GapMind for catabolism of small carbon sources

 

Protein 16258 in Escherichia coli BW25113

Annotation: b2149 fused methyl-galactoside transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Length: 506 amino acids

Source: Keio in FitnessBrowser

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-cellobiose catabolism mglA hi Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 100% 100% 993 Inositol transport system ATP-binding protein 49% 469.9
D-galactose catabolism mglA hi Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 100% 100% 993 Inositol transport system ATP-binding protein 49% 469.9
D-glucose catabolism mglA hi Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 100% 100% 993 Inositol transport system ATP-binding protein 49% 469.9
lactose catabolism mglA hi Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 100% 100% 993 Inositol transport system ATP-binding protein 49% 469.9
D-maltose catabolism mglA hi Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 100% 100% 993 Inositol transport system ATP-binding protein 49% 469.9
sucrose catabolism mglA hi Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 100% 100% 993 Inositol transport system ATP-binding protein 49% 469.9
trehalose catabolism mglA hi Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 100% 100% 993 Inositol transport system ATP-binding protein 49% 469.9
myo-inositol catabolism PS417_11890 med Inositol transport system ATP-binding protein (characterized) 49% 97% 469.9 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 100% 993.0
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) 45% 99% 449.9 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 100% 993.0
L-fucose catabolism HSERO_RS05250 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 45% 96% 443 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 100% 993.0
D-ribose catabolism rbsA med ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized) 46% 98% 434.5 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 100% 993.0
D-xylose catabolism xylK_Tm med Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) 42% 96% 394.8 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 100% 993.0
D-galactose catabolism BPHYT_RS16930 med Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 43% 96% 394 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 100% 993.0
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) 39% 98% 379.4 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 100% 993.0
D-mannose catabolism HSERO_RS03640 lo Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 40% 95% 377.5 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 100% 993.0
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% 96% 363.2 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 100% 993.0
L-arabinose catabolism araG lo L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 40% 97% 362.1 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 100% 993.0
L-arabinose catabolism gguA lo GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 38% 97% 358.2 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 100% 993.0
D-galactose catabolism gguA lo GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 38% 97% 358.2 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 100% 993.0
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) 39% 99% 352.8 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 100% 993.0
L-arabinose catabolism araVsh lo ABC transporter related (characterized, see rationale) 38% 99% 346.3 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 100% 993.0
D-fructose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 38% 96% 344.7 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 100% 993.0
sucrose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 38% 96% 344.7 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 100% 993.0
2'-deoxyinosine catabolism nupA lo Purine/cytidine ABC transporter ATP-binding protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized) 34% 98% 304.3 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 100% 993.0
L-fucose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 32% 94% 285.4 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 100% 993.0
L-rhamnose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 32% 94% 285.4 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 100% 993.0
D-lactate catabolism PGA1_c12640 lo D-lactate transporter, ATP-binding component (characterized) 31% 89% 125.9 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 100% 993.0

Sequence Analysis Tools

View 16258 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MVSSTTPSSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLF
GIYQKDSGTILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMF
VDQDKMYRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSL
TEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDK
IIAMMVGRSLNQRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGA
KRTDIVETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGF
NSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRW
LLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMS
NGLVSGIVDTKTTTQNEILRLASLHL

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