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 (2,946) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 45,114 221,022 90
Proteins 44,439 219,509 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 process0.25950.09336Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.82470.1522Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.91851Least InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.000013770.0001753Moderately InformativeDirect
Biological Process (BP)cellular amino acid metabolic process0.0024140.0000004645Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.18020.3091Moderately InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.17540.0002997Moderately InformativeInherited
Biological Process (BP)single-organism biosynthetic process0.049530.01153Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.017480.1105Moderately InformativeInherited
Biological Process (BP)lipid metabolic process0.99041Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.9310.5368Moderately InformativeInherited
Biological Process (BP)sulfur amino acid metabolic process0.000000000041540.0000007019InformativeDirect
Biological Process (BP)carbohydrate biosynthetic process0.0009830.0000003599InformativeDirect
Biological Process (BP)cellular metabolic compound salvage0.00000073240.00000006872InformativeDirect
Biological Process (BP)sulfur compound biosynthetic process0.00000096540.00001946InformativeDirect
Biological Process (BP)alpha-amino acid biosynthetic process0.0019660.3746InformativeInherited
Biological Process (BP)cellular carbohydrate metabolic process0.0056620.003112InformativeInherited
Biological Process (BP)polysaccharide metabolic process0.0037290.00001116InformativeInherited
Biological Process (BP)aspartate family amino acid metabolic process0.000023840.008907InformativeInherited
Biological Process (BP)lipopolysaccharide metabolic process0.00072690.00000004704Highly InformativeDirect
Biological Process (BP)cellular polysaccharide biosynthetic process0.0000079950.00000001035Highly InformativeDirect
Biological Process (BP)amino acid salvage0.000000000038080.0000000000001194Highly InformativeDirect
Biological Process (BP)L-methionine biosynthetic process0.016550.00002873Highly InformativeInherited
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)oxidoreductase activity0.000048560.0000000002304Moderately InformativeDirect
Molecular Function (MF)isomerase activity0.00066320Moderately InformativeDirect
Molecular Function (MF)racemase and epimerase activity0.0013070.1503InformativeInherited
Molecular Function (MF)oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.0000000000013870Highly InformativeDirect
Molecular Function (MF)racemase and epimerase activity, acting on carbohydrates and derivatives0.00000035210.000000002637Highly InformativeDirect
Molecular Function (MF)hormone binding0.0000013950.00002816Highly InformativeDirect
Molecular Function (MF)dioxygenase activity0.0000000093680Highly 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 0.09336 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.1522 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound 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 1 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.0002997 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0.0000004645 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0.0001753 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.3091 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.01153 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.1105 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.8827 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.9097 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.9041 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.8558 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.7446 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.8515 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.9012 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.5368 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) sulfur amino acid metabolic process 0.0000007019 Informative Direct
Biological Process (BP) polysaccharide metabolic process 0.00001116 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.0000003599 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 0.00000006872 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0.00001946 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.3746 Informative Inherited
Biological Process (BP) cellular carbohydrate metabolic process 0.003112 Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 0.01199 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.05864 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.05994 Informative Inherited
Biological Process (BP) aspartate family amino acid metabolic process 0.008907 Informative Inherited
Biological Process (BP) hexose metabolic process 0.8196 Informative Inherited
Biological Process (BP) lipopolysaccharide metabolic process 0.00000004704 Highly Informative Direct
Biological Process (BP) nucleotide-sugar metabolic process 0.000002795 Highly Informative Direct
Biological Process (BP) cellular polysaccharide biosynthetic process 0.00000001035 Highly Informative Direct
Biological Process (BP) amino acid salvage 0.0000000000001194 Highly Informative Direct
Biological Process (BP) L-methionine biosynthetic process 0.00002873 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0.0000000002304 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) cation binding 0.0006493 Moderately Informative Direct
Molecular Function (MF) lyase activity 0.1291 Moderately Informative Inherited
Molecular Function (MF) intramolecular oxidoreductase activity 0.000005261 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0.00288 Informative Inherited
Molecular Function (MF) racemase and epimerase activity 0.1503 Informative Inherited
Molecular Function (MF) iron ion binding 0.00006221 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on single donors with incorporation of molecular oxygen 0 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 0.00008442 Highly Informative Direct
Molecular Function (MF) racemase and epimerase activity, acting on carbohydrates and derivatives 0.000000002637 Highly Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity, interconverting aldoses and ketoses 0 Highly Informative Direct
Molecular Function (MF) hormone binding 0.00002816 Highly Informative Direct
Molecular Function (MF) dioxygenase activity 0 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-lyases0.000002917Moderately 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 derivatives0.0000005017InformativeDirect
Enzyme Commission (EC)In linear amidines0Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details) Document: HP 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)genital system0Least InformativeDirect
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 stage0.0001454InformativeDirect

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)Lyases0.0000002877Least InformativeDirect
Enzyme Commission (EC)Transferring phosphorous-containing groups1Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0.9109Moderately InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds1Moderately InformativeInherited
Enzyme Commission (EC)Carbon-carbon lyases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on single donors with incorporation of molecular oxygen0InformativeDirect
Enzyme Commission (EC)Carbon-nitrogen lyases0InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0.9059InformativeInherited
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)Lyases acting on amides, amidines, etc0Highly InformativeDirect
Enzyme Commission (EC)Interconverting aldoses and ketoses, and related compounds0.0000000003216Highly InformativeDirect
Enzyme Commission (EC)Acting on carbohydrates and derivatives0.00000001123Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor0.000000147Highly InformativeDirect
Enzyme Commission (EC)In linear amidines0.09711Highly InformativeInherited

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 processLipopolysaccharide biosynthesis0.0000000000285Highly InformativeDirect
Biological processAuxin signaling pathway0.00000000004284Highly InformativeDirect
Biological processAntibiotic biosynthesis0.0000000002256Highly InformativeDirect
Biological processGluconeogenesis0.0007141Highly InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentVacuole0.000000000000004758InformativeDirect
Cellular componentCell wall0.0006668Highly InformativeDirect
DomainSignal0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0.0008634Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionNickel0InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationLyase0.000000000006176Moderately InformativeDirect
Post-translational modificationDioxygenase0Highly InformativeDirect
Post-translational modificationStorage protein0Highly InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationGlycoprotein0.00000000000004807Least InformativeDirect
Post-translational modificationThioether bond0.000000000000003548Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0.000000000000001345Least 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 metabolism8.993e-16Moderately InformativeDirect
UniPathway (UP)aromatic compound degradation0.000000000000004664Moderately InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis0.000004382Moderately InformativeDirect
UniPathway (UP)alcohol metabolism0.001087Moderately InformativeInherited
UniPathway (UP)nucleotide metabolism0.2794Moderately InformativeInherited
UniPathway (UP)energy metabolism0.4299Moderately 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)ureide metabolism0InformativeDirect
UniPathway (UP)glycan degradation0InformativeDirect
UniPathway (UP)L-methionine biosynthesis0InformativeDirect
UniPathway (UP)nucleotide-sugar biosynthesis0.00000000000004515InformativeDirect
UniPathway (UP)flavonoid metabolism0.000000000001436InformativeDirect
UniPathway (UP)phenylpropanoid degradation0.00000000003696InformativeDirect
UniPathway (UP)amine and polyamine biosynthesis0.00000000008373InformativeDirect
UniPathway (UP)antibiotic biosynthesis0.00002945InformativeDirect
UniPathway (UP)polyol degradation0.02812InformativeInherited
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)myo-inositol degradation into acetyl-CoA0.000000000000467Highly InformativeDirect
UniPathway (UP)LPS O-antigen biosynthesis0.000000000002579Highly InformativeDirect
UniPathway (UP)L-cysteine metabolism0.000000804Highly InformativeDirect
UniPathway (UP)bacilysin biosynthesis0.0004688Highly 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) · Human Phenotype (HP) · 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) · Human Phenotype (HP) · 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 ]