GapMind for catabolism of small carbon sources

 

Protein 3607108 in Dinoroseobacter shibae DFL-12

Annotation: FitnessBrowser__Dino:3607108

Length: 498 amino acids

Source: Dino in FitnessBrowser

Candidate for 30 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
2'-deoxyinosine catabolism H281DRAFT_01113 hi deoxynucleoside transporter, ATPase component (characterized) 46% 97% 420.2 m-Inositol ABC transporter, ATPase component (itaA) 38% 352.1
D-mannose catabolism HSERO_RS03640 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 41% 95% 382.1 deoxynucleoside transporter, ATPase component 46% 420.2
myo-inositol catabolism PS417_11890 lo m-Inositol ABC transporter, ATPase component (itaA) (characterized) 38% 94% 352.1 deoxynucleoside transporter, ATPase component 46% 420.2
D-ribose catabolism rbsA lo Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) 39% 95% 348.6 deoxynucleoside transporter, ATPase component 46% 420.2
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) 39% 95% 344.4 deoxynucleoside transporter, ATPase component 46% 420.2
D-xylose catabolism xylK_Tm lo Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) 39% 95% 343.2 deoxynucleoside transporter, ATPase component 46% 420.2
myo-inositol catabolism iatA lo 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) 39% 97% 337.4 deoxynucleoside transporter, ATPase component 46% 420.2
L-fucose catabolism HSERO_RS05250 lo Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 37% 95% 328.9 deoxynucleoside transporter, ATPase component 46% 420.2
D-cellobiose catabolism mglA lo 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) 38% 97% 327.4 deoxynucleoside transporter, ATPase component 46% 420.2
D-glucose catabolism mglA lo 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) 38% 97% 327.4 deoxynucleoside transporter, ATPase component 46% 420.2
lactose catabolism mglA lo 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) 38% 97% 327.4 deoxynucleoside transporter, ATPase component 46% 420.2
D-maltose catabolism mglA lo 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) 38% 97% 327.4 deoxynucleoside transporter, ATPase component 46% 420.2
sucrose catabolism mglA lo 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) 38% 97% 327.4 deoxynucleoside transporter, ATPase component 46% 420.2
trehalose catabolism mglA lo 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) 38% 97% 327.4 deoxynucleoside transporter, ATPase component 46% 420.2
D-xylose catabolism xylG lo 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) 38% 97% 327.4 deoxynucleoside transporter, ATPase component 46% 420.2
D-fructose catabolism frcA lo ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 40% 91% 314.3 deoxynucleoside transporter, ATPase component 46% 420.2
sucrose catabolism frcA lo ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 40% 91% 314.3 deoxynucleoside transporter, ATPase component 46% 420.2
D-galactose catabolism ytfR lo galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) 35% 100% 312.8 deoxynucleoside transporter, ATPase component 46% 420.2
L-arabinose catabolism araVsh lo ABC transporter related (characterized, see rationale) 35% 100% 305.8 deoxynucleoside transporter, ATPase component 46% 420.2
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% 97% 302.8 deoxynucleoside transporter, ATPase component 46% 420.2
D-fructose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 34% 94% 302.8 deoxynucleoside transporter, ATPase component 46% 420.2
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% 97% 302.8 deoxynucleoside transporter, ATPase component 46% 420.2
sucrose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 34% 94% 302.8 deoxynucleoside transporter, ATPase component 46% 420.2
L-arabinose catabolism araG lo L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 35% 95% 302 deoxynucleoside transporter, ATPase component 46% 420.2
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) 36% 98% 302 deoxynucleoside transporter, ATPase component 46% 420.2
D-galactose catabolism mglA lo Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 34% 97% 295.4 deoxynucleoside transporter, ATPase component 46% 420.2
D-galactose catabolism BPHYT_RS16930 lo Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 35% 94% 290.8 deoxynucleoside transporter, ATPase component 46% 420.2
L-fucose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 36% 97% 280 deoxynucleoside transporter, ATPase component 46% 420.2
L-rhamnose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 36% 97% 280 deoxynucleoside transporter, ATPase component 46% 420.2
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 33% 94% 148.3 deoxynucleoside transporter, ATPase component 46% 420.2

Sequence Analysis Tools

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Sequence

MSSDHDTAFIDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEP
ATAGTVQIAGQEHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKF
RAVRDIARAALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEK
EVRRLQGIIRMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTY
HMTGRDVPEVPPSDVAAGAQTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLLGCGRTSV
AKALFGLVTPDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVG
RLDAHTSGGFLDMTGLAKEASDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAPR
VLILNGPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRIID
ALEGTALTEDDLAHRLAS

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