GapMind for catabolism of small carbon sources

 

Protein 8502321 in Desulfovibrio vulgaris Miyazaki F

Annotation: FitnessBrowser__Miya:8502321

Length: 537 amino acids

Source: Miya in FitnessBrowser

Candidate for 32 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
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) 39% 97% 346.3 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
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) 32% 100% 287.7 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 39% 346.3
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) 32% 100% 287.7 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 39% 346.3
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) 32% 100% 287.7 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 39% 346.3
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) 32% 100% 287.7 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 39% 346.3
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) 32% 100% 287.7 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 39% 346.3
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) 32% 100% 287.7 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 39% 346.3
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) 32% 100% 287.7 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
D-mannose catabolism HSERO_RS03640 lo Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 35% 91% 281.2 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
L-fucose catabolism HSERO_RS05250 lo Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 33% 94% 280.4 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
myo-inositol catabolism PS417_11890 lo Inositol transport system ATP-binding protein (characterized) 34% 96% 278.9 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
D-galactose catabolism mglA lo Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized) 33% 98% 276.6 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
D-ribose catabolism rbsA lo ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized) 33% 98% 274.6 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
D-galactose catabolism BPHYT_RS16930 lo Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 32% 100% 271.2 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
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) 33% 94% 263.1 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
D-xylose catabolism xylK_Tm lo Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) 33% 94% 259.6 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
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) 32% 99% 258.1 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
D-fructose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 32% 96% 251.1 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
sucrose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 32% 96% 251.1 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
L-arabinose catabolism araG lo L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 32% 98% 250.8 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
D-fructose catabolism frcA lo ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 33% 96% 246.5 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
sucrose catabolism frcA lo ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 33% 96% 246.5 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
D-galactose catabolism ytfR lo galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) 32% 93% 241.1 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
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) 33% 96% 235 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
L-arabinose catabolism araVsh lo ABC transporter related (characterized, see rationale) 31% 95% 234.6 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
2'-deoxyinosine catabolism H281DRAFT_01113 lo deoxynucleoside transporter, ATPase component (characterized) 30% 97% 232.3 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
L-fucose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 32% 97% 229.2 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
L-rhamnose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 32% 97% 229.2 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 36% 92% 154.1 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 31% 88% 128.6 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 34% 86% 124.4 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 34% 86% 124.4 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 42% 360.5

Sequence Analysis Tools

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Sequence

MSDTPHTHAAVAPETPRRVRETHAHLPPVVRLDGICKSFGKVRANHDITLDIRPGCIKAL
LGENGAGKSTLMSILAGKLRQDAGTIVVDGVPTVFASPRDALRAGIGMVYQHFMLVDSMT
VAENVLLGQSPDMLLRPARMRDEVAALAERYGLAVDPAARVGGLSMGERQRVEILKLLYR
DSRVLILDEPTAVLTPRETDQLFEAMWRMADQGKALVFISHKLQEVLTVADEIAILRRGE
VVDEFSEADVPNQTVLANRMVGRDVVLQVDAKRLTPVDTVLSVEHLSGAGLSDVSLQVRR
GEIVAIAGVAGNGQKELVEAICGLARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQ
GLATCRHLDLVDNFLLTTRNQFAKGVFLDRTEATNAVKRVVWEYNVQPGDITAPARALSG
GNLQKLVIGREFFRKPEVIVAENPTQGLDISATEEVWGRLLEARSTSGVLLVTGDLNEAL
ELADRIAVMYRGRFIDVFDKDDTAKVQAIGLMMAGVRPDDADGPGVADKAVEAEGRA

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