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 (400) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 9,966 10,156 7
Proteins 9,851 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 0.00000007558 Least Informative Direct
Biological Process (BP) response to stimulus 0.00002379 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.0007628 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.6647 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 0.01111 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) developmental process 0.9982 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) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.9555 Least Informative Inherited
Biological Process (BP) immune system process 0 Moderately Informative Direct
Biological Process (BP) defense response 0.0000000002722 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.00000001134 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.0000003073 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 0.000000865 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0000009988 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 0.0000017 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.000008124 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.00001874 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.00006984 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.0576 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.5212 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.6648 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.179 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.006906 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.02768 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.1706 Moderately Informative Inherited
Biological Process (BP) regulation of phosphorus metabolic process 0.1028 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.2871 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.8278 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 0.4105 Moderately Informative Inherited
Biological Process (BP) tissue development 0.9232 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.01953 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.7611 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.6671 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.1476 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) regulation of response to external stimulus 0.0000000000003143 Informative Direct
Biological Process (BP) positive regulation of immune system process 0.0000000005539 Informative Direct
Biological Process (BP) protein oligomerization 0.0000001099 Informative Direct
Biological Process (BP) immune response 0.0000002447 Informative Direct
Biological Process (BP) regulation of immune response 0.000001302 Informative Direct
Biological Process (BP) positive regulation of intracellular signal transduction 0.000002534 Informative Direct
Biological Process (BP) regulation of cytokine production 0.000009271 Informative Direct
Biological Process (BP) regulation of defense response 0.000026 Informative Direct
Biological Process (BP) regulation of MAPK cascade 0.00003713 Informative Direct
Biological Process (BP) positive regulation of phosphate metabolic process 0.0001264 Informative Direct
Biological Process (BP) regulation of locomotion 0.0001384 Informative Direct
Biological Process (BP) regulation of protein localization 0.0002447 Informative Direct
Biological Process (BP) muscle system process 0.0007017 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.5199 Informative Inherited
Biological Process (BP) positive regulation of gene expression 1 Informative Inherited
Biological Process (BP) cell proliferation 0.01797 Informative Inherited
Biological Process (BP) response to lipid 0.003111 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.3891 Informative Inherited
Biological Process (BP) cellular response to hormone stimulus 0.331 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.456 Informative Inherited
Biological Process (BP) defense response to other organism 0.9618 Informative Inherited
Biological Process (BP) immune effector process 1 Informative Inherited
Biological Process (BP) protein catabolic process 0.05013 Informative Inherited
Biological Process (BP) proteolysis 0.9419 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.07849 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.142 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.3245 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 1 Informative Inherited
Biological Process (BP) positive regulation of catabolic process 0.4264 Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 0.06606 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.235 Informative Inherited
Biological Process (BP) response to acid chemical 0.5483 Informative Inherited
Biological Process (BP) tube development 0.1077 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.1668 Informative Inherited
Biological Process (BP) epithelium development 0.457 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.02399 Informative Inherited
Biological Process (BP) ncRNA metabolic process 0.08489 Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.05162 Informative Inherited
Biological Process (BP) single-organism membrane organization 0.2613 Informative Inherited
Biological Process (BP) cell cycle process 0.5514 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.1593 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 0.0000000003875 Highly Informative Direct
Biological Process (BP) positive regulation of MAPK cascade 0.00000006089 Highly Informative Direct
Biological Process (BP) stem cell proliferation 0.000001087 Highly Informative Direct
Biological Process (BP) innate immune response 0.000002572 Highly Informative Direct
Biological Process (BP) response to virus 0.000002886 Highly Informative Direct
Biological Process (BP) regulation of neural precursor cell proliferation 0.000003197 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 0.000006282 Highly Informative Direct
Biological Process (BP) ubiquitin-dependent protein catabolic process 0.000006313 Highly Informative Direct
Biological Process (BP) cellular response to steroid hormone stimulus 0.00002284 Highly Informative Direct
Biological Process (BP) neural tube development 0.00006918 Highly Informative Direct
Biological Process (BP) negative regulation of cytoskeleton organization 0.0000703 Highly Informative Direct
Biological Process (BP) immune response-activating signal transduction 0.00009085 Highly Informative Direct
Biological Process (BP) regulation of protein complex disassembly 0.0001467 Highly Informative Direct
Biological Process (BP) response to glucocorticoid 0.0001684 Highly Informative Direct
Biological Process (BP) mitotic cell cycle phase transition 0.0002116 Highly Informative Direct
Biological Process (BP) plasma membrane organization 0.0002921 Highly Informative Direct
Biological Process (BP) protein ubiquitination 0.0004698 Highly Informative Direct
Biological Process (BP) regulation of protein stability 0.0006687 Highly Informative Direct
Biological Process (BP) gene silencing 0.0006968 Highly Informative Direct
Biological Process (BP) regulation of translation 0.1446 Highly Informative Inherited
Biological Process (BP) negative regulation of sequence-specific DNA binding transcription factor activity 0.01215 Highly Informative Inherited
Biological Process (BP) regulation of gene expression, epigenetic 0.1976 Highly Informative Inherited
Biological Process (BP) cellular response to growth factor stimulus 0.001373 Highly Informative Inherited
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0.1978 Highly Informative Inherited
Biological Process (BP) regulation of microtubule polymerization or depolymerization 0.07556 Highly Informative Inherited
Biological Process (BP) wound healing 0.03481 Highly Informative Inherited
Molecular Function (MF) transferase activity 0 Least Informative Direct
Molecular Function (MF) binding 0.00001323 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.3288 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.703 Moderately Informative Inherited
Molecular Function (MF) cation binding 0.4307 Moderately Informative Inherited
Molecular Function (MF) anion binding 1 Moderately Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.5131 Moderately Informative Inherited
Molecular Function (MF) molecular transducer activity 0.000000000001811 Informative Direct
Molecular Function (MF) receptor activity 0.0000000006142 Informative Direct
Molecular Function (MF) zinc ion binding 0.00002104 Informative Direct
Molecular Function (MF) chromatin binding 0.00009271 Informative Direct
Molecular Function (MF) carboxylic acid binding 0.000789 Informative Direct
Molecular Function (MF) RNA binding 0.1105 Informative Inherited
Molecular Function (MF) lipid binding 0.07172 Informative Inherited
Molecular Function (MF) ubiquitin-protein transferase activity 0 Highly Informative Direct
Molecular Function (MF) amino acid binding 0.00002957 Highly Informative Direct
Cellular Component (CC) 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 0.0000000000001845 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 1 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.2121 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.3144 Moderately Informative Inherited
Cellular Component (CC) chromosome 1 Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0.02147 Informative Inherited
Cellular Component (CC) cytoplasmic ribonucleoprotein granule 0 Highly Informative Direct
Cellular Component (CC) sarcolemma 0.00008882 Highly Informative Direct
Cellular Component (CC) microtubule associated complex 0.0001944 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.04772 Highly Informative Inherited
Cellular Component (CC) chromatin 0.1956 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 variant0.000001611Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.00006937Moderately 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 processApoptosis0.0000002102Moderately InformativeDirect
Biological processInnate immunity0InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processAntiviral defense0Highly InformativeDirect
Biological processRNA-mediated gene silencing0.0000000009038Highly InformativeDirect
Biological processExocytosis0.0000000009049Highly InformativeDirect
Cellular componentCytoplasm0.0000000000008556Least InformativeDirect
Cellular componentNucleus0.000000002434Least InformativeDirect
Cellular componentCytoskeleton0.0000000002541Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0.000000003438Moderately InformativeDirect
Cellular componentCell projection0.0001042Moderately InformativeDirect
Cellular componentMicrotubule0.000000000001165InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainBromodomain0.000000000001632Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.0000002158Moderately InformativeDirect
Post-translational modificationRepressor0.0000472Moderately InformativeDirect
Post-translational modificationMuscle protein0.000006802Highly InformativeDirect
Post-translational modificationAcetylation0.000000000007941Least 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 ]