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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 (2,953) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 45,244 271,234 90
Proteins 44,557 268,138 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)organonitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)primary metabolic process11Least InformativeInherited
Biological Process (BP)biosynthetic process0.21410.01307Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process10.9942Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process11Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process11Least InformativeInherited
Biological Process (BP)macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.24260.007217Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.000063780.0000001228Moderately InformativeDirect
Biological Process (BP)sulfur compound metabolic process0.000099110.0005174Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process0.1560.1414Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.72390.06971Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.53660.06009Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.85130.1309Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.69720.1262Moderately InformativeInherited
Biological Process (BP)lipid metabolic process0.94411Moderately InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.020850.0000006067Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.07610.08344Moderately InformativeInherited
Biological Process (BP)carbohydrate biosynthetic process0.00026480.0000000003156InformativeDirect
Biological Process (BP)cellular metabolic compound salvage0.00000015920.00000000137InformativeDirect
Biological Process (BP)cellular carbohydrate metabolic process0.00047380.00001454InformativeDirect
Biological Process (BP)sulfur compound biosynthetic process0.0000069040.00009897InformativeDirect
Biological Process (BP)alpha-amino acid biosynthetic process0.0058850.2994InformativeInherited
Biological Process (BP)polysaccharide metabolic process0.0019730.00000005473InformativeInherited
Biological Process (BP)liposaccharide metabolic process0.011140.00004316InformativeInherited
Biological Process (BP)aspartate family amino acid metabolic process0.000085560.008319InformativeInherited
Biological Process (BP)lipopolysaccharide metabolic process0.00015190.00000007873Highly InformativeDirect
Biological Process (BP)cellular polysaccharide biosynthetic process0.0000040660.000000000006343Highly InformativeDirect
Biological Process (BP)L-methionine salvage0.00000000000059420Highly InformativeDirect
Biological Process (BP)nucleotide-sugar metabolic process0.0013920.000000001123Highly InformativeInherited
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)oxidoreductase activity0.0000024980.00000000004828Moderately InformativeDirect
Molecular Function (MF)isomerase activity0.00000013940Moderately InformativeDirect
Molecular Function (MF)racemase and epimerase activity0.0031560.108InformativeInherited
Molecular Function (MF)oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.0000000000000073520Highly InformativeDirect
Molecular Function (MF)racemase and epimerase activity, acting on carbohydrates and derivatives0.0000000034170.00000000001565Highly InformativeDirect
Molecular Function (MF)hormone binding0.0000016580.0003519Highly InformativeDirect
Molecular Function (MF)dioxygenase activity0.00000000011840Highly InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on the aldehyde or oxo group of donors0.1480.58Highly InformativeInherited

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) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.01307 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.9942 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.007217 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.0000006067 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0.0000001228 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0.0005174 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.08344 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.1414 Moderately Informative Inherited
Biological Process (BP) reproduction 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.1309 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.06971 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.06009 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.1262 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.1745 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.191 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.02067 Moderately Informative Inherited
Biological Process (BP) polysaccharide metabolic process 0.00000005473 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.0000000003156 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 0.00000000137 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 0.00001454 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0.00009897 Informative Direct
Biological Process (BP) liposaccharide metabolic process 0.00004316 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.2994 Informative Inherited
Biological Process (BP) reproductive system development 0.3038 Informative Inherited
Biological Process (BP) post-embryonic development 0.6462 Informative Inherited
Biological Process (BP) single organism reproductive process 1 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 1 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.09475 Informative Inherited
Biological Process (BP) aspartate family amino acid metabolic process 0.008319 Informative Inherited
Biological Process (BP) monosaccharide metabolic process 0.03242 Informative Inherited
Biological Process (BP) lipopolysaccharide metabolic process 0.00000007873 Highly Informative Direct
Biological Process (BP) nucleotide-sugar metabolic process 0.000000001123 Highly Informative Direct
Biological Process (BP) cellular polysaccharide biosynthetic process 0.000000000006343 Highly Informative Direct
Biological Process (BP) seed development 0.0002333 Highly Informative Direct
Biological Process (BP) L-methionine salvage 0 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0.00000000004828 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) metal ion binding 0.179 Moderately Informative Inherited
Molecular Function (MF) lyase activity 0.1263 Moderately Informative Inherited
Molecular Function (MF) intramolecular oxidoreductase activity 0.00000568 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0.01313 Informative Inherited
Molecular Function (MF) racemase and epimerase activity 0.108 Informative Inherited
Molecular Function (MF) iron ion binding 0.000003563 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 0.0001745 Highly Informative Direct
Molecular Function (MF) racemase and epimerase activity, acting on carbohydrates and derivatives 0.00000000001565 Highly Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity, interconverting aldoses and ketoses 0.000000164 Highly Informative Direct
Molecular Function (MF) hormone binding 0.0003519 Highly Informative Direct
Molecular Function (MF) dioxygenase activity 0 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the aldehyde or oxo group of donors 0.58 Highly Informative Inherited

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

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 processAuxin signaling pathway0.0000000003684Highly InformativeDirect
Biological processLipopolysaccharide biosynthesis0.000000000707Highly InformativeDirect
Biological processAntibiotic biosynthesis0.00000001696Highly InformativeDirect
Cellular componentSecreted0.000000000002024Moderately InformativeDirect
Cellular componentVacuole0.000000000000159InformativeDirect
Cellular componentApoplast0Highly InformativeDirect
DiseaseAllergen0.00000000004881Moderately InformativeDirect
DomainSignal0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionNickel0InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationLyase0.000000008161Moderately InformativeDirect
Post-translational modificationGlycosyltransferase0InformativeDirect
Post-translational modificationStorage protein0Highly InformativeDirect
Post-translational modificationDioxygenase0Highly InformativeDirect
Post-translational modificationDisulfide bond9.634e-16Least InformativeDirect
Post-translational modificationGlycoprotein0.000000000000002852Least InformativeDirect
Post-translational modificationThioether bond0Highly InformativeDirect

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 [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) · 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.


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) · UniProtKB KeyWords (KW) · Internal database links ]