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 5.783e-08 Least Informative Direct
Biological Process (BP) response to stimulus 2.164e-05 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.0003797 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.539 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.9256 Least Informative Inherited
Biological Process (BP) developmental process 0.9975 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 2.866e-08 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 4.352e-08 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 3.239e-07 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 1.057e-06 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 1.177e-05 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 2.853e-05 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 5.527e-05 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0001443 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.02418 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.166 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.1429 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.4881 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.01622 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.6802 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.07126 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.8058 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.9982 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.3767 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.985 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.004022 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.7467 Moderately Informative Inherited
Biological Process (BP) system process 1 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.1586 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 1.083e-11 Informative Direct
Biological Process (BP) defense response 9.426e-10 Informative Direct
Biological Process (BP) regulation of intracellular protein kinase cascade 1.454e-08 Informative Direct
Biological Process (BP) positive regulation of signal transduction 1.461e-08 Informative Direct
Biological Process (BP) protein oligomerization 9.607e-08 Informative Direct
Biological Process (BP) immune response 2.697e-07 Informative Direct
Biological Process (BP) regulation of immune response 1.497e-06 Informative Direct
Biological Process (BP) regulation of cytokine production 8.441e-06 Informative Direct
Biological Process (BP) regulation of defense response 4.621e-05 Informative Direct
Biological Process (BP) regulation of locomotion 0.0001393 Informative Direct
Biological Process (BP) muscle system process 0.0007264 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.5243 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.1062 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.07499 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.3901 Informative Inherited
Biological Process (BP) response to hormone stimulus 0.4292 Informative Inherited
Biological Process (BP) cell cycle process 0.3583 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.166 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.01751 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.07167 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.9406 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.2917 Informative Inherited
Biological Process (BP) response to lipid 0.002837 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 1 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.3487 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.3547 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.1673 Informative Inherited
Biological Process (BP) ncRNA metabolic process 0.08419 Informative Inherited
Biological Process (BP) response to other organism 0.1614 Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.05022 Informative Inherited
Biological Process (BP) cellular membrane organization 0.1343 Informative Inherited
Biological Process (BP) protein catabolic process 0.04912 Informative Inherited
Biological Process (BP) proteolysis 0.9381 Informative Inherited
Biological Process (BP) response to wounding 0.2701 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.1735 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 4.185e-11 Highly Informative Direct
Biological Process (BP) innate immune response 1e-06 Highly Informative Direct
Biological Process (BP) stem cell proliferation 1.188e-06 Highly Informative Direct
Biological Process (BP) regulation of neural precursor cell proliferation 2.255e-06 Highly Informative Direct
Biological Process (BP) response to virus 2.711e-06 Highly Informative Direct
Biological Process (BP) ubiquitin-dependent protein catabolic process 4.888e-06 Highly Informative Direct
Biological Process (BP) regulation of protein catabolic process 5.225e-06 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 8.108e-06 Highly Informative Direct
Biological Process (BP) cell cycle phase 1.064e-05 Highly Informative Direct
Biological Process (BP) cellular response to steroid hormone stimulus 1.977e-05 Highly Informative Direct
Biological Process (BP) neural tube development 6.931e-05 Highly Informative Direct
Biological Process (BP) negative regulation of cytoskeleton organization 8.756e-05 Highly Informative Direct
Biological Process (BP) immune response-activating signal transduction 8.765e-05 Highly Informative Direct
Biological Process (BP) response to glucocorticoid stimulus 0.0001511 Highly Informative Direct
Biological Process (BP) regulation of protein complex disassembly 0.0001601 Highly Informative Direct
Biological Process (BP) mitotic cell cycle phase transition 0.0001718 Highly Informative Direct
Biological Process (BP) positive regulation of catabolic process 0.0002619 Highly Informative Direct
Biological Process (BP) positive regulation of MAPK cascade 0.0004176 Highly Informative Direct
Biological Process (BP) protein ubiquitination 0.0004292 Highly Informative Direct
Biological Process (BP) regulation of protein stability 0.0006344 Highly Informative Direct
Biological Process (BP) gene silencing 0.0006461 Highly Informative Direct
Biological Process (BP) cellular response to growth factor stimulus 0.001229 Highly Informative Inherited
Biological Process (BP) regulation of gene expression, epigenetic 0.2167 Highly Informative Inherited
Biological Process (BP) negative regulation of sequence-specific DNA binding transcription factor activity 0.5449 Highly Informative Inherited
Biological Process (BP) regulation of translation 0.1741 Highly Informative Inherited
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0.1999 Highly Informative Inherited
Biological Process (BP) regulation of microtubule polymerization or depolymerization 0.08574 Highly Informative Inherited
Biological Process (BP) wound healing 0.1245 Highly Informative Inherited
Molecular Function (MF) binding 1.046e-05 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.3698 Moderately Informative Inherited
Molecular Function (MF) cation binding 0.4321 Moderately Informative Inherited
Molecular Function (MF) anion binding 1 Moderately Informative Inherited
Molecular Function (MF) ligase activity, forming carbon-nitrogen bonds 0 Informative Direct
Molecular Function (MF) molecular transducer activity 3.457e-12 Informative Direct
Molecular Function (MF) receptor activity 1.101e-09 Informative Direct
Molecular Function (MF) zinc ion binding 1.951e-05 Informative Direct
Molecular Function (MF) chromatin binding 6.713e-05 Informative Direct
Molecular Function (MF) carboxylic acid binding 0.0007239 Informative Direct
Molecular Function (MF) RNA binding 0.2368 Informative Inherited
Molecular Function (MF) lipid binding 0.06851 Informative Inherited
Molecular Function (MF) small conjugating protein ligase activity 0 Highly Informative Direct
Molecular Function (MF) amino acid binding 2.67e-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 2.083e-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 0.3964 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.5627 Moderately Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0.02888 Informative Inherited
Cellular Component (CC) chromosome 1 Informative Inherited
Cellular Component (CC) cytoplasmic mRNA processing body 0 Highly Informative Direct
Cellular Component (CC) sarcolemma 9.193e-05 Highly Informative Direct
Cellular Component (CC) microtubule associated complex 0.0002046 Highly Informative Direct
Cellular Component (CC) chromatin 0.5449 Highly Informative Inherited
Cellular Component (CC) nuclear chromosome part 0.03165 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 phenotype0.1837Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeletal muscle morphology0.0779InformativeInherited
Mammalian Phenotype (MP)abnormal skeletal muscle fiber morphology0.02392Highly 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 processApoptosis2.103e-07Moderately InformativeDirect
Biological processInnate immunity0InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processAntiviral defense0Highly InformativeDirect
Biological processRNA-mediated gene silencing9.104e-10Highly InformativeDirect
Biological processExocytosis9.106e-10Highly InformativeDirect
Cellular componentCytoplasm8.57e-13Least InformativeDirect
Cellular componentNucleus2.323e-09Least InformativeDirect
Cellular componentCytoskeleton2.462e-10Moderately InformativeDirect
Cellular componentCytoplasmic vesicle3.231e-09Moderately InformativeDirect
Cellular componentCell projection0.0001Moderately InformativeDirect
Cellular componentMicrotubule1.18e-12InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainBromodomain1.663e-12Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationDevelopmental protein2.198e-07Moderately InformativeDirect
Post-translational modificationRepressor4.217e-05Moderately InformativeDirect
Post-translational modificationMuscle protein6.84e-06Highly InformativeDirect
Post-translational modificationAcetylation7.912e-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 ]