GapMind for catabolism of small carbon sources

 

Protein SM_b20713 in Sinorhizobium meliloti 1021

Annotation: SM_b20713 sugar uptake ABC transporter ATP-binding protein

Length: 513 amino acids

Source: Smeli in FitnessBrowser

Candidate for 22 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
myo-inositol catabolism PS417_11890 hi Inositol transport system ATP-binding protein (characterized) 64% 95% 630.6 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 51% 490.0
D-cellobiose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 51% 99% 490 Inositol transport system ATP-binding protein 64% 630.6
D-galactose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 51% 99% 490 Inositol transport system ATP-binding protein 64% 630.6
D-glucose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 51% 99% 490 Inositol transport system ATP-binding protein 64% 630.6
lactose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 51% 99% 490 Inositol transport system ATP-binding protein 64% 630.6
D-maltose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 51% 99% 490 Inositol transport system ATP-binding protein 64% 630.6
sucrose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 51% 99% 490 Inositol transport system ATP-binding protein 64% 630.6
trehalose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 51% 99% 490 Inositol transport system ATP-binding protein 64% 630.6
L-fucose catabolism HSERO_RS05250 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 50% 98% 487.6 Inositol transport system ATP-binding protein 64% 630.6
D-ribose catabolism rbsA med Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) 45% 96% 444.1 Inositol transport system ATP-binding protein 64% 630.6
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) 48% 99% 442.2 Inositol transport system ATP-binding protein 64% 630.6
D-xylose catabolism xylK_Tm med Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) 46% 96% 424.9 Inositol transport system ATP-binding protein 64% 630.6
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) 44% 96% 423.3 Inositol transport system ATP-binding protein 64% 630.6
D-galactose catabolism BPHYT_RS16930 med Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 44% 96% 417.5 Inositol transport system ATP-binding protein 64% 630.6
xylitol catabolism PS417_12065 med 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) 44% 99% 398.3 Inositol transport system ATP-binding protein 64% 630.6
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% 98% 383.6 Inositol transport system ATP-binding protein 64% 630.6
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% 98% 383.6 Inositol transport system ATP-binding protein 64% 630.6
D-galactose catabolism ytfR med galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) 41% 97% 382.1 Inositol transport system ATP-binding protein 64% 630.6
L-arabinose catabolism araG med L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 41% 98% 376.3 Inositol transport system ATP-binding protein 64% 630.6
D-fructose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 39% 97% 354 Inositol transport system ATP-binding protein 64% 630.6
sucrose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 39% 97% 354 Inositol transport system ATP-binding protein 64% 630.6
2'-deoxyinosine catabolism H281DRAFT_01113 lo deoxynucleoside transporter, ATPase component (characterized) 39% 95% 352.4 Inositol transport system ATP-binding protein 64% 630.6

Sequence Analysis Tools

View SM_b20713 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

MTLSPTTMAAVRASGAVPKSEYLLTAEGVRKEFPGVVALDDVEFKLKRGTVHALMGENGA
GKSTLMKILAGIYYPDQGEVKLRGAGIRLKSPLDALENGIAMIHQELNLMPFMTVAENIW
IRREPKNRFGFVDHGEMRRMTAKLFERLKIDLDPEIEVRHLSVANRQMVEIAKAVSYESD
VLIMDEPTSALTEREVAHLFEIIRDLRSQGIGIVYITHKMNELFEIADEFSVFRDGKYIG
THLSNEVTRDDIIRMMVGREITQMFPKEEVPIGDVVLSVKNLTLNGVFRDVSFDVRAGEI
LGVAGLVGSGRSNVAETLFGVTPASSGTIAIDGKEVVIDSANKAIRHRMAFLTEDRKDTG
CLLILDILENMQIAVLQDKFVKRGFVSEREVTAACEEMSRKLRVKTPNLQERVENLSGGN
QQKVLIGRWLLTNPRILILDEPTRGIDVGAKAEIHRLVTELARNGVAVIMISSEMPEVLG
MSDRIMVMHEGRVTGILDRAEATQIKVMELAAR

This GapMind analysis is from Sep 17 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 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