SUPERFAMILY 1.75 HMM library and genome assignments server


Zn-finger domain of Sec23/24 superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   Rubredoxin-like [ 57769] (17)
Superfamily:   Zn-finger domain of Sec23/24 [ 82919]
Families:   Zn-finger domain of Sec23/24 [ 82920] (2)


Superfamily statistics
Genomes (466) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 2,341 1,884 4
Proteins 2,339 1,884 4


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) localization 9.334e-08 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.000384 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.294 Least Informative Inherited
Biological Process (BP) developmental process 0.1002 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.4684 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.02042 Least Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.0008488 Moderately Informative Direct
Biological Process (BP) regulation of localization 8.844e-07 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 9.138e-05 Moderately Informative Direct
Biological Process (BP) cellular localization 1.002e-08 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.006147 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.4814 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.1506 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.3168 Moderately Informative Inherited
Biological Process (BP) organ development 0.02865 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.6247 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.0606 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.001791 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.001309 Moderately Informative Inherited
Biological Process (BP) protein complex assembly 6.115e-05 Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 0.0001267 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.0002592 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 4.318e-06 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.0005726 Informative Direct
Biological Process (BP) regulation of organelle organization 0.0005671 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 9.035e-05 Informative Direct
Biological Process (BP) embryonic organ development 3.82e-05 Informative Direct
Biological Process (BP) embryonic morphogenesis 0.0007036 Informative Direct
Biological Process (BP) anatomical structure formation involved in morphogenesis 5.666e-05 Informative Direct
Biological Process (BP) positive regulation of transport 0.000169 Informative Direct
Biological Process (BP) regulation of intracellular transport 0.07503 Informative Inherited
Biological Process (BP) regulation of secretion 0.1694 Informative Inherited
Biological Process (BP) organ morphogenesis 0.0118 Informative Inherited
Biological Process (BP) generation of neurons 0.001248 Informative Inherited
Biological Process (BP) membrane organization 0.00104 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.03339 Informative Inherited
Biological Process (BP) vesicle organization 1.798e-07 Highly Informative Direct
Biological Process (BP) regulation of protein complex assembly 0.0005941 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 8.004e-10 Highly Informative Direct
Biological Process (BP) embryonic organ morphogenesis 3.423e-07 Highly Informative Direct
Biological Process (BP) positive regulation of secretion 2.52e-08 Highly Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 2.972e-06 Highly Informative Direct
Cellular Component (CC) membrane 0.0009076 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000946 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1.543e-09 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.02852 Least Informative Inherited
Cellular Component (CC) protein complex 0.001336 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.0009719 Moderately Informative Direct
Cellular Component (CC) endomembrane system 4.179e-13 Moderately Informative Direct
Cellular Component (CC) organelle membrane 6.016e-12 Moderately Informative Direct
Cellular Component (CC) vesicle 0 Moderately Informative Direct
Cellular Component (CC) coated vesicle 0 Informative Direct
Cellular Component (CC) Golgi apparatus 0.03502 Informative Inherited
Cellular Component (CC) transport vesicle 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 2.429e-05 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 8.26e-08 Highly Informative Direct

Document: GO annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0Least InformativeDirect
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0Least InformativeDirect
Worm Phenotype (WP)cell organization biogenesis variant0Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0Moderately InformativeDirect
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0Moderately InformativeDirect
Worm Phenotype (WP)germline nuclear positioning variant0InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0InformativeDirect
Worm Phenotype (WP)germ cell compartment size variant0Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processProtein transport0Moderately InformativeDirect
Biological processER-Golgi transport0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCytoplasm1.96e-07Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationAcetylation0.0003515Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR006895 SSF82919 Protein matches
Abstract

COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex [PubMed11535824]. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation [PubMed12239560].

Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain , an all-helical region , and a C-terminal gelsolin-like domain . This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex.

More information about these proteins can be found at Protein of the Month: Zinc Fingers.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · 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 2 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 Zn-finger domain of Sec23/24 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 2 hidden Markov models representing the Zn-finger domain of Sec23/24 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]