SUPERFAMILY 1.75 HMM library and genome assignments server


EPT/RTPC-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   IF3-like [ 55199] (8)
Superfamily:   EPT/RTPC-like [ 55205] (2)
Families:   RNA 3'-terminal phosphate cyclase, RPTC [ 55206]
  Enolpyruvate transferase, EPT [ 55209] (2)


Superfamily statistics
Genomes (3,150) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 7,852 46,057 14
Proteins 7,522 43,592 13


Functional annotation
General category Information
Detailed category RNA processing

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Molecular Function (MF)transferase activity, transferring alkyl or aryl (other than methyl) groups4.372e-101.255e-13InformativeDirect

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) single-organism metabolic process 0.1893 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.06639 Least Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.001498 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 1.255e-13 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

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EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases1Least InformativeInherited
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Hydro-lyases0.008955Moderately InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as accep0.001493Moderately InformativeInherited
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than meth1Moderately InformativeInherited
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.002834Moderately InformativeInherited
Enzyme Commission (EC)Acting on phosphates0InformativeDirect
Enzyme Commission (EC)Ligases that form phosphoric-ester bonds1InformativeInherited
Enzyme Commission (EC)Shikimate kinase0Highly InformativeDirect
Enzyme Commission (EC)Shikimate dehydrogenase0Highly InformativeDirect
Enzyme Commission (EC)3-phosphoshikimate 1-carboxyvinyltransferase0Highly InformativeDirect
Enzyme Commission (EC)3-dehydroquinate synthase0Highly InformativeDirect
Enzyme Commission (EC)3-dehydroquinate dehydratase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Yeast Phenotype (YP)

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YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

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AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Transferring phosphorous-containing groups1Least InformativeInherited
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0.00151Moderately InformativeInherited
Enzyme Commission (EC)Acting on the CH-OH group of donors0.003627Moderately InformativeInherited
Enzyme Commission (EC)Carbon-oxygen lyases0.4279Moderately InformativeInherited
Enzyme Commission (EC)Ligases1Moderately InformativeInherited
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.0004424InformativeDirect
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited
Enzyme Commission (EC)Shikimate dehydrogenase0Highly InformativeDirect
Enzyme Commission (EC)3-phosphoshikimate 1-carboxyvinyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Shikimate kinase0Highly InformativeDirect
Enzyme Commission (EC)3-dehydroquinate dehydratase0Highly InformativeDirect
Enzyme Commission (EC)3-dehydroquinate synthase0Highly InformativeDirect
Enzyme Commission (EC)Ligases that form phosphoric-ester bonds1Highly 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 processCell cycle0Moderately InformativeDirect
Biological processCell shape0InformativeDirect
Biological processCell wall biogenesis/degradation0InformativeDirect
Biological processAromatic amino acid biosynthesis0Highly InformativeDirect
Biological processPeptidoglycan synthesis0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionNADP8.495e-06InformativeDirect
Molecular functionPyruvate0Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)metabolic intermediate biosynthesis0Moderately InformativeDirect
UniPathway (UP)cellular component biogenesis0Moderately InformativeDirect
UniPathway (UP)peptidoglycan biosynthesis0InformativeDirect
UniPathway (UP)chorismate biosynthesis0Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR013792 SSF55205 Protein matches
Abstract

This entry represents an alpha/beta domain consisting of alternating beta-strands and alpha helices in two layer. This domain is found in RNA 3'-terminal phosphate cyclase (RPTC), where it occurs as a duplication of three repeats of this fold packed together around a pseudo three-fold axis [PubMed10673421]. RNA cyclases are a family of RNA-modifying enzymes that catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA. These cyclases contain an insert alpha/beta domain with a thioredoxin topology .

This domain is also found in enolpyruvate transferase, where it occurs as a duplication of six repeats of this fold organised into two RPTC-like domains [PubMed9485407, PubMed15995357]. Enolpyruvate transferase is the first enzyme in bacterial peptidoglycan biosynthesis, catalysing the transfer of enolpyruvate from phosphoenolpyruvate to UDP-N-acetyl-glucosamine.


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) · Yeast Phenotype (YP) · 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 5 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 EPT/RTPC-like 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 5 hidden Markov models representing the EPT/RTPC-like 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) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]