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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 (441) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 2,295 1,832 4
Proteins 2,293 1,829 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 1.313e-09 Least Informative Direct
Biological Process (BP) biosynthetic process 0.3628 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.04606 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.005652 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.4538 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.9194 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.0002334 Moderately Informative Direct
Biological Process (BP) organelle organization 4.912e-05 Moderately Informative Direct
Biological Process (BP) cellular localization 1.711e-13 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0008852 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.02083 Moderately Informative Inherited
Biological Process (BP) immune system process 0.01525 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.08493 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.6612 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.1041 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.01359 Moderately Informative Inherited
Biological Process (BP) protein transport 2.61e-06 Informative Direct
Biological Process (BP) cellular membrane organization 3.327e-06 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.0003077 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.02759 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.4684 Informative Inherited
Biological Process (BP) protein glycosylation 1.725e-08 Highly Informative Direct
Biological Process (BP) vesicle organization 6.108e-10 Highly Informative Direct
Biological Process (BP) antigen processing and presentation 2.651e-06 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 1.256e-06 Highly Informative Direct
Biological Process (BP) post-translational protein modification 2.99e-09 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 2.522e-07 Highly Informative Direct
Biological Process (BP) organelle localization 0.1267 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 2.502e-05 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.02495 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.03062 Least Informative Inherited
Cellular Component (CC) protein complex 0.2106 Least Informative Inherited
Cellular Component (CC) membrane 0.07605 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 7.996e-06 Moderately Informative Direct
Cellular Component (CC) endomembrane system 4.622e-09 Moderately Informative Direct
Cellular Component (CC) organelle membrane 1.367e-07 Moderately Informative Direct
Cellular Component (CC) vesicle 7.484e-10 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0.0001556 Informative Direct
Cellular Component (CC) coated vesicle 0 Informative Direct
Cellular Component (CC) Golgi apparatus 0.006171 Informative Inherited
Cellular Component (CC) vesicle membrane 9.956e-12 Highly Informative Direct
Cellular Component (CC) transport vesicle 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle part 8.236e-10 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 3.883e-07 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

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)shoot apex0Least InformativeDirect
Plant ANatomical entity (PAN)shoot internode0Least InformativeDirect
Plant ANatomical entity (PAN)root0Least InformativeDirect
Plant ANatomical entity (PAN)plant embryo0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)vascular leaf0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)sepal0Least InformativeDirect
Plant ANatomical entity (PAN)petal0Least InformativeDirect
Plant ANatomical entity (PAN)stem0Least InformativeDirect
Plant ANatomical entity (PAN)pedicel0Least InformativeDirect
Plant ANatomical entity (PAN)androecium0Least InformativeDirect
Plant ANatomical entity (PAN)gynoecium0Least InformativeDirect
Plant ANatomical entity (PAN)leaf lamina0Least InformativeDirect
Plant ANatomical entity (PAN)collective leaf structure0Least InformativeDirect
Plant ANatomical entity (PAN)stalk0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)phyllome apex0Least InformativeDirect
Plant ANatomical entity (PAN)microgametophyte0Least 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 componentCytoplasm1.033e-07Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least 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) · 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) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.