GapMind for catabolism of small carbon sources

 

Protein 8502321 in Desulfovibrio vulgaris Miyazaki F

Annotation: DvMF_3029 ABC transporter related (RefSeq)

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

View 8502321 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

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 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