GapMind for catabolism of small carbon sources

 

Protein WP_084937078.1 in Pantoea rwandensis LMG 26275

Annotation: NCBI__GCF_002095475.1:WP_084937078.1

Length: 506 amino acids

Source: GCF_002095475.1 in NCBI

Candidate for 11 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) 89% 100% 901 Inositol transport system ATP-binding protein 47% 461.5
D-cellobiose catabolism mglA hi Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 89% 100% 897.9 Inositol transport system ATP-binding protein 47% 461.5
D-glucose catabolism mglA hi Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 89% 100% 897.9 Inositol transport system ATP-binding protein 47% 461.5
lactose catabolism mglA hi Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 89% 100% 897.9 Inositol transport system ATP-binding protein 47% 461.5
D-maltose catabolism mglA hi Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 89% 100% 897.9 Inositol transport system ATP-binding protein 47% 461.5
sucrose catabolism mglA hi Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 89% 100% 897.9 Inositol transport system ATP-binding protein 47% 461.5
trehalose catabolism mglA hi Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 89% 100% 897.9 Inositol transport system ATP-binding protein 47% 461.5
myo-inositol catabolism PS417_11890 med Inositol transport system ATP-binding protein (characterized) 47% 96% 461.5 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 89% 901.0
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% 443.4 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 89% 901.0
L-fucose catabolism HSERO_RS05250 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 45% 94% 434.5 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 89% 901.0
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) 40% 100% 358.2 Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 89% 901.0

Sequence Analysis Tools

View WP_084937078.1 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

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MASENPTAQREYLLEMTNVSKSFPGVKALDNVNLKVRPHSVHALMGENGAGKSTLLKCLF
GIYKKDTGSILFQGEEIDYKSSKEALENGVSMVHQELNLVLQRNVMDNMWLGRYPRKGVF
VDQDKMYRDTKAIFDELDIDIDPRDKVANLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSL
TEKEVNHLFTIIRKLKDRGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDK
IIAMMVGRSLNQRFPDKTNVPGETILEVRHLTSLRQPSIRDISFDLRKGEILGIAGLVGA
KRTDIVETLFGIREKSGGTIKLHGKAINNHSANEAINHGFALVTEERRSTGIYAYLDIGF
NSLISNIKKYKSNIGLLDNKRMKSDTQWVIDSMRVKTPGHHTQIGSLSGGNQQKVIIGRW
LLTQPEILMLDEPTRGIDVGAKFEIYQLISELAKKEKGIIIISSEMPELLGITDRILVMS
NGLVAGIVETKTTSQNEILRLASLHL

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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