SUPERFAMILY 1.75 HMM library and genome assignments server


RmlC-like cupins superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Double-stranded beta-helix [ 51181] (7)
Superfamily:   RmlC-like cupins [ 51182] (24)
Families:   dTDP-sugar isomerase [ 51183] (4)
  Glucose-6-phosphate isomerase, GPI [ 89403]
  Hypothetical protein TM1112 [ 89406]
  TM1287-like [ 89409] (4)
  TM1459-like [ 101976] (2)
  Germin/Seed storage 7S protein [ 51187] (4)
  YlbA-like [ 101979] (4)
  Pirin-like [ 101984] (2)
  Quercetin 2,3-dioxygenase-like [ 75035] (2)
  Type I phosphomannose isomerase [ 51191] (3)
  Homogentisate dioxygenase [ 51194]
  Acireductone dioxygenase [ 82191]
  KduI-like [ 110318]
  Ureidoglycolate hydrolase AllA [ 117312]
  Probable transcriptional regulator VC1968, C-terminal domain [ 117315]
  YML079-like [ 117318] (3)
  PA5104-like [ 141609]
  MJ0764-like [ 141612]
  Cysteine dioxygenase type I [ 141615]
  3-hydroxyanthranilic acid dioxygenase-like [ 141618]
  Acetylacetone-cleaving enzyme-like [ 159293]
  VPA0057-like [ 159296]
  Gentisate 1,2-dioxygenase-like [ 159299]
  EutQ-like [ 159304]


Superfamily statistics
Genomes (2,302) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 34,747 100,522 90
Proteins 34,280 99,646 84


Functional annotation
General category Metabolism
Detailed category Nitrogen metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)cellular macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)biosynthetic process0.0430.01184Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.61870.1143Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.73770.9047Least InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.029860.04716Moderately InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.0019854.236e-05Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.014120.04661Moderately InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.010556.045e-07Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.0025070.001911Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.022340.2143Moderately InformativeInherited
Biological Process (BP)cellular lipid metabolic process0.62420.6172Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.78230.2186Moderately InformativeInherited
Biological Process (BP)lipid biosynthetic process0.38140.5335Moderately InformativeInherited
Biological Process (BP)sulfur amino acid metabolic process2.979e-122.38e-09InformativeDirect
Biological Process (BP)polysaccharide metabolic process5.445e-051.541e-06InformativeDirect
Biological Process (BP)aspartate family amino acid metabolic process1.485e-064.42e-05InformativeDirect
Biological Process (BP)amine biosynthetic process7.828e-103.906e-09InformativeDirect
Biological Process (BP)carbohydrate biosynthetic process4.748e-052.768e-06InformativeDirect
Biological Process (BP)cellular metabolic compound salvage4.049e-071.741e-08InformativeDirect
Biological Process (BP)cellular carbohydrate metabolic process3.749e-063.064e-06InformativeDirect
Biological Process (BP)sulfur compound biosynthetic process5.776e-074.724e-06InformativeDirect
Biological Process (BP)alpha-amino acid biosynthetic process0.00086430.03708InformativeInherited
Biological Process (BP)lipopolysaccharide biosynthetic process0.00025241.007e-05Highly InformativeDirect
Biological Process (BP)amino acid salvage1.982e-117.835e-15Highly InformativeDirect
Biological Process (BP)L-methionine biosynthetic process0.012161.188e-05Highly InformativeInherited
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)oxidoreductase activity2.582e-072.878e-11Moderately InformativeDirect
Molecular Function (MF)isomerase activity7.968e-050Moderately InformativeDirect
Molecular Function (MF)intramolecular oxidoreductase activity0.58323.947e-05InformativeInherited
Molecular Function (MF)racemase and epimerase activity0.00016220.01049InformativeInherited
Molecular Function (MF)oxidoreductase activity, acting on single donors with incorporation of molecular oxygen1.42e-120Highly InformativeDirect
Molecular Function (MF)racemase and epimerase activity, acting on carbohydrates and derivatives4.276e-091.012e-11Highly InformativeDirect
Molecular Function (MF)intramolecular oxidoreductase activity, interconverting aldoses and ketoses0.00066980Highly InformativeDirect
Molecular Function (MF)hormone binding2.637e-072.865e-06Highly InformativeDirect
Molecular Function (MF)dioxygenase activity3.691e-090Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) biosynthetic process 0.01184 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.9047 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.1143 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 6.045e-07 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 4.236e-05 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.04716 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.04661 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.2143 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.001911 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.3611 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.5342 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.2186 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.5023 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.779 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.8728 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.6172 Moderately Informative Inherited
Biological Process (BP) lipid biosynthetic process 0.5335 Moderately Informative Inherited
Biological Process (BP) sulfur amino acid metabolic process 2.38e-09 Informative Direct
Biological Process (BP) polysaccharide metabolic process 1.541e-06 Informative Direct
Biological Process (BP) aspartate family amino acid metabolic process 4.42e-05 Informative Direct
Biological Process (BP) amine biosynthetic process 3.906e-09 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 2.768e-06 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 1.741e-08 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 3.064e-06 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 4.724e-06 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.03708 Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 0.006463 Informative Inherited
Biological Process (BP) lipopolysaccharide biosynthetic process 1.007e-05 Highly Informative Direct
Biological Process (BP) nucleotide-sugar metabolic process 2.323e-05 Highly Informative Direct
Biological Process (BP) amino acid salvage 7.835e-15 Highly Informative Direct
Biological Process (BP) L-methionine biosynthetic process 1.188e-05 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 2.878e-11 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) cation binding 0.0006652 Moderately Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity 3.947e-05 Informative Direct
Molecular Function (MF) racemase and epimerase activity 0.01049 Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on single donors with incorporation of molecular oxygen 0 Highly Informative Direct
Molecular Function (MF) racemase and epimerase activity, acting on carbohydrates and derivatives 1.012e-11 Highly Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity, interconverting aldoses and ketoses 0 Highly Informative Direct
Molecular Function (MF) hormone binding 2.865e-06 Highly Informative Direct
Molecular Function (MF) dioxygenase activity 0 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) chromosome 0.6192 Informative Inherited
Cellular Component (CC) kinetochore 0.0001588 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Lyases0.5417Least InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases1Least InformativeInherited
Enzyme Commission (EC)Intramolecular oxidoreductases0Moderately InformativeDirect
Enzyme Commission (EC)Hydro-lyases2.917e-06Moderately InformativeDirect
Enzyme Commission (EC)Racemases and epimerases1Moderately InformativeInherited
Enzyme Commission (EC)Carboxy-lyases0.8946Moderately InformativeInherited
Enzyme Commission (EC)Acting on single donors with incorporation of mole0InformativeDirect
Enzyme Commission (EC)Interconverting aldoses and ketoses, and related c0InformativeDirect
Enzyme Commission (EC)Acting on carbohydrates and derivatives5.017e-07InformativeDirect
Enzyme Commission (EC)In linear amidines0Highly InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)seed development stage0.0001175InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Lyases0.6574Least InformativeInherited
Enzyme Commission (EC)Transferring phosphorous-containing groups1Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0.0001029Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0.002825Moderately InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Carbon-carbon lyases1Moderately InformativeInherited
Enzyme Commission (EC)Intramolecular oxidoreductases0InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0.8918InformativeInherited
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors1InformativeInherited
Enzyme Commission (EC)Racemases and epimerases1InformativeInherited
Enzyme Commission (EC)With incorporation of two atoms of oxygen0Highly InformativeDirect
Enzyme Commission (EC)In linear amidines0Highly InformativeDirect
Enzyme Commission (EC)Interconverting aldoses and ketoses, and related compounds3.142e-10Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor2.532e-08Highly InformativeDirect
Enzyme Commission (EC)Acting on carbohydrates and derivatives6.611e-07Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0Moderately InformativeDirect
Biological processMethionine biosynthesis0Highly InformativeDirect
Biological processPhenylalanine catabolism0Highly InformativeDirect
Biological processPurine metabolism0Highly InformativeDirect
Biological processPyridine nucleotide biosynthesis0Highly InformativeDirect
Biological processRhamnose metabolism0Highly InformativeDirect
Biological processTyrosine catabolism0Highly InformativeDirect
Biological processLipopolysaccharide biosynthesis2.26e-11Highly InformativeDirect
Biological processAuxin signaling pathway3.062e-11Highly InformativeDirect
Biological processAntibiotic biosynthesis7.181e-08Highly InformativeDirect
Biological processGluconeogenesis0.0006817Highly InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentVacuole2.522e-15InformativeDirect
Cellular componentCell wall0.000455Highly InformativeDirect
DomainSignal0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0.0006044Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionNickel0InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationDioxygenase0Highly InformativeDirect
Post-translational modificationStorage protein0Highly InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationGlycoprotein1.282e-14Least InformativeDirect
Post-translational modificationThioether bond3.05e-15Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism2.426e-15Least InformativeDirect
UniPathway (UP)biopolymer metabolism1Least InformativeInherited
UniPathway (UP)cofactor metabolism1Least InformativeInherited
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)aromatic compound metabolism1Least InformativeInherited
UniPathway (UP)lipid metabolism1Least InformativeInherited
UniPathway (UP)nitrogen metabolism0Moderately InformativeDirect
UniPathway (UP)amino-acid degradation0Moderately InformativeDirect
UniPathway (UP)glycan metabolism0Moderately InformativeDirect
UniPathway (UP)amine and polyamine metabolism8.878e-16Moderately InformativeDirect
UniPathway (UP)aromatic compound degradation2.82e-14Moderately InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis4.124e-06Moderately InformativeDirect
UniPathway (UP)alcohol metabolism0.001045Moderately InformativeInherited
UniPathway (UP)nucleotide metabolism0.2789Moderately InformativeInherited
UniPathway (UP)energy metabolism0.4217Moderately InformativeInherited
UniPathway (UP)biopolymer biosynthesis1Moderately InformativeInherited
UniPathway (UP)carbohydrate biosynthesis1Moderately InformativeInherited
UniPathway (UP)lipid biosynthesis1Moderately InformativeInherited
UniPathway (UP)cellular component biogenesis1Moderately InformativeInherited
UniPathway (UP)membrane lipid metabolism1Moderately InformativeInherited
UniPathway (UP)NAD(+) biosynthesis0InformativeDirect
UniPathway (UP)glycan degradation0InformativeDirect
UniPathway (UP)L-methionine biosynthesis0InformativeDirect
UniPathway (UP)nucleotide-sugar biosynthesis4.815e-14InformativeDirect
UniPathway (UP)flavonoid metabolism3.14e-13InformativeDirect
UniPathway (UP)phenylpropanoid degradation7.414e-12InformativeDirect
UniPathway (UP)amine and polyamine biosynthesis6.713e-11InformativeDirect
UniPathway (UP)alcohol degradation7.173e-06InformativeDirect
UniPathway (UP)antibiotic biosynthesis2.626e-05InformativeDirect
UniPathway (UP)lipopolysaccharide biosynthesis1InformativeInherited
UniPathway (UP)ectoine biosynthesis0Highly InformativeDirect
UniPathway (UP)GDP-alpha-D-mannose biosynthesis0Highly InformativeDirect
UniPathway (UP)L-phenylalanine degradation0Highly InformativeDirect
UniPathway (UP)(S)-allantoin degradation0Highly InformativeDirect
UniPathway (UP)pectin degradation0Highly InformativeDirect
UniPathway (UP)flavonoid degradation0Highly InformativeDirect
UniPathway (UP)L-methionine biosynthesis via salvage pathway0Highly InformativeDirect
UniPathway (UP)organosulfur metabolism1.495e-14Highly InformativeDirect
UniPathway (UP)myo-inositol degradation into acetyl-CoA4.763e-13Highly InformativeDirect
UniPathway (UP)LPS O-antigen biosynthesis5.661e-13Highly InformativeDirect
UniPathway (UP)L-cysteine metabolism6.852e-07Highly InformativeDirect
UniPathway (UP)bacilysin biosynthesis0.0006811Highly InformativeDirect

Document: UP 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 [PubMed10802738]. 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 [PubMed11062559]; auxin-binding protein [PubMed12065401]; seed storage protein 7S [PubMed11124907]; acireductone dioxygenase [PubMed12402029]; as well as three proteins that have metal-binding sites similar to that of germine, namely quercetin 2,3-dioxygenase [PubMed11839311], phosphomannose isomerase [PubMed8612079] and homogentisate dioxygenase [PubMed10876237], the last three sharing a 2-domain fold with storage protein 7s.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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.


Alignments of sequences to 68 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.


Browse and view proteins in genomes which have different domain combinations including a RmlC-like cupins domain.


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.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 68 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.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]