GapMind for catabolism of small carbon sources

 

catabolism of small carbon sources in Algoriphagus machipongonensis PR1

Pathways are sorted by completeness. Sort by name instead.

Pathway Steps
rhamnose Echvi_1617, rhaM, rhaA, rhaB, rhaD, tpi, aldA
citrate citM, acn, icd
gluconate gntT, gntK, gnd
xylose Echvi_1871, xylA, xylB
asparagine ans, glt
fructose glcP, scrK
alanine alsT
aspartate glt
fumarate sdcL
L-malate sdlC
succinate sdc
threonine snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
trehalose lacA, lacC, lacB, klh, SSS-glucose, glk
L-lactate Shew_2731, Shew_2732, lldE, lldF, lldG
glycerol glpF, glpK, glpD, tpi
proline ectP, put1, putA
sucrose ams, glcP, scrK
lactose lacA', lacC', lacB', klh, SSS-glucose, glk
glucose SSS-glucose, glk
glutamate gltP, gdhA
D-lactate larD, D-LDH
serine snatA, sdaB
pyruvate yjcH, actP
leucine leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
galacturonate exuT, uxaC, uxaB, uxaA, kdgK, eda
propionate putP, prpE, pccA, pccB, epi, mcm-large, mcm-small
tyrosine aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
deoxyribose deoP, deoK, deoC, adh, acs
galactose sglS, galK, galT, galE, pgmA
histidine permease, hutH, hutU, hutI, hutG
arginine rocE, rocF, rocD, PRO3, put1, putA
deoxyinosine nupC, deoD, deoB, deoC, adh, acs
thymidine nupC, deoA, deoB, deoC, adh, acs
phenylalanine aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
glucuronate dctP, dctQ, dctM, uxaC, uxuB, uxuA, kdgK, eda
arabinose Echvi_1880, xacB, xacC, xacD, xacE, xacF
isoleucine Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small
ethanol etoh-dh-nad, adh, acs
fucose fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
acetate actP, acs
ribose rbsU, rbsK
cellobiose bgl, SSS-glucose, glk
maltose susB, SSS-glucose, glk
glucose-6-P uhpT
2-oxoglutarate kgtP
putrescine puuP, patA, patD, gabT, gabD
glucosamine gamP, nagB
D-serine cycA, dsdA
NAG nagEcba, nagA, nagB
citrulline AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
mannitol PLT5, mt2d, scrK
mannose STP6, man-isomerase, scrK
sorbitol SOT, sdh, scrK
xylitol PLT5, xdhA, xylB
deoxyribonate deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
valine Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small
D-alanine cycA, dadA
tryptophan aroP, tnaA
lysine lysP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
myoinositol iolT, iolG, iolM, iolN, iolO, uxaE, uxuB, uxuA, kdgK, eda
4-hydroxybenzoate pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
phenylacetate paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2

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