GapMind for catabolism of small carbon sources

 

Protein GFF3463 in Pseudomonas simiae WCS417

Annotation: PS417_17730 ribonucleotide-diphosphate reductase subunit alpha

Length: 502 amino acids

Source: WCS417 in FitnessBrowser

Candidate for 22 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-fucose catabolism HSERO_RS05250 hi Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 45% 95% 420.6 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 44% 409.5
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) 44% 100% 409.5 m-Inositol ABC transporter, ATPase component (itaA) 43% 405.6
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) 44% 100% 409.5 m-Inositol ABC transporter, ATPase component (itaA) 43% 405.6
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) 44% 100% 409.5 m-Inositol ABC transporter, ATPase component (itaA) 43% 405.6
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) 44% 100% 409.5 m-Inositol ABC transporter, ATPase component (itaA) 43% 405.6
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) 44% 100% 409.5 m-Inositol ABC transporter, ATPase component (itaA) 43% 405.6
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) 44% 100% 409.5 m-Inositol ABC transporter, ATPase component (itaA) 43% 405.6
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) 44% 100% 409.5 m-Inositol ABC transporter, ATPase component (itaA) 43% 405.6
myo-inositol catabolism PS417_11890 med m-Inositol ABC transporter, ATPase component (itaA) (characterized) 43% 95% 405.6 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 44% 409.5
D-xylose catabolism xylK_Tm med Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) 42% 97% 399.8 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 44% 409.5
D-fructose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 42% 94% 362.1 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 44% 409.5
sucrose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 42% 94% 362.1 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 44% 409.5
D-galactose catabolism ytfR med galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) 42% 97% 357.8 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 44% 409.5
D-galactose catabolism mglA lo Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized) 40% 97% 375.2 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 44% 409.5
D-galactose catabolism BPHYT_RS16930 lo Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 39% 97% 364 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 44% 409.5
L-arabinose catabolism araVsh lo ABC transporter related (characterized, see rationale) 40% 100% 360.1 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 44% 409.5
L-arabinose catabolism gguA lo GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 40% 98% 359 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 44% 409.5
D-galactose catabolism gguA lo GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 40% 98% 359 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 44% 409.5
2'-deoxyinosine catabolism H281DRAFT_01113 lo deoxynucleoside transporter, ATPase component (characterized) 37% 96% 324.7 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 44% 409.5
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) 38% 99% 322 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 44% 409.5
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) 35% 99% 310.1 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 44% 409.5
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 36% 97% 167.2 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 44% 409.5

Sequence Analysis Tools

View GFF3463 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

MSSLLKLENICKRYPGVQALKSINLQVERGEIHALLGENGAGKSTLMKILGGVEHQDEGQ
ILIDGQAQQFATYRDAIAAGIGIVFQEFSLIPYLTAVENIFLGHELSNRFGLLRKREMVE
ASEALFKRLGVTIDLQCAVKHLSVAEQQFVEIAKALALDARLLVLDEPTATLTPSEAELL
FEIMRELKRQGVAVIFISHHLEEIFQVCDRISVLRDGGNVGVTDVADSDIDHLVEMMVGR
RLACSFPPKPTRERGPLLLEVKDIQLVRNGPHNRFQLHKGEILGFAGLVGSGRTELALGM
MGALPSVSKDVWLRGEKITLDDPAQALAHGIGLLPESRKSEGLITDFSIRENISLNNLPK
YQNASGLIDKNRECASVEGLMKQLSIKAPSSESRVFNLSGGNQQKVVIARWINHHCDVLV
FDEPTRGIDVGAKAQIYALMRSLTEQGYAIIMISSELPEIIGMCDRVAVFHKGAIVKLLE
ASAVNPQEVMRHATGGSSEYVH

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