GapMind for catabolism of small carbon sources

 

Protein GFF2274 in Phaeobacter inhibens BS107

Annotation: PGA1_c23060 ribose import ATP-binding protein RbsA

Length: 503 amino acids

Source: Phaeo in FitnessBrowser

Candidate for 34 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism mglA hi 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) 49% 100% 465.7 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 435.6
D-glucose catabolism mglA hi 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) 49% 100% 465.7 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 435.6
lactose catabolism mglA hi 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) 49% 100% 465.7 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 435.6
D-maltose catabolism mglA hi 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) 49% 100% 465.7 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 435.6
sucrose catabolism mglA hi 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) 49% 100% 465.7 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 435.6
trehalose catabolism mglA hi 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) 49% 100% 465.7 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 435.6
D-xylose catabolism xylG hi 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) 49% 100% 465.7 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 46% 435.6
D-ribose catabolism rbsA med ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized) 46% 98% 435.6 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 49% 465.7
L-fucose catabolism HSERO_RS05250 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 47% 94% 433.3 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 49% 465.7
myo-inositol catabolism PS417_11890 med Inositol transport system ATP-binding protein (characterized) 44% 96% 427.2 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 49% 465.7
D-xylose catabolism xylK_Tm med Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) 45% 97% 425.2 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 49% 465.7
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% 97% 418.7 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 49% 465.7
D-mannose catabolism HSERO_RS03640 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 44% 97% 416.8 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 49% 465.7
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) 44% 98% 406.8 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 49% 465.7
D-galactose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 43% 97% 396.4 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 49% 465.7
D-galactose catabolism BPHYT_RS16930 med Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 42% 96% 389.4 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 49% 465.7
L-arabinose catabolism araG med L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 42% 100% 378.3 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 49% 465.7
D-fructose catabolism fruK med Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 40% 100% 367.1 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 49% 465.7
sucrose catabolism fruK med Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 40% 100% 367.1 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 49% 465.7
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% 98% 365.9 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 49% 465.7
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% 98% 365.9 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 49% 465.7
D-fructose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 43% 94% 363.2 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 49% 465.7
sucrose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 43% 94% 363.2 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 49% 465.7
L-arabinose catabolism araVsh lo ABC transporter related (characterized, see rationale) 39% 100% 358.6 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 49% 465.7
D-galactose catabolism ytfR lo galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) 38% 100% 340.1 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 49% 465.7
2'-deoxyinosine catabolism H281DRAFT_01113 lo deoxynucleoside transporter, ATPase component (characterized) 38% 97% 337.4 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 49% 465.7
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) 38% 99% 332.4 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 49% 465.7
L-fucose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 36% 98% 307 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 49% 465.7
L-rhamnose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 36% 98% 307 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 49% 465.7
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) 36% 98% 288.9 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 49% 465.7
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 36% 94% 167.9 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 49% 465.7
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 36% 94% 156.8 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 49% 465.7
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 36% 96% 153.3 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 49% 465.7
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 36% 96% 153.3 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 49% 465.7

Sequence Analysis Tools

View GFF2274 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

MTEQSPVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPD
EGQIIVAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAE
LEAKTNAILEKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEK
VVLFEVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMM
IGRKLDLSRNEAHHELGEVALEVRGLSCGSLFEDVNFEVRRGEVVGFYGLVGAGRTEIAE
TLFGLRNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNMTLPQV
DDLKAGPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNVL
IVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTF
TSEEVTEENLIAAISGLDTEKVA

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