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Zinc beta-ribbon superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   Rubredoxin-like [ 57769] (17)
Superfamily:   Zinc beta-ribbon [ 57783] (5)
Families:   Transcriptional factor domain [ 57784] (4)
  DNA primase zinc finger [ 57792] (2)
  Prokaryotic DNA topoisomerase I, a C-terminal fragment [ 57795]
  Putative zinc binding domain [ 118285]
  PhnA zinc-binding domain [ 144191]


Superfamily statistics
Genomes (3,235) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 15,648 70,509 16
Proteins 13,103 54,777 14


Functional annotation
General category Other
Detailed category Unknown function

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.00000000003949 Least Informative Direct
Biological Process (BP) primary metabolic process 0.000002674 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) biological regulation 0.1433 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.8537 Least Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0.000000000000003764 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.00001182 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0006597 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.004983 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.3213 Moderately Informative Inherited
Biological Process (BP) immune system process 0.3745 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.8468 Moderately Informative Inherited
Biological Process (BP) system development 0.9013 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.001173 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.00179 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.6425 Moderately Informative Inherited
Biological Process (BP) transcription, DNA-templated 0 Informative Direct
Biological Process (BP) response to oxidative stress 0.00006223 Informative Direct
Biological Process (BP) regulation of transcription, DNA-templated 0.005959 Informative Inherited
Biological Process (BP) chromosome organization 0.004922 Informative Inherited
Biological Process (BP) DNA metabolic process 0.1352 Informative Inherited
Biological Process (BP) myeloid cell differentiation 0.000007295 Highly Informative Direct
Molecular Function (MF) transferase activity 0.4782 Least Informative Inherited
Molecular Function (MF) binding 0.07905 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.00008868 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0.0009136 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.007698 Moderately Informative Inherited
Molecular Function (MF) metal ion binding 0.009686 Moderately Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 0.00000000006337 Informative Direct
Molecular Function (MF) DNA binding 0.00000007722 Informative Direct
Molecular Function (MF) zinc ion binding 0.000002956 Informative Direct
Molecular Function (MF) enzyme binding 0.03172 Informative Inherited
Molecular Function (MF) macromolecular complex binding 0.02684 Informative Inherited
Molecular Function (MF) RNA polymerase activity 0 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.000000008224 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.0000007003 Highly Informative Direct
Molecular Function (MF) transcription factor activity, transcription factor binding 1 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.00000005981 Least Informative Direct
Cellular Component (CC) macromolecular complex 0.00000005976 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0004169 Least Informative Direct
Cellular Component (CC) transferase complex 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.00000000006516 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.000000005938 Moderately Informative Direct
Cellular Component (CC) transferase complex, transferring phosphorus-containing groups 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0.0000001128 Informative Direct
Cellular Component (CC) protein-DNA complex 0.006346 Informative Inherited
Cellular Component (CC) DNA-directed RNA polymerase II, core complex 0.000007604 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)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0.00009124Least InformativeDirect
Enzyme Commission (EC)DNA-directed RNA polymerase0.000000001471InformativeDirect
Enzyme Commission (EC)Sole sub-subclass for isomerases that do not belon1InformativeInherited
Enzyme Commission (EC)DNA topoisomerase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect
Mammalian Phenotype (MP)prenatal lethality0Moderately InformativeDirect
Mammalian Phenotype (MP)embryonic lethality prior to organogenesis0.0007437InformativeDirect

Document: MP 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

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0Least InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)cell0Moderately InformativeDirect
Zebrafish Anatomy (ZA)hematopoietic system0InformativeDirect
Zebrafish Anatomy (ZA)circulating cell0InformativeDirect

Document: ZA 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)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)egg0Moderately InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0.7021Least InformativeInherited
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0.03783Moderately InformativeInherited
Enzyme Commission (EC)DNA topoisomerase0Highly InformativeDirect
Enzyme Commission (EC)DNA-directed RNA polymerase0.0001103Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA replication0InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentDNA-directed RNA polymerase0Highly InformativeDirect
Cellular componentPrimosome0Highly InformativeDirect
Coding sequence diversityAlternative initiation0.00001824Moderately InformativeDirect
Developmental stageLate protein0.00000002586Least InformativeDirect
DomainRepeat0.0004345Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMagnesium0.000000000001337Least InformativeDirect
Post-translational modificationTransferase0.03186Least InformativeInherited
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationIsomerase0.000000000006559Moderately InformativeDirect
Post-translational modificationActivator0.000005815Moderately InformativeDirect
Post-translational modificationTopoisomerase0Highly InformativeDirect
Post-translational modificationOxidation0.000000001939InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · 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.


Alignments of sequences to 13 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 Zinc beta-ribbon 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 13 hidden Markov models representing the Zinc beta-ribbon 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 · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]