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 (399) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 9,960 10,156 7
Proteins 9,845 10,063 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 6.078e-08 Least Informative Direct
Biological Process (BP) response to stimulus 2.389e-05 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.0004263 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.5465 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.9328 Least Informative Inherited
Biological Process (BP) developmental process 0.9984 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 response to stimulus 2.679e-08 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 3.376e-08 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 3.282e-07 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 6.335e-07 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 1.607e-05 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 2.397e-05 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 4.791e-05 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0001559 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.02597 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.1683 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.1507 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.5037 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.01472 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.6752 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.6817 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.07881 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.8174 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.3813 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.004894 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.7672 Moderately Informative Inherited
Biological Process (BP) system process 1 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.1489 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) protein modification by small protein conjugation or removal 0 Informative Direct
Biological Process (BP) positive regulation of immune system process 8.527e-12 Informative Direct
Biological Process (BP) defense response 9.704e-10 Informative Direct
Biological Process (BP) positive regulation of signal transduction 1.392e-08 Informative Direct
Biological Process (BP) regulation of intracellular protein kinase cascade 1.815e-08 Informative Direct
Biological Process (BP) protein oligomerization 1.048e-07 Informative Direct
Biological Process (BP) immune response 2.555e-07 Informative Direct
Biological Process (BP) regulation of immune response 1.373e-06 Informative Direct
Biological Process (BP) regulation of cytokine production 8.933e-06 Informative Direct
Biological Process (BP) regulation of defense response 4.332e-05 Informative Direct
Biological Process (BP) regulation of locomotion 0.0001348 Informative Direct
Biological Process (BP) regulation of protein localization 0.0001915 Informative Direct
Biological Process (BP) muscle system process 0.0007261 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.527 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.1088 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.07381 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.3864 Informative Inherited
Biological Process (BP) response to hormone stimulus 0.4282 Informative Inherited
Biological Process (BP) positive regulation of protein metabolic process 0.7814 Informative Inherited
Biological Process (BP) cell cycle process 0.3588 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.1694 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.01584 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.06836 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.933 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.319 Informative Inherited
Biological Process (BP) response to lipid 0.003031 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 1 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.3371 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.3547 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.1636 Informative Inherited
Biological Process (BP) ncRNA metabolic process 0.08385 Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.05104 Informative Inherited
Biological Process (BP) cellular membrane organization 0.1362 Informative Inherited
Biological Process (BP) protein catabolic process 0.04913 Informative Inherited
Biological Process (BP) proteolysis 0.9457 Informative Inherited
Biological Process (BP) response to wounding 0.2678 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.1725 Informative Inherited
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) regulation of innate immune response 4.002e-11 Highly Informative Direct
Biological Process (BP) innate immune response 9.444e-07 Highly Informative Direct
Biological Process (BP) stem cell proliferation 1.082e-06 Highly Informative Direct
Biological Process (BP) response to virus 2.672e-06 Highly Informative Direct
Biological Process (BP) regulation of neural precursor cell proliferation 3.289e-06 Highly Informative Direct
Biological Process (BP) ubiquitin-dependent protein catabolic process 4.873e-06 Highly Informative Direct
Biological Process (BP) regulation of protein catabolic process 5.41e-06 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 7.153e-06 Highly Informative Direct
Biological Process (BP) cell cycle phase 1.073e-05 Highly Informative Direct
Biological Process (BP) cellular response to steroid hormone stimulus 2.042e-05 Highly Informative Direct
Biological Process (BP) neural tube development 6.858e-05 Highly Informative Direct
Biological Process (BP) negative regulation of cytoskeleton organization 8.183e-05 Highly Informative Direct
Biological Process (BP) immune response-activating signal transduction 9.073e-05 Highly Informative Direct
Biological Process (BP) response to glucocorticoid stimulus 0.0001527 Highly Informative Direct
Biological Process (BP) regulation of protein complex disassembly 0.0001569 Highly Informative Direct
Biological Process (BP) mitotic cell cycle phase transition 0.0001701 Highly Informative Direct
Biological Process (BP) positive regulation of catabolic process 0.0002705 Highly Informative Direct
Biological Process (BP) positive regulation of MAPK cascade 0.0003366 Highly Informative Direct
Biological Process (BP) protein ubiquitination 0.0004477 Highly Informative Direct
Biological Process (BP) regulation of protein stability 0.0006385 Highly Informative Direct
Biological Process (BP) gene silencing 0.0006618 Highly Informative Direct
Biological Process (BP) cellular response to growth factor stimulus 0.001244 Highly Informative Inherited
Biological Process (BP) regulation of gene expression, epigenetic 0.2107 Highly Informative Inherited
Biological Process (BP) negative regulation of sequence-specific DNA binding transcription factor activity 0.5419 Highly Informative Inherited
Biological Process (BP) regulation of translation 0.1682 Highly Informative Inherited
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0.1988 Highly Informative Inherited
Biological Process (BP) regulation of microtubule polymerization or depolymerization 0.08458 Highly Informative Inherited
Biological Process (BP) wound healing 0.1265 Highly Informative Inherited
Molecular Function (MF) binding 1.254e-05 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.3731 Moderately Informative Inherited
Molecular Function (MF) cation binding 0.4289 Moderately Informative Inherited
Molecular Function (MF) anion binding 1 Moderately Informative Inherited
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) molecular transducer activity 3.52e-12 Informative Direct
Molecular Function (MF) receptor activity 1.087e-09 Informative Direct
Molecular Function (MF) zinc ion binding 1.954e-05 Informative Direct
Molecular Function (MF) chromatin binding 8.116e-05 Informative Direct
Molecular Function (MF) carboxylic acid binding 0.0007601 Informative Direct
Molecular Function (MF) RNA binding 0.2295 Informative Inherited
Molecular Function (MF) lipid binding 0.06947 Informative Inherited
Molecular Function (MF) small conjugating protein ligase activity 0 Highly Informative Direct
Molecular Function (MF) amino acid binding 2.796e-05 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 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) ribonucleoprotein complex 1.684e-13 Moderately Informative Direct
Cellular Component (CC) plasma membrane 1 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 1 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.3903 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.5572 Moderately Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0.02781 Informative Inherited
Cellular Component (CC) chromosome 1 Informative Inherited
Cellular Component (CC) cytoplasmic mRNA processing body 0 Highly Informative Direct
Cellular Component (CC) sarcolemma 9.133e-05 Highly Informative Direct
Cellular Component (CC) microtubule associated complex 0.0001949 Highly Informative Direct
Cellular Component (CC) chromatin 0.5318 Highly Informative Inherited
Cellular Component (CC) nuclear chromosome part 0.0333 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 phenotype0.1881Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeletal muscle morphology0.07914InformativeInherited
Mammalian Phenotype (MP)abnormal skeletal muscle fiber morphology0.02412Highly 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 processApoptosis2.102e-07Moderately InformativeDirect
Biological processInnate immunity0InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processAntiviral defense0Highly InformativeDirect
Biological processRNA-mediated gene silencing9.038e-10Highly InformativeDirect
Biological processExocytosis9.049e-10Highly InformativeDirect
Cellular componentCytoplasm8.556e-13Least InformativeDirect
Cellular componentNucleus2.434e-09Least InformativeDirect
Cellular componentCytoskeleton2.541e-10Moderately InformativeDirect
Cellular componentCytoplasmic vesicle3.438e-09Moderately InformativeDirect
Cellular componentCell projection0.0001042Moderately InformativeDirect
Cellular componentMicrotubule1.165e-12InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainBromodomain1.632e-12Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationDevelopmental protein2.158e-07Moderately InformativeDirect
Post-translational modificationRepressor4.72e-05Moderately InformativeDirect
Post-translational modificationMuscle protein6.802e-06Highly InformativeDirect
Post-translational modificationAcetylation7.941e-12Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)protein ubiquitination0Moderately InformativeDirect

Document: UP 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) · UniProtKB UniPathway (UP) ]

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) · UniProtKB UniPathway (UP) · Internal database links ]