GapMind for catabolism of small carbon sources

 

Protein WP_008507134.1 in Brucella inopinata BO1

Annotation: NCBI__GCF_000182725.1:WP_008507134.1

Length: 492 amino acids

Source: GCF_000182725.1 in NCBI

Candidate for 19 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
xylitol catabolism PS417_12065 hi D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale) 52% 99% 475.3 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 426.4
D-ribose catabolism rbsA med ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized) 46% 97% 426.4 m-Inositol ABC transporter, ATPase component (itaA) 46% 425.2
myo-inositol catabolism PS417_11890 med m-Inositol ABC transporter, ATPase component (itaA) (characterized) 46% 94% 425.2 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 426.4
D-cellobiose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 42% 97% 379.8 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 426.4
D-galactose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 42% 97% 379.8 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 426.4
D-glucose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 42% 97% 379.8 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 426.4
lactose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 42% 97% 379.8 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 426.4
D-maltose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 42% 97% 379.8 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 426.4
sucrose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 42% 97% 379.8 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 426.4
trehalose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 42% 97% 379.8 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 426.4
L-rhamnose catabolism rhaT' med RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized) 42% 96% 378.6 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 426.4
D-mannose catabolism HSERO_RS03640 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 43% 95% 377.1 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 426.4
D-xylose catabolism xylG med Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 42% 99% 373.2 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 426.4
myo-inositol catabolism iatA med Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized) 42% 94% 366.3 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 426.4
L-arabinose catabolism araG med L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 41% 97% 352.8 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 426.4
D-galactose catabolism BPHYT_RS16930 med Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 41% 95% 346.3 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 426.4
L-arabinose catabolism araVsh lo ABC transporter related (characterized, see rationale) 37% 99% 332.8 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 426.4
D-fructose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 36% 96% 307.8 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 426.4
sucrose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 36% 96% 307.8 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 426.4

Sequence Analysis Tools

View WP_008507134.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MEFLLDVEGLRKSFGGVAALRDGRLQLRAGSVHALCGGNGAGKSTFLKILMGIHARDGGH
IRRRGKEVTYSSPAEALQAGIAIIEQELSPVPHMTVAENIYLGREPLRRFGGIDFKTMNL
NAQKLLDQLEFKIRANQFMMNLSVAQVQLVEIAKALSHDAEVIFMDEPTSAIGEKEAQQL
FAAIERLKASGKGIVYVSHRLSEIFQIADSYTVFRDGSYIDSGDLGGITRAELIHMIVGR
ELGEEYIKTNAPTEIPGVEVSGLSAPGKITDISFTAHKGEIFGIYGLMGSGRSEIFNCLF
GLEKASEGTIRLEGEPVTVRRPADAMALGLAFVTEDRKLTGLNLGDSVRNNICLASLPEM
SPHFSMNRRAESAASREMIERFRIKVAHDTMAVSGLSGGNQQKVVLGKWFLRKPRVLLLD
EPTRGVDVGAKQEIYRIICEFAAQGGTVVMVSSEIDEVLGMSDRIMVMRGGQSVGIYRRA
ETDAQSLVHLST

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