GapMind for catabolism of small carbon sources

 

Protein WP_004127105.1 in Rhizobium freirei PRF 81

Annotation: NCBI__GCF_000359745.1:WP_004127105.1

Length: 513 amino acids

Source: GCF_000359745.1 in NCBI

Candidate for 27 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) 65% 95% 624.8 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 49% 469.2
L-fucose catabolism HSERO_RS05250 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 50% 98% 479.6 Inositol transport system ATP-binding protein 65% 624.8
D-cellobiose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 49% 99% 469.2 Inositol transport system ATP-binding protein 65% 624.8
D-galactose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 49% 99% 469.2 Inositol transport system ATP-binding protein 65% 624.8
D-glucose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 49% 99% 469.2 Inositol transport system ATP-binding protein 65% 624.8
lactose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 49% 99% 469.2 Inositol transport system ATP-binding protein 65% 624.8
D-maltose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 49% 99% 469.2 Inositol transport system ATP-binding protein 65% 624.8
sucrose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 49% 99% 469.2 Inositol transport system ATP-binding protein 65% 624.8
trehalose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 49% 99% 469.2 Inositol transport system ATP-binding protein 65% 624.8
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) 47% 99% 443.4 Inositol transport system ATP-binding protein 65% 624.8
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% 95% 440.3 Inositol transport system ATP-binding protein 65% 624.8
D-galactose catabolism BPHYT_RS16930 med Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 45% 96% 422.2 Inositol transport system ATP-binding protein 65% 624.8
D-xylose catabolism xylK_Tm med Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) 46% 96% 418.3 Inositol transport system ATP-binding protein 65% 624.8
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) 43% 96% 411 Inositol transport system ATP-binding protein 65% 624.8
D-mannose catabolism HSERO_RS03640 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 43% 95% 407.1 Inositol transport system ATP-binding protein 65% 624.8
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% 394.4 Inositol transport system ATP-binding protein 65% 624.8
L-arabinose catabolism araG med L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 42% 97% 389 Inositol transport system ATP-binding protein 65% 624.8
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) 43% 97% 387.9 Inositol transport system ATP-binding protein 65% 624.8
D-galactose catabolism ytfR med galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) 40% 98% 377.9 Inositol transport system ATP-binding protein 65% 624.8
D-fructose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 41% 93% 370.2 Inositol transport system ATP-binding protein 65% 624.8
sucrose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 41% 93% 370.2 Inositol transport system ATP-binding protein 65% 624.8
L-arabinose catabolism gguA lo GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 39% 98% 368.2 Inositol transport system ATP-binding protein 65% 624.8
D-galactose catabolism gguA lo GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 39% 98% 368.2 Inositol transport system ATP-binding protein 65% 624.8
D-fructose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 39% 97% 359 Inositol transport system ATP-binding protein 65% 624.8
sucrose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 39% 97% 359 Inositol transport system ATP-binding protein 65% 624.8
2'-deoxyinosine catabolism H281DRAFT_01113 lo deoxynucleoside transporter, ATPase component (characterized) 37% 95% 342.8 Inositol transport system ATP-binding protein 65% 624.8
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) 37% 96% 320.1 Inositol transport system ATP-binding protein 65% 624.8

Sequence Analysis Tools

View WP_004127105.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MVVSPSTMAAVRASGVVPNAAYLLSAEGIRKEFPGVLALDDVSFHLKRGTVHALMGENGA
GKSTLMKILAGIYIPDQGDVRLKGVEIRLKSPLDALENGIAMIHQELNLMPYMTVAENIW
IRREPKNRFGFVDHTEMRRKTEELFHRLNISIDPEIQVRELSVANRQMVEIAKAVSYNSD
VLIMDEPTSALTEREVAHLFQIIRDLRTQGIGIVYITHKMNELFEIADEFSVFRDGKYIG
THASTDVTRDDIIRMMVGREITQMFPKEEVPIGETVLSVKDLSLDGVFSNVSFDVRAGEI
LGVAGLVGSGRSNVAETIFGVTPASSGTIQLFGKAATISSPADAIRHRMAFLTEDRKDTG
CLLILSVLENMQVAVLHDKFVRGGFVQEGPIEQACEEMAKKLRVKTPNLDERIENLSGGN
QQKALIGRWMLTNPRILILDEPTRGIDVGAKAEIHRLVTEMARNGVAVIMISSEMPEVLG
MSDRIMVMHEGRVTGFLDRADATQVKVMELAAQ

This GapMind analysis is from Sep 24 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 (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