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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 (3,238) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 15,693 76,532 16
Proteins 13,146 64,156 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) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.00000000002444 Least Informative Direct
Biological Process (BP) primary metabolic process 0.000001652 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.8589 Least Informative Inherited
Biological Process (BP) biological regulation 0.1494 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0.000000000000005563 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.02257 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.003201 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.001118 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.6274 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.004809 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.335 Moderately Informative Inherited
Biological Process (BP) immune system process 0.3787 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.8321 Moderately Informative Inherited
Biological Process (BP) animal organ development 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.001126 Moderately Informative Inherited
Biological Process (BP) transcription, DNA-templated 0 Informative Direct
Biological Process (BP) response to oxidative stress 0.00005923 Informative Direct
Biological Process (BP) chromosome organization 0.004773 Informative Inherited
Biological Process (BP) hemopoiesis 0.002489 Informative Inherited
Biological Process (BP) DNA metabolic process 0.1262 Informative Inherited
Biological Process (BP) myeloid cell differentiation 0.000008586 Highly Informative Direct
Molecular Function (MF) binding 0.04808 Least Informative Inherited
Molecular Function (MF) transferase activity 0.4592 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.00009554 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0.0008036 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.007015 Moderately Informative Inherited
Molecular Function (MF) metal ion binding 0.00944 Moderately Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 0.00000000006835 Informative Direct
Molecular Function (MF) DNA binding 0.0000001011 Informative Direct
Molecular Function (MF) zinc ion binding 0.000003013 Informative Direct
Molecular Function (MF) enzyme binding 0.03068 Informative Inherited
Molecular Function (MF) macromolecular complex binding 0.02986 Informative Inherited
Molecular Function (MF) RNA polymerase activity 0 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.00000001264 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.0000009593 Highly Informative Direct
Molecular Function (MF) transcription factor activity, transcription factor binding 1 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.00000005323 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0003899 Least Informative Direct
Cellular Component (CC) protein complex 0.9396 Least Informative Inherited
Cellular Component (CC) transferase complex 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.00000000006689 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.000000006862 Moderately Informative Direct
Cellular Component (CC) transferase complex, transferring phosphorus-containing groups 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0.0000000884 Informative Direct
Cellular Component (CC) protein-DNA complex 0.006791 Informative Inherited
Cellular Component (CC) DNA-directed RNA polymerase II, core complex 0.000006423 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

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 initiation0.00001993Moderately InformativeDirect
Developmental stageLate protein0.00000002528Least InformativeDirect
DomainRepeat0.0004007Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMagnesium0.000000000001177Least InformativeDirect
Post-translational modificationTransferase0.03109Least InformativeInherited
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationIsomerase0.000000000006291Moderately InformativeDirect
Post-translational modificationActivator0.000005821Moderately InformativeDirect
Post-translational modificationTopoisomerase0Highly InformativeDirect
Post-translational modificationOxidation0.000000002736InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · 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 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) · UniProtKB KeyWords (KW) · Internal database links ]