GapMind for catabolism of small carbon sources

 

Protein BWI76_RS00275 in Klebsiella michiganensis M5al

Annotation: FitnessBrowser__Koxy:BWI76_RS00275

Length: 501 amino acids

Source: Koxy in FitnessBrowser

Candidate for 29 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 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized) 95% 100% 919.5 RbsA, component of The probable autoinducer-2 (AI-2;, a furanosyl borate diester: 3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyltetrahydrofuro[3,2-d][1,3,2]dioxaborolan-2-uide) uptake porter (Shao et al., 2007) (50-70% identical to RbsABC of E. coli; TC# 3.A.1.2.1) 72% 701.4
myo-inositol catabolism PS417_11890 med m-Inositol ABC transporter, ATPase component (itaA) (characterized) 50% 94% 481.1 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
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) 47% 100% 447.6 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
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) 47% 100% 447.6 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
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) 47% 100% 447.6 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
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) 47% 100% 447.6 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
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) 47% 100% 447.6 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
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) 47% 100% 447.6 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
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% 100% 447.6 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
L-fucose catabolism HSERO_RS05250 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 47% 96% 435.3 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
D-galactose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized) 45% 98% 430.6 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
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) 45% 96% 423.3 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
D-mannose catabolism HSERO_RS03640 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 45% 95% 420.2 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
D-xylose catabolism xylK_Tm med Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) 44% 96% 417.2 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
L-arabinose catabolism araG med L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 43% 98% 406.8 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
D-galactose catabolism BPHYT_RS16930 med Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 44% 96% 405.2 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
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) 42% 98% 394.4 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
D-fructose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 44% 93% 389.8 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
sucrose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 44% 93% 389.8 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
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% 99% 379.8 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
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% 99% 379.8 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
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% 367.5 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
L-arabinose catabolism araVsh lo ABC transporter related (characterized, see rationale) 39% 100% 360.9 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
D-galactose catabolism ytfR lo galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) 39% 98% 356.7 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
D-fructose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 40% 98% 355.9 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
sucrose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 40% 98% 355.9 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
L-fucose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 36% 92% 291.2 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
L-rhamnose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 36% 92% 291.2 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 37% 96% 168.7 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 95% 919.5

Sequence Analysis Tools

View BWI76_RS00275 at FitnessBrowser

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MEALLQLKGIDKAFPGVKALSGASLNVYPGRVMALVGENGAGKSTMMKVLTGIYARDAGS
LLWLGKETTFNGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYA
EADKLLAKLNLRFNSQKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESL
FRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLDEDLLIEMMVGR
KLEDQYPRLDKAPGAVRLKVDNLCGSGVENISFILRQGEILGVAGLMGAGRTELMKVLYG
ALPRSSGSVTLDGREVVARSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFS
RGGGSLKHKDEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILD
EPTRGVDVGAKKEIYQLINQFKAEGLSIILVSSEMPEVLGMSDRIMVMHEGHLGGEFTRE
QATQEVLMAAAVGKLNRVNQE

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 (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