GapMind for catabolism of small carbon sources

 

Protein PfGW456L13_2121 in Pseudomonas fluorescens GW456-L13

Annotation: L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Length: 514 amino acids

Source: pseudo13_GW456_L13 in FitnessBrowser

Candidate for 34 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-galactose catabolism BPHYT_RS16930 hi Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 88% 100% 879 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
L-arabinose catabolism araG hi L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 60% 98% 582.4 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 45% 415.2
D-ribose catabolism rbsA med ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized) 45% 98% 415.2 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
myo-inositol catabolism PS417_11890 med Inositol transport system ATP-binding protein (characterized) 42% 96% 394.8 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
D-cellobiose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 42% 97% 391.3 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
D-galactose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 42% 97% 391.3 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
D-glucose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 42% 97% 391.3 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
lactose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 42% 97% 391.3 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
D-maltose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 42% 97% 391.3 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
sucrose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 42% 97% 391.3 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
trehalose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 42% 97% 391.3 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
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) 45% 96% 389.8 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
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% 98% 386 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
D-mannose catabolism HSERO_RS03640 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 41% 96% 380.2 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
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) 42% 97% 370.5 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
L-fucose catabolism HSERO_RS05250 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 41% 95% 368.2 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
D-fructose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 44% 89% 354 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
sucrose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 44% 89% 354 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
D-xylose catabolism xylK_Tm lo Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) 40% 97% 357.5 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
D-galactose catabolism ytfR lo galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) 38% 98% 345.9 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
L-arabinose catabolism araVsh lo ABC transporter related (characterized, see rationale) 38% 98% 331.6 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
D-fructose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 38% 91% 317.4 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
sucrose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 38% 91% 317.4 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
L-arabinose catabolism gguA lo GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 36% 98% 315.8 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
D-galactose catabolism gguA lo GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 36% 98% 315.8 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
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) 37% 99% 301.2 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
2'-deoxyinosine catabolism H281DRAFT_01113 lo deoxynucleoside transporter, ATPase component (characterized) 36% 96% 294.3 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
2'-deoxyinosine catabolism nupA lo RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized) 33% 96% 266.9 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
L-fucose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 36% 92% 261.2 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
L-rhamnose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 36% 92% 261.2 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 33% 92% 140.6 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 93% 133.3 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 93% 133.3 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 32% 93% 128.3 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.4

Sequence Analysis Tools

View PfGW456L13_2121 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

MHAQTIQHEHSLTGSLRFNGIGKTFPGVKALDNISFVAHPGQVHALMGENGAGKSTLLKI
LGGAYTPCSGALQIGERTMDFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASF
GLINRSTLRQQALACLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTS
SLSAREIDRLMAIIGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFDDMSQLT
HDQLVTCMVGRDIQDIYDYRPRQRGAVALKVDGLLGPGLREPVSFEVHKGEILGLFGLVG
AGRTELLRLLSGLARHSAGQLKLRGHELKLRSPRDAIAAGILLCPEDRKKEGILPLASVA
ENINISARGAHSTFGCLLRGLWEKDNAEQQIKALKVKTPNAAQKIMYLSGGNQQKAILGR
WLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAAEGIAVIVVSSDLMEVMGISDRILVL
CEGALRGELSREQANESNLLQLALPRQRADGVAN

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