo, acdH, ech, bch, mmsB, mmsA, prpC, acnD, prpF, acn, prpB
4-hydroxybenzoate pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
threonine snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
deoxyribose drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
glucosamine gamP, nagB
mannitol mtlE, mtlF, mtlG, mtlK, mt2d, scrK
alanine cycA
tryptophan aroP, kynA, kynB, kyn, hpaH, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, ackA, pta
lysine argT, hisM, hisQ, hisP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
lactose lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
rhamnose BPHYT_RS34250, BPHYT_RS34245, BPHYT_RS34240, LRA1, LRA2, LRA3, LRA5, LRA6
deoxyinosine H281DRAFT_01115, H281DRAFT_01114, H281DRAFT_01113, H281DRAFT_01112, deoD, deoB, deoC, adh, ackA, pta
maltose susB, gtsA, gtsB, gtsC, gtsD, glk
sucrose ams, gtsA, gtsB, gtsC, gtsD, glk
thymidine nupC, deoA, deoB, deoC, adh, ackA, pta
xylitol PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
glucose-6-P uhpT
D-serine cycA, dsdA

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 17 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