SUPERFAMILY 1.75 HMM library and genome assignments server

Helical domain of Sec23/24 superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   ERP29 C domain-like [ 47932] (2)
Superfamily:   Helical domain of Sec23/24 [ 81811]
Families:   Helical domain of Sec23/24 [ 81812] (2)


Superfamily statistics
Genomes (495) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,520 2,642 4
Proteins 2,517 2,637 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 0.000000000009528 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0002765 Least Informative Direct
Biological Process (BP) positive regulation of biological process 0.1038 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.3832 Least Informative Inherited
Biological Process (BP) developmental process 0.03249 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.1014 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.701 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.4317 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.9021 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.6753 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.9307 Least Informative Inherited
Biological Process (BP) cellular localization 0.0000003824 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.000005051 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0.00056 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.04762 Moderately Informative Inherited
Biological Process (BP) single-organism organelle organization 0.004238 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.231 Moderately Informative Inherited
Biological Process (BP) organ development 0.2716 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.0287 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.01935 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.1608 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.4147 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.01478 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.08194 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.002428 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.01619 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.2256 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.001627 Moderately Informative Inherited
Biological Process (BP) immune system process 0.01753 Moderately Informative Inherited
Biological Process (BP) positive regulation of transport 0.0000009604 Informative Direct
Biological Process (BP) single-organism membrane organization 0.000001693 Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 0.000003401 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 0.00007741 Informative Direct
Biological Process (BP) single-organism intracellular transport 0.00007965 Informative Direct
Biological Process (BP) tube development 0.0001541 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.00019 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.0006073 Informative Direct
Biological Process (BP) embryonic organ development 0.0008089 Informative Direct
Biological Process (BP) regulation of secretion 0.01437 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.004293 Informative Inherited
Biological Process (BP) organelle localization 0.5197 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.007197 Informative Inherited
Biological Process (BP) organ morphogenesis 0.07594 Informative Inherited
Biological Process (BP) single-organism cellular localization 0.04456 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.01116 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.02993 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.003803 Informative Inherited
Biological Process (BP) muscle structure development 0.001512 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.02057 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.009382 Informative Inherited
Biological Process (BP) Golgi vesicle transport 0.000000000006151 Highly Informative Direct
Biological Process (BP) vesicle organization 0.000000002097 Highly Informative Direct
Biological Process (BP) post-translational protein modification 0.00000000229 Highly Informative Direct
Biological Process (BP) protein glycosylation 0.0000000204 Highly Informative Direct
Biological Process (BP) respiratory system development 0.00000002911 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0.0000000969 Highly Informative Direct
Biological Process (BP) antigen processing and presentation 0.000001541 Highly Informative Direct
Biological Process (BP) establishment or maintenance of cell polarity 0.00001041 Highly Informative Direct
Biological Process (BP) embryonic organ morphogenesis 0.00001147 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 0.00001562 Highly Informative Direct
Biological Process (BP) muscle organ development 0.0001002 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.00000001006 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00005423 Least Informative Direct
Cellular Component (CC) membrane 0.000876 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.00265 Least Informative Inherited
Cellular Component (CC) protein complex 0.003512 Least Informative Inherited
Cellular Component (CC) vesicle 0 Moderately Informative Direct
Cellular Component (CC) bounding membrane of organelle 0 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 0.0000003819 Moderately Informative Direct
Cellular Component (CC) membrane region 0.0178 Moderately Informative Inherited
Cellular Component (CC) coated vesicle 0 Highly Informative Direct
Cellular Component (CC) transport vesicle 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 0.000004682 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.0000124 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)organism metabolism processing variant0Least InformativeDirect
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0Moderately InformativeDirect
Worm Phenotype (WP)cell organization biogenesis 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)flower0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight 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 componentCytoplasm0.00000005892Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationAcetylation0.0004103Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR006900 SSF81811 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 the all-helical domain, which forms an approximately 105-residue segment with the C-terminal 30 residues. The linker between alpha-M and alpha-N contacts Sar1.


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 Helical 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 Helical 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 ]