GapMind for catabolism of small carbon sources

 

Protein PfGW456L13_3911 in Pseudomonas fluorescens GW456-L13

Annotation: Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Length: 517 amino acids

Source: pseudo13_GW456_L13 in FitnessBrowser

Candidate for 33 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-ribose catabolism rbsA hi Sugar ABC transporter ATP-binding protein (characterized, see rationale) 92% 100% 920.6 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 41% 354.8
L-fucose catabolism HSERO_RS05250 hi Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 44% 94% 376.3 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 41% 354.8
D-galactose catabolism BPHYT_RS16930 hi Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 42% 97% 367.9 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 41% 354.8
D-cellobiose catabolism mglA 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) 41% 99% 354.8 Inositol transport system ATP-binding protein 39% 350.9
D-galactose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 39% 97% 354.8 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 41% 354.8
D-glucose catabolism mglA 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) 41% 99% 354.8 Inositol transport system ATP-binding protein 39% 350.9
lactose catabolism mglA 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) 41% 99% 354.8 Inositol transport system ATP-binding protein 39% 350.9
D-maltose catabolism mglA 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) 41% 99% 354.8 Inositol transport system ATP-binding protein 39% 350.9
sucrose catabolism mglA 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) 41% 99% 354.8 Inositol transport system ATP-binding protein 39% 350.9
trehalose catabolism mglA 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) 41% 99% 354.8 Inositol transport system ATP-binding protein 39% 350.9
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) 41% 99% 354.8 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 39% 354.8
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) 40% 99% 334.3 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 41% 354.8
myo-inositol catabolism PS417_11890 lo Inositol transport system ATP-binding protein (characterized) 39% 94% 350.9 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 41% 354.8
D-xylose catabolism xylK_Tm lo Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) 38% 98% 340.5 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 41% 354.8
L-arabinose catabolism araG lo L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 39% 97% 339 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 41% 354.8
D-mannose catabolism HSERO_RS03640 lo Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 39% 98% 332.8 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 41% 354.8
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% 100% 328.6 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 41% 354.8
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% 100% 328.6 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 41% 354.8
D-fructose catabolism frcA lo ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 39% 94% 321.6 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 41% 354.8
sucrose catabolism frcA lo ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 39% 94% 321.6 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 41% 354.8
D-galactose catabolism ytfR lo galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) 40% 93% 317 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 41% 354.8
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% 313.9 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 41% 354.8
2'-deoxyinosine catabolism H281DRAFT_01113 lo deoxynucleoside transporter, ATPase component (characterized) 36% 97% 303.5 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 41% 354.8
D-fructose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 35% 97% 299.7 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 41% 354.8
sucrose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 35% 97% 299.7 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 41% 354.8
L-arabinose catabolism araVsh lo ABC transporter related (characterized, see rationale) 36% 97% 297.7 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 41% 354.8
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) 36% 96% 289.3 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 41% 354.8
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) 36% 98% 287 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 41% 354.8
L-fucose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 35% 96% 272.3 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 41% 354.8
L-rhamnose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 35% 96% 272.3 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 41% 354.8
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 35% 96% 132.9 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 41% 354.8
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 35% 96% 132.9 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 41% 354.8
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 33% 96% 131 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 41% 354.8

Sequence Analysis Tools

View PfGW456L13_3911 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

MSVCAPNAVLSVSGIGKTYAQPVLAGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTP
TTGQMQYQGQDYRPGSRAQAEALGIRMVMQELNLLPTLSVAENLFLDNLPSKGGWISRKQ
LRKAAIEAMAHVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTARE
VEMLFEQITRLQSRGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTL
MVGRELGEHIDMGARKIGAPVLTVNGLSRSDKVRDVSFEVRAGEIFGISGLIGAGRTELL
RLIFGADIADSGTIALGAPAQVINVRSPVDAVGHGIALITEDRKGEGLLLTQSIGANIAL
GNMPGISGAGFVDNDKERALAQRQIDAMRIRSSGPAQLVSELSGGNQQKVVIGRWLERDC
SVLLFDEPTRGIDVGAKFDIYNLLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGSLI
DTFDRDSWTQDELLAAAFAGYQKRDAQLVEAAPRDLP

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