SUPERFAMILY 1.75 HMM library and genome assignments server


B-box zinc-binding domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   B-box zinc-binding domain [ 57844]
Superfamily:   B-box zinc-binding domain [ 57845]
Families:   B-box zinc-binding domain [ 57846] (7)


Superfamily statistics
Genomes (358) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 8,652 8,795 7
Proteins 8,552 8,721 7


Functional annotation
General category General
Detailed category Ion binding

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) protein metabolic process 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 3.18e-08 Least Informative Direct
Biological Process (BP) response to stimulus 1.003e-05 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.0001592 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.5959 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.7883 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) immune system process 0 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 6.694e-09 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 2.7e-08 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 6.36e-08 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 1.094e-06 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 1.379e-05 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 4.636e-05 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 5.705e-05 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0001609 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) macromolecule catabolic process 0.05851 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.01229 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.1227 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.1599 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.3845 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.01768 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.6364 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.04469 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.7607 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.3724 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.9721 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.003622 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.9697 Moderately Informative Inherited
Biological Process (BP) system process 0.9814 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.1975 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of immune system process 2.032e-11 Informative Direct
Biological Process (BP) defense response 6.757e-10 Informative Direct
Biological Process (BP) regulation of intracellular protein kinase cascade 1.353e-08 Informative Direct
Biological Process (BP) positive regulation of signal transduction 1.459e-08 Informative Direct
Biological Process (BP) immune response 1.59e-07 Informative Direct
Biological Process (BP) regulation of immune response 2.431e-06 Informative Direct
Biological Process (BP) regulation of cytokine production 4.348e-06 Informative Direct
Biological Process (BP) regulation of defense response 7.029e-05 Informative Direct
Biological Process (BP) regulation of locomotion 0.0001053 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.09291 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.06715 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.385 Informative Inherited
Biological Process (BP) protein complex assembly 0.001083 Informative Inherited
Biological Process (BP) response to hormone stimulus 0.4192 Informative Inherited
Biological Process (BP) positive regulation of protein metabolic process 0.7665 Informative Inherited
Biological Process (BP) cell cycle process 0.4811 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.1853 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.01577 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.05794 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.9003 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.2589 Informative Inherited
Biological Process (BP) response to lipid 0.002881 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 1 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.3337 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.5578 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.1409 Informative Inherited
Biological Process (BP) ncRNA metabolic process 0.06507 Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.03988 Informative Inherited
Biological Process (BP) membrane organization 0.1531 Informative Inherited
Biological Process (BP) protein catabolic process 0.03876 Informative Inherited
Biological Process (BP) proteolysis 0.8927 Informative Inherited
Biological Process (BP) response to wounding 0.2575 Informative Inherited
Biological Process (BP) regulation of response to biotic stimulus 0 Highly Informative Direct
Biological Process (BP) regulation of multi-organism process 0 Highly Informative Direct
Biological Process (BP) positive regulation of defense response 0 Highly Informative Direct
Biological Process (BP) positive regulation of sequence-specific DNA binding transcription factor activity 0 Highly Informative Direct
Biological Process (BP) immune response-regulating signaling pathway 0 Highly Informative Direct
Biological Process (BP) regulation of innate immune response 6.329e-11 Highly Informative Direct
Biological Process (BP) activation of immune response 1.381e-10 Highly Informative Direct
Biological Process (BP) innate immune response 2.724e-07 Highly Informative Direct
Biological Process (BP) regulation of protein depolymerization 7.795e-07 Highly Informative Direct
Biological Process (BP) regulation of neural precursor cell proliferation 9.424e-07 Highly Informative Direct
Biological Process (BP) response to virus 1.872e-06 Highly Informative Direct
Biological Process (BP) regulation of protein catabolic process 2.508e-06 Highly Informative Direct
Biological Process (BP) ubiquitin-dependent protein catabolic process 2.776e-06 Highly Informative Direct
Biological Process (BP) negative regulation of cytoskeleton organization 2.992e-06 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 6.712e-06 Highly Informative Direct
Biological Process (BP) cell cycle phase 2.732e-05 Highly Informative Direct
Biological Process (BP) plasma membrane organization 4.862e-05 Highly Informative Direct
Biological Process (BP) neural tube development 5.343e-05 Highly Informative Direct
Biological Process (BP) mitotic cell cycle phase transition 0.0001769 Highly Informative Direct
Biological Process (BP) positive regulation of MAPK cascade 0.0002768 Highly Informative Direct
Biological Process (BP) negative regulation of protein complex disassembly 0.0003231 Highly Informative Direct
Biological Process (BP) regulation of protein stability 0.000446 Highly Informative Direct
Biological Process (BP) protein ubiquitination 0.0005166 Highly Informative Direct
Biological Process (BP) gene silencing 0.0006325 Highly Informative Direct
Biological Process (BP) cellular response to growth factor stimulus 0.0006872 Highly Informative Direct
Biological Process (BP) cell proliferation 0.01312 Highly Informative Inherited
Biological Process (BP) cellular response to organic cyclic compound 0.1039 Highly Informative Inherited
Biological Process (BP) response to corticosteroid stimulus 0.1911 Highly Informative Inherited
Biological Process (BP) regulation of gene expression, epigenetic 0.4694 Highly Informative Inherited
Biological Process (BP) negative regulation of sequence-specific DNA binding transcription factor activity 0.5445 Highly Informative Inherited
Biological Process (BP) regulation of translation 0.1678 Highly Informative Inherited
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0.2213 Highly Informative Inherited
Biological Process (BP) regulation of microtubule polymerization or depolymerization 0.08289 Highly Informative Inherited
Biological Process (BP) wound healing 0.1167 Highly Informative Inherited
Molecular Function (MF) binding 3.866e-06 Least Informative Direct
Molecular Function (MF) anion binding 1 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.2591 Moderately Informative Inherited
Molecular Function (MF) cation binding 0.3026 Moderately Informative Inherited
Molecular Function (MF) ligase activity, forming carbon-nitrogen bonds 0 Informative Direct
Molecular Function (MF) molecular transducer activity 1.274e-12 Informative Direct
Molecular Function (MF) receptor activity 4.219e-10 Informative Direct
Molecular Function (MF) carboxylic acid binding 0.0005518 Informative Direct
Molecular Function (MF) RNA binding 0.2508 Informative Inherited
Molecular Function (MF) transition metal ion binding 0.03103 Informative Inherited
Molecular Function (MF) cytoskeletal protein binding 0.01979 Informative Inherited
Molecular Function (MF) lipid binding 0.2454 Informative Inherited
Molecular Function (MF) small conjugating protein ligase activity 0 Highly Informative Direct
Molecular Function (MF) amino acid binding 1.995e-05 Highly Informative Direct
Molecular Function (MF) tubulin binding 0.2398 Highly Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 5.404e-14 Least Informative Direct
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 2.059e-13 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 1 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) nuclear part 1 Moderately Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0.05985 Informative Inherited
Cellular Component (CC) chromosome 1 Informative Inherited
Cellular Component (CC) cytoplasmic mRNA processing body 0 Highly Informative Direct
Cellular Component (CC) sarcolemma 6.881e-05 Highly Informative Direct
Cellular Component (CC) microtubule associated complex 0.0001174 Highly Informative Direct
Cellular Component (CC) chromatin 0.8606 Highly Informative Inherited
Cellular Component (CC) nuclear chromosome part 0.08424 Highly Informative Inherited

Document: GO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)muscle phenotype0.1828Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeletal muscle morphology0.07281InformativeInherited
Mammalian Phenotype (MP)abnormal muscle fiber morphology0.002572Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.004183Least InformativeInherited
Worm Phenotype (WP)protein aggregation variant1.611e-06Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant6.937e-05Moderately InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect
Fly Phenotype (FP)increased mortality0Least InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system0Least InformativeDirect
Fly Anatomy (FA)cell0Least InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis2.336e-07Moderately InformativeDirect
Biological processInnate immunity0InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processAntiviral defense0Highly InformativeDirect
Biological processRNA-mediated gene silencing8.99e-10Highly InformativeDirect
Biological processExocytosis1.019e-09Highly InformativeDirect
Cellular componentCytoplasm1.118e-11Least InformativeDirect
Cellular componentNucleus1.236e-08Least InformativeDirect
Cellular componentCytoplasmic vesicle2.443e-09Moderately InformativeDirect
Cellular componentCytoskeleton5.009e-09Moderately InformativeDirect
Cellular componentMicrotubule1.056e-12InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainBromodomain1.886e-12Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationDevelopmental protein2.664e-07Moderately InformativeDirect
Post-translational modificationRepressor4.395e-05Moderately InformativeDirect
Post-translational modificationMuscle protein7.422e-06Highly InformativeDirect
Post-translational modificationAcetylation7.529e-12Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · 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 7 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 B-box zinc-binding domain 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 7 hidden Markov models representing the B-box zinc-binding domain 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]