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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 (3,231) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 15,595 70,509 16
Proteins 13,057 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) heterocycle metabolic 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) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.00000000006555 Least Informative Direct
Biological Process (BP) primary metabolic process 0.000002887 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) biological regulation 0.2327 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.8572 Least Informative Inherited
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) nucleobase-containing compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0.000000000000007239 Moderately Informative Direct
Biological Process (BP) regulation of cellular metabolic process 0.000136 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0004009 Moderately Informative Direct
Biological Process (BP) organelle organization 0.6445 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0.001364 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.2716 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 0.003916 Moderately Informative Inherited
Biological Process (BP) immune system process 0.3126 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.6136 Moderately Informative Inherited
Biological Process (BP) system development 0.7245 Moderately Informative Inherited
Biological Process (BP) response to stress 0.4955 Moderately Informative Inherited
Biological Process (BP) transcription, DNA-templated 0 Informative Direct
Biological Process (BP) response to oxidative stress 0.0000656 Informative Direct
Biological Process (BP) regulation of transcription, DNA-templated 0.03859 Informative Inherited
Biological Process (BP) DNA metabolic process 0.1497 Informative Inherited
Biological Process (BP) chromosome organization 0.002025 Highly Informative Inherited
Biological Process (BP) hemopoiesis 0.001912 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.5129 Least Informative Inherited
Molecular Function (MF) binding 0.2445 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.00004689 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0.0009973 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.009309 Moderately Informative Inherited
Molecular Function (MF) metal ion binding 0.008866 Moderately Informative Inherited
Molecular Function (MF) protein binding 1 Moderately Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 0.00000000009006 Informative Direct
Molecular Function (MF) DNA binding 0.00000003256 Informative Direct
Molecular Function (MF) zinc ion binding 0.00000262 Informative Direct
Molecular Function (MF) enzyme binding 0.03032 Informative Inherited
Molecular Function (MF) macromolecular complex binding 0.1083 Informative Inherited
Molecular Function (MF) RNA polymerase activity 0 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.000000001379 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.000006074 Highly Informative Direct
Molecular Function (MF) transcription factor activity, transcription factor binding 1 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.0000001344 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0006681 Least Informative Direct
Cellular Component (CC) protein complex 0.9782 Least Informative Inherited
Cellular Component (CC) transferase complex 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0000000000122 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.000000005563 Moderately Informative Direct
Cellular Component (CC) DNA-directed RNA polymerase complex 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0.0000003423 Informative Direct
Cellular Component (CC) DNA-directed RNA polymerase II, core complex 0.00001633 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 lethality0.49InformativeInherited

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)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 groups0.7122Least InformativeInherited
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0.03935Moderately InformativeInherited
Enzyme Commission (EC)DNA topoisomerase0Highly InformativeDirect
Enzyme Commission (EC)DNA-directed RNA polymerase0.0001168Highly 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 initiation0.00001794Moderately InformativeDirect
Developmental stageLate protein0.00000002636Least InformativeDirect
DomainRepeat0.0003817Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Post-translational modificationTransferase0.02446Least InformativeInherited
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationIsomerase0.000000000007903Moderately InformativeDirect
Post-translational modificationActivator0.000005451Moderately InformativeDirect
Post-translational modificationTopoisomerase0Highly InformativeDirect
Post-translational modificationOxidation0.000000001218Highly InformativeDirect

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 ]