SUPERFAMILY 1.75 HMM library and genome assignments server


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 (3,188) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 15,165 35,542 16
Proteins 12,688 28,114 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 aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 5.506e-13 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.9563 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.7743 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.01932 Least Informative Inherited
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 7.551e-05 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.0007611 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.02913 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.001395 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.1644 Moderately Informative Inherited
Biological Process (BP) transcription, DNA-dependent 0 Informative Direct
Biological Process (BP) transcription from RNA polymerase II promoter 1 Highly Informative Inherited
Molecular Function (MF) binding 0.8517 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.001085 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.03599 Moderately Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 8.074e-13 Informative Direct
Molecular Function (MF) enzyme binding 0.002862 Informative Inherited
Molecular Function (MF) DNA binding 0.002297 Informative Inherited
Molecular Function (MF) transcription factor binding 2.682e-07 Highly Informative Direct
Molecular Function (MF) protein complex binding 9.275e-05 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 1.859e-05 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) protein complex 4.009e-10 Least Informative Direct
Cellular Component (CC) intracellular organelle part 3.301e-07 Least Informative Direct
Cellular Component (CC) nuclear part 2.071e-12 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0 Moderately Informative Direct
Cellular Component (CC) nucleoplasm part 1.229e-05 Informative Direct
Cellular Component (CC) nuclear DNA-directed RNA polymerase complex 8.627e-15 Informative Direct
Cellular Component (CC) DNA-directed RNA polymerase II, core complex 5.442e-05 Highly Informative Direct
Cellular Component (CC) transcription factor complex 1.594e-07 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)Nucleotidyltransferases9.124e-05Least InformativeDirect
Enzyme Commission (EC)DNA-directed RNA polymerase1.471e-09InformativeDirect
Enzyme Commission (EC)Sole sub-subclass for isomerases that do not belon1InformativeInherited
Enzyme Commission (EC)DNA topoisomerase0Highly InformativeDirect

Document: EC 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

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)gamete0Moderately 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 phosphorous-containing groups0.1175Least InformativeInherited
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0.0001092Moderately InformativeDirect
Enzyme Commission (EC)DNA topoisomerase0Highly InformativeDirect
Enzyme Commission (EC)DNA-directed RNA polymerase1.012e-09Highly 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 initiation1.384e-05Moderately InformativeDirect
Developmental stageLate protein1.337e-08Least InformativeDirect
DomainRepeat0.0001673Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Post-translational modificationTransferase0.002184Least InformativeInherited
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationIsomerase5.562e-12Moderately InformativeDirect
Post-translational modificationActivator2.999e-06Moderately InformativeDirect
Post-translational modificationTopoisomerase0Highly InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]