SUPERFAMILY 1.75 HMM library and genome assignments server


t-snare proteins superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   STAT-like [ 47654] (6)
Superfamily:   t-snare proteins [ 47661]
Families:   t-snare proteins [ 47662] (5)


Superfamily statistics
Genomes (530) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 6,084 7,080 13
Proteins 6,056 7,068 13


Functional annotation
General category Processes_IC
Detailed category Transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Cellular Component (CC)intracellular membrane-bounded organelle0.44630.002163Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.65274.177e-14Least InformativeInherited
Cellular Component (CC)Golgi apparatus8.282e-050InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) localization 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 7.154e-12 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1.768e-07 Least Informative Direct
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.2018 Least Informative Inherited
Biological Process (BP) cellular localization 0 Moderately Informative Direct
Biological Process (BP) system process 1.018e-07 Moderately Informative Direct
Biological Process (BP) organelle organization 0.0004282 Moderately Informative Direct
Biological Process (BP) macromolecule localization 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.2381 Moderately Informative Inherited
Biological Process (BP) reproduction 0.03969 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.3458 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.8522 Moderately Informative Inherited
Biological Process (BP) vesicle-mediated transport 0 Informative Direct
Biological Process (BP) secretion by cell 0 Informative Direct
Biological Process (BP) cellular membrane organization 3.722e-15 Informative Direct
Biological Process (BP) transmission of nerve impulse 9.067e-15 Informative Direct
Biological Process (BP) cell-cell signaling 2.316e-11 Informative Direct
Biological Process (BP) protein transport 1.116e-06 Informative Direct
Biological Process (BP) protein localization to organelle 0.8997 Informative Inherited
Biological Process (BP) organelle localization 0.03819 Informative Inherited
Biological Process (BP) response to nutrient levels 0.004581 Informative Inherited
Biological Process (BP) single organism reproductive process 0.597 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.7093 Informative Inherited
Biological Process (BP) neurotransmitter transport 0 Highly Informative Direct
Biological Process (BP) vesicle organization 0 Highly Informative Direct
Biological Process (BP) organelle fusion 0 Highly Informative Direct
Biological Process (BP) regulation of neurotransmitter levels 0 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 1.761e-14 Highly Informative Direct
Biological Process (BP) cellular membrane fusion 1.075e-13 Highly Informative Direct
Biological Process (BP) exocytosis 1.054e-09 Highly Informative Direct
Biological Process (BP) autophagy 1.252e-08 Highly Informative Direct
Biological Process (BP) establishment of vesicle localization 9.058e-08 Highly Informative Direct
Biological Process (BP) cellular response to starvation 4.974e-05 Highly Informative Direct
Biological Process (BP) establishment of protein localization to organelle 0.1136 Highly Informative Inherited
Biological Process (BP) synaptic vesicle localization 0.01111 Highly Informative Inherited
Biological Process (BP) signal release 0.0242 Highly Informative Inherited
Biological Process (BP) female pregnancy 0.009195 Highly Informative Inherited
Molecular Function (MF) binding 8.996e-14 Least Informative Direct
Cellular Component (CC) cytoplasmic part 4.177e-14 Least Informative Direct
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) protein complex 6.948e-10 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.6831 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.002163 Least Informative Inherited
Cellular Component (CC) organelle membrane 1.622e-13 Moderately Informative Direct
Cellular Component (CC) vesicle 6.379e-08 Moderately Informative Direct
Cellular Component (CC) endomembrane system 5.381e-06 Moderately Informative Direct
Cellular Component (CC) cytosol 1 Moderately Informative Inherited
Cellular Component (CC) plasma membrane 0.001298 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 0 Informative Direct
Cellular Component (CC) vacuolar part 1.384e-09 Informative Direct
Cellular Component (CC) endosome 4.611e-09 Informative Direct
Cellular Component (CC) cell-cell junction 0.0007924 Informative Direct
Cellular Component (CC) synapse part 0.001632 Informative Inherited
Cellular Component (CC) coated vesicle 0.1308 Informative Inherited
Cellular Component (CC) SNARE complex 0 Highly Informative Direct
Cellular Component (CC) trans-Golgi network 4.17e-13 Highly Informative Direct
Cellular Component (CC) Golgi membrane 5.86e-05 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.000111 Highly Informative Direct
Cellular Component (CC) endosomal part 0.0003073 Highly Informative Direct
Cellular Component (CC) apical plasma membrane 0.0004409 Highly Informative Direct
Cellular Component (CC) clathrin-coated vesicle 0.7767 Highly Informative Inherited

Document: GO annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant2.487e-06Least InformativeDirect
Worm Phenotype (WP)endocytic transport defect3.985e-10Moderately InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP 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
Fly Anatomy (FA)multi-tissue structure0Least InformativeDirect
Fly Anatomy (FA)reproductive system0Moderately InformativeDirect
Fly Anatomy (FA)germline cyst0InformativeDirect
Fly Anatomy (FA)ovariole0InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)pollen tube cell2.754e-05InformativeDirect
Plant structure DEvelopment stage (PDE)pollen development stage0.0001036Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)M germinated pollen stage4.764e-05InformativeDirect

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 processNeurotransmitter transport0Highly InformativeDirect
Biological processExocytosis1.243e-09Highly InformativeDirect
Biological processAutophagy2.273e-07Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle1.167e-11Moderately InformativeDirect
Cellular componentCell junction0.0001115Moderately InformativeDirect
Cellular componentSynapse2.113e-07InformativeDirect
Cellular componentSynaptosome3.911e-05Highly InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect
Post-translational modificationPhosphoprotein3.127e-08Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR010989 SSF47661 Protein matches
Abstract

Soluble N-ethylmaleimide attachment protein receptor (SNARE) proteins are a family of membrane-associated proteins characterised by an alpha-helical coiled-coil domain called the SNARE motif [PubMed12827282]. These proteins are classified as v-SNAREs and t-SNAREs based on their localisation on vesicle or target membrane; another classification scheme defines R-SNAREs and Q-SNAREs, as based on the conserved arginine or glutamine residue in the centre of the SNARE motif. SNAREs are localised to distinct membrane compartments of the secretory and endocytic trafficking pathways, and contribute to the specificity of intracellular membrane fusion processes.

The t-SNARE domain consists of a 4-helical bundle with a coiled-coil twist. The SNARE motif contributes to the fusion of two membranes. SNARE motifs fall into four classes: homologues of syntaxin 1a (t-SNARE), VAMP-2 (v-SNARE), and the N- and C-terminal SNARE motifs of SNAP-25. It is thought that one member from each class interacts to form a SNARE complex.

The SNARE motif represented in this entry is found in the N-terminal domains of certain syntaxin family members: syntaxin 1a, which is required for neurotransmitter release[PubMed10913252], syntaxin 6, which is found in endosomal transport vesicles [PubMed12082176], yeast Sso1p [PubMed11839791], and Vam3p, a yeast syntaxin essential for vacuolar fusion [PubMed11224573]. The SNARE motifs in these proteins share structural similarity, despite having a low level of sequence similarity.


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-quality) · Gene Ontology (high-coverage) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · 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 6 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 t-snare proteins 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 6 hidden Markov models representing the t-snare proteins 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-quality) · Gene Ontology (high-coverage) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]