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RmlC-like cupins superfamily
SCOP classification
Superfamily statistics
Functional annotation
General category | Metabolism |
Detailed category | Nitrogen metabolism and transport |
Document: Function annotation of SCOP domain superfamilies
Enzyme Commission (EC) (show details)
Highlighted in gray are those with FDR_all>0.001
Document: EC annotation of SCOP domains
Human Phenotype (HP) (show details)
Highlighted in gray are those with FDR_all>0.001
Document: HP annotation of SCOP domains
Worm Phenotype (WP) (show details)
Highlighted in gray are those with FDR_all>0.001
Document: WP annotation of SCOP domains
Yeast Phenotype (YP) (show details)
Highlighted in gray are those with FDR_all>0.001
Document: YP annotation of SCOP domains
Xenopus Anatomy (XA) (show details)
Highlighted in gray are those with FDR_all>0.001
Document: XA annotation of SCOP domains
Arabidopsis Plant Ontology (AP) (show details)
Highlighted in gray are those with FDR_all>0.001
Document: AP annotation of SCOP domains
Enzyme Commission (EC) (show details)
Highlighted in gray are those with FDR_all>0.001
| EC term | FDR (all) | IC level | SDEC level | Annotation (direct or inherited) |
Enzyme Commission (EC) | Acireductone dioxygenase (Fe(2+)-requiring) | 0 | 2.952 | -- | DIRECT |
Enzyme Commission (EC) | Guanosine phosphorylase | 0 | 2.952 | -- | DIRECT |
Enzyme Commission (EC) | Pyrimidine-nucleoside phosphorylase | 0 | 2.952 | -- | DIRECT |
Enzyme Commission (EC) | Uridine phosphorylase | 0 | 2.952 | -- | DIRECT |
Enzyme Commission (EC) | Thymidine phosphorylase | 0 | 2.35 | -- | DIRECT |
Enzyme Commission (EC) | Mannose-1-phosphate guanylyltransferase | 0 | 2.651 | -- | DIRECT |
Enzyme Commission (EC) | Peptidyl-glutamate 4-carboxylase | 0 | 2.952 | -- | DIRECT |
Enzyme Commission (EC) | Ectoine synthase | 0 | 2.952 | -- | DIRECT |
Enzyme Commission (EC) | Ureidoglycolate lyase | 0 | 2.651 | -- | DIRECT |
Enzyme Commission (EC) | dTDP-4-dehydrorhamnose 3,5-epimerase | 0 | 2.952 | -- | DIRECT |
Enzyme Commission (EC) | 5-dehydro-4-deoxy-D-glucuronate isomerase | 0 | 2.952 | -- | DIRECT |
Enzyme Commission (EC) | 5-deoxy-glucuronate isomerase | 0 | 2.952 | -- | DIRECT |
Enzyme Commission (EC) | Mannose-6-phosphate isomerase | 0 | 2.651 | -- | DIRECT |
Enzyme Commission (EC) | Oxalate oxidase | 0.00000000001425 | 2.952 | -- | DIRECT |
Enzyme Commission (EC) | Oxalate decarboxylase | 0.00000000001425 | 2.952 | -- | DIRECT |
Enzyme Commission (EC) | Dimethylpropiothetin dethiomethylase | 0.0000000001043 | 2.952 | -- | DIRECT |
Enzyme Commission (EC) | Acireductone dioxygenase (Ni(2+)-requiring) | 0.0000000004384 | 2.952 | -- | DIRECT |
Enzyme Commission (EC) | (S)-ureidoglycine aminohydrolase | 0.000000001382 | 2.952 | -- | DIRECT |
Enzyme Commission (EC) | 3-((4R)-4-hydroxycyclohexa-1,5-dien-1-yl)-2-oxopropanoate isomerase | 0.000000001382 | 2.952 | -- | DIRECT |
Enzyme Commission (EC) | Homogentisate 1,2-dioxygenase | 0.00000002207 | 2.952 | -- | DIRECT |
Enzyme Commission (EC) | 3-hydroxyanthranilate 3,4-dioxygenase | 0.000002699 | 2.952 | -- | DIRECT |
Enzyme Commission (EC) | Hydro-lyases | 0.0005006 | 1.166 | -- | DIRECT |
Enzyme Commission (EC) | Carbon-sulfur lyases | 0.08348 | 2.049 | -- | INHERITED FROM: Dimethylpropiothetin dethiomethylase |
Enzyme Commission (EC) | Transferases | 1 | 0.3035 | -- | INHERITED FROM: Guanosine phosphorylase || Pyrimidine-nucleoside phosphorylase || Uridine phosphorylase || Mannose-1-phosphate guanylyltransferase || Thymidine phosphorylase || Pentosyltransferases || Glycosyltransferases |
Enzyme Commission (EC) | Oxidoreductases | 0 | 0.6234 | Least Informative | DIRECT |
Enzyme Commission (EC) | Lyases | 0.002675 | 0.6918 | Least Informative | INHERITED FROM: Oxalate decarboxylase || Carbon-nitrogen lyases || Ureidoglycolate lyase || Ectoine synthase || Peptidyl-glutamate 4-carboxylase || Lyases acting on amides, amidines, etc || Hydro-lyases || Dimethylpropiothetin dethiomethylase |
Enzyme Commission (EC) | Transferring phosphorus-containing groups | 1 | 0.5453 | Least Informative | INHERITED FROM: Mannose-1-phosphate guanylyltransferase |
Enzyme Commission (EC) | Hydrolases | 1 | 0.3541 | Least Informative | INHERITED FROM: (S)-ureidoglycine aminohydrolase |
Enzyme Commission (EC) | Glycosyltransferases | 0 | 1.204 | Moderately Informative | DIRECT |
Enzyme Commission (EC) | Isomerases | 0 | 0.8446 | Moderately Informative | DIRECT |
Enzyme Commission (EC) | Carbon-oxygen lyases | 0.804 | 1.012 | Moderately Informative | INHERITED FROM: Ectoine synthase || Hydro-lyases |
Enzyme Commission (EC) | Nucleotidyltransferases | 1 | 0.9432 | Moderately Informative | INHERITED FROM: Mannose-1-phosphate guanylyltransferase |
Enzyme Commission (EC) | Acting on carbon-nitrogen bonds, other than peptide bonds | 1 | 1.094 | Moderately Informative | INHERITED FROM: (S)-ureidoglycine aminohydrolase |
Enzyme Commission (EC) | Carbon-carbon lyases | 1 | 1.101 | Moderately Informative | INHERITED FROM: Oxalate decarboxylase || Peptidyl-glutamate 4-carboxylase |
Enzyme Commission (EC) | Acting on single donors with incorporation of molecular oxygen (oxygenases). The oxygen incorporated | 0 | 1.673 | Informative | DIRECT |
Enzyme Commission (EC) | Pentosyltransferases | 0 | 1.447 | Informative | DIRECT |
Enzyme Commission (EC) | Intramolecular oxidoreductases | 0 | 1.35 | Informative | DIRECT |
Enzyme Commission (EC) | Carbon-nitrogen lyases | 0.000000000007824 | 1.673 | Informative | DIRECT |
Enzyme Commission (EC) | Carboxy-lyases | 0.9703 | 1.253 | Informative | INHERITED FROM: Oxalate decarboxylase || Peptidyl-glutamate 4-carboxylase |
Enzyme Commission (EC) | Acting on the aldehyde or oxo group of donors | 1 | 1.42 | Informative | INHERITED FROM: Oxalate oxidase || With oxygen as acceptor |
Enzyme Commission (EC) | Racemases and epimerases | 1 | 1.447 | Informative | INHERITED FROM: Acting on carbohydrates and derivatives || dTDP-4-dehydrorhamnose 3,5-epimerase |
Enzyme Commission (EC) | With incorporation of two atoms of oxygen | 0 | 1.91 | Highly Informative | DIRECT |
Enzyme Commission (EC) | Lyases acting on amides, amidines, etc | 0 | 1.998 | Highly Informative | DIRECT |
Enzyme Commission (EC) | Interconverting aldoses and ketoses | 0.0000001298 | 1.776 | Highly Informative | DIRECT |
Enzyme Commission (EC) | With oxygen as acceptor | 0.0000007274 | 1.998 | Highly Informative | DIRECT |
Enzyme Commission (EC) | Acting on carbohydrates and derivatives | 0.000001365 | 1.776 | Highly Informative | DIRECT |
Enzyme Commission (EC) | In linear amidines | 0.1628 | 1.952 | Highly Informative | INHERITED FROM: (S)-ureidoglycine aminohydrolase |
Enzyme Commission (EC) | Carbon-sulfur lyases | 1 | 2.049 | Highly Informative | INHERITED FROM: Dimethylpropiothetin dethiomethylase |
Enzyme Commission (EC) | Transposing C=C bonds | 1 | 1.776 | Highly Informative | INHERITED FROM: 3-((4R)-4-hydroxycyclohexa-1,5-dien-1-yl)-2-oxopropanoate isomerase |
Document: EC annotation of SCOP domains
UniProtKB KeyWords (KW) (show details)
Highlighted in gray are those with FDR_all>0.001
Document: KW annotation of SCOP domains
InterPro annotation
Cross references | IPR011051 SSF51182 Protein matches |
Abstract | RmlC (dTDP (deoxythimodone diphosphates)-4-dehydrorhamnose 3,5-epimerase) is a dTDP-sugar isomerase enzyme involved in the synthesis of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria [10802738]. RmlC is a dimer, each monomer being formed from two beta-sheets arranged in a beta-sandwich, where the substrate-binding site is located between the two sheets of both monomers.
Other protein families contain domains that share this fold, including glucose-6-phosphate isomerase ; germin, a metal-binding protein with oxalate oxidase and superoxide dismutases activities [11062559]; auxin-binding protein [12065401]; seed storage protein 7S [11124907]; acireductone dioxygenase [12402029]; as well as three proteins that have metal-binding sites similar to that of germine, namely quercetin 2,3-dioxygenase [11839311], phosphomannose isomerase [8612079] and homogentisate dioxygenase [10876237], the last three sharing a 2-domain fold with storage protein 7s.
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InterPro database
PDBeMotif information about ligands, sequence and structure motifs
PDBeMotif resource
Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]
Internal database links
Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry
out SCOP domain assignments to all genomes at the superfamily level.
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Alignments of sequences to 100 models
in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical
are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.
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Browse and view proteins in genomes which have
different domain combinations including a RmlC-like cupins domain.
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Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.
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Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.
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There are 100 hidden Markov models representing the RmlC-like cupins superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.
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Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]
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