GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Burkholderia phytofirmans PsJN

Pathways are sorted by name. Sort by completeness instead.

Pathway Steps
acetate actP, ackA, pta
D-alanine mctP, dadA
alanine cycA
arabinose araF, araG, araH, xacB, xacC, xacD, xacE, xacF
arginine artJ, artM, artP, artQ, astA, astB, astC, astD, astE
asparagine ans, aatJ, aatQ, aatM, aatP
aspartate aatJ, aatQ, aatM, aatP
cellobiose bgl, gtsA, gtsB, gtsC, gtsD, glk
citrate citA, acn, icd
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
deoxyinosine H281DRAFT_01115, H281DRAFT_01114, H281DRAFT_01113, H281DRAFT_01112, deoD, deoB, deoC, adh, ackA, pta
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
deoxyribose drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
ethanol etoh-dh-nad, adh, ackA, pta
fructose frcA, frcB, frcC, scrK
fucose BPHYT_RS34250, BPHYT_RS34245, BPHYT_RS34240, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
fumarate dctA
galactose ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
galacturonate exuT, udh, uxuL, garD, kdgD, dopDH
gluconate gadh1, gadh2, gadh3, kguT, kguK, kguD, edd, eda
glucose gtsA, gtsB, gtsC, gtsD, glk
glucose-6-P uhpT
glucosamine gamP, nagB
glucuronate exuT, udh, uxuL, gudD, garL, garR, garK
glutamate gltI, gltJ, gltK, gltL, gdhA
glycerol glpS, glpT, glpP, glpQ, glpV, glpK, glpD, tpi
histidine BPHYT_RS24000, BPHYT_RS24005, BPHYT_RS24010, BPHYT_RS24015, hutH, hutU, hutI, hutF, hutG'
isoleucine livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB
4-hydroxybenzoate pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
D-lactate mctP, glcD, glcE, glcF
L-lactate mctP, lldE, lldF, lldG
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 argT, hisM, hisQ, hisP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
L-malate dctA
maltose susB, gtsA, gtsB, gtsC, gtsD, glk
mannitol mtlE, mtlF, mtlG, mtlK, mt2d, scrK
mannose frcA, frcB, frcC, man-isomerase, scrK
myoinositol PGA1_c07300, PGA1_c07310, PGA1_c07320, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
NAG nagF, nagEcb, nagA, nagB
2-oxoglutarate kgtP
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 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
propionate mctC, prpE, prpC, acnD, prpF, acn, prpB
putrescine potA, potB, potC, potD, puuA, puuB, puuC, puuD, gabT, gabD
pyruvate mctC
rhamnose BPHYT_RS34250, BPHYT_RS34245, BPHYT_RS34240, LRA1, LRA2, LRA3, LRA5, LRA6
ribose rbsA, rbsB, rbsC, rbsK
D-serine cycA, dsdA
serine Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, sdaB
sorbitol mtlE, mtlF, mtlG, mtlK, sdh, scrK
succinate dctA
sucrose ams, gtsA, gtsB, gtsC, gtsD, glk
threonine snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
thymidine nupC, deoA, deoB, deoC, adh, ackA, pta
trehalose treF, gtsA, gtsB, gtsC, gtsD, glk
tryptophan aroP, kynA, kynB, kyn, hpaH, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, ackA, pta
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, prpC, acnD, prpF, acn, prpB
xylitol PS417_12065, PS417_12060, PS417_12055, 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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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