GapMind for catabolism of small carbon sources

 

Protein WP_040660822.1 in Oscillibacter ruminantium GH1

Annotation: NCBI__GCF_000307265.1:WP_040660822.1

Length: 499 amino acids

Source: GCF_000307265.1 in NCBI

Candidate for 27 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-galactose catabolism mglA hi Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized) 61% 98% 612.5 Inositol transport system ATP-binding protein 48% 455.3
D-cellobiose catabolism mglA hi Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 60% 98% 609 Inositol transport system ATP-binding protein 48% 455.3
D-glucose catabolism mglA hi Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 60% 98% 609 Inositol transport system ATP-binding protein 48% 455.3
lactose catabolism mglA hi Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 60% 98% 609 Inositol transport system ATP-binding protein 48% 455.3
D-maltose catabolism mglA hi Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 60% 98% 609 Inositol transport system ATP-binding protein 48% 455.3
sucrose catabolism mglA hi Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 60% 98% 609 Inositol transport system ATP-binding protein 48% 455.3
trehalose catabolism mglA hi Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 60% 98% 609 Inositol transport system ATP-binding protein 48% 455.3
myo-inositol catabolism PS417_11890 med Inositol transport system ATP-binding protein (characterized) 48% 96% 455.3 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 61% 612.5
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) 44% 99% 417.2 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 61% 612.5
D-ribose catabolism rbsA med ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized) 44% 98% 415.2 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 61% 612.5
D-xylose catabolism xylK_Tm med Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) 43% 96% 404.4 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 61% 612.5
L-fucose catabolism HSERO_RS05250 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 43% 95% 402.1 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 61% 612.5
D-galactose catabolism BPHYT_RS16930 med Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 43% 96% 387.9 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 61% 612.5
L-arabinose catabolism araG med L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 41% 98% 378.6 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 61% 612.5
D-fructose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 43% 93% 369.8 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 61% 612.5
sucrose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 43% 93% 369.8 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 61% 612.5
L-arabinose catabolism gguA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 41% 97% 367.5 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 61% 612.5
D-galactose catabolism gguA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 41% 97% 367.5 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 61% 612.5
D-mannose catabolism HSERO_RS03640 lo Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 39% 96% 375.2 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 61% 612.5
myo-inositol catabolism iatA lo 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) 39% 97% 357.8 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 61% 612.5
xylitol catabolism PS417_12065 lo 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) 39% 100% 346.3 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 61% 612.5
L-rhamnose catabolism rhaT' lo 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) 37% 96% 342.4 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 61% 612.5
L-arabinose catabolism araVsh lo ABC transporter related (characterized, see rationale) 38% 100% 341.3 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 61% 612.5
D-galactose catabolism ytfR lo galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) 39% 99% 341.3 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 61% 612.5
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 33% 96% 148.7 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 61% 612.5
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 97% 141.4 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 61% 612.5
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 97% 141.4 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 61% 612.5

Sequence Analysis Tools

View WP_040660822.1 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

MGQEVLLQMTDISKEFPGVKALDHVSLTVKPGTVHALMGENGAGKSTLMKCLFGIYGKDE
GKIFLEGKEVSFKSSKEAMESGVAMVHQELNQALKRSVMDNIWLGRYPTIGGVMVNEKKM
YADTKAIFDDLGIDVDPHRIMSTIPVSQRQMVEIAKAVSYNSKVVVFDEPTSSLTEQEVE
HLFRIINMLRDRGVGIIYISHKMAEILQISDEVTIMRDGCWVATKSAGELDTATIIKLMV
GRELGNQFPIKTNTPGEVYLEVEHLTAQYSQLEDVSFSARRGEILGLAGLDASGRTETLE
NIFGIATRKSGTIRLGGREVKNRNSRESIRNGFALLTEERRATGIFGILSIRENTVISSL
KKHLRAGFILNDKTMRQDTQWSIDAMRTKTPSQHTKIRSLSGGNQQKVILGRWLLTNPEV
LLLDEPTRGIDVGAKFEIYQLIIDLANKGKTVLMVSSEMPELLGVCDRILVMSGGRLAGE
VDAKSTTQEEIMTLAAKYV

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