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 (542) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 6,346 7,080 13
Proteins 6,317 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 organelle0.38210.000256Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.66480Least InformativeInherited
Cellular Component (CC)Golgi apparatus0.00013590InformativeDirect

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) cellular component organization or biogenesis 0.0000000000002596 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000699 Least Informative Direct
Biological Process (BP) positive regulation of biological process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) cellular localization 0 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.000001034 Moderately Informative Direct
Biological Process (BP) single-organism organelle organization 0.000002786 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.5046 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.2 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.1124 Moderately Informative Inherited
Biological Process (BP) reproductive process 0.007823 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.8003 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.4346 Moderately Informative Inherited
Biological Process (BP) single-organism membrane organization 0 Informative Direct
Biological Process (BP) secretion by cell 0 Informative Direct
Biological Process (BP) vesicle-mediated transport 0 Informative Direct
Biological Process (BP) synaptic transmission 0 Informative Direct
Biological Process (BP) protein transport 0.00000001198 Informative Direct
Biological Process (BP) cellular response to external stimulus 0.0004148 Informative Direct
Biological Process (BP) multi-multicellular organism process 0.0007246 Informative Direct
Biological Process (BP) organelle localization 0.0216 Informative Inherited
Biological Process (BP) single organism reproductive process 0.008205 Informative Inherited
Biological Process (BP) single-organism intracellular transport 0.002229 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.3735 Informative Inherited
Biological Process (BP) protein localization to organelle 0.9446 Informative Inherited
Biological Process (BP) single-organism cellular localization 1 Informative Inherited
Biological Process (BP) response to nutrient levels 0.004983 Informative Inherited
Biological Process (BP) membrane fusion 0 Highly Informative Direct
Biological Process (BP) neurotransmitter transport 0 Highly Informative Direct
Biological Process (BP) organelle fusion 0 Highly Informative Direct
Biological Process (BP) vesicle organization 0 Highly Informative Direct
Biological Process (BP) regulation of neurotransmitter levels 0 Highly Informative Direct
Biological Process (BP) macroautophagy 0.00000000001356 Highly Informative Direct
Biological Process (BP) signal release 0.00000000004796 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 0.0000000002294 Highly Informative Direct
Biological Process (BP) exocytosis 0.0000000004834 Highly Informative Direct
Biological Process (BP) regulation of synaptic transmission 0.00004395 Highly Informative Direct
Biological Process (BP) meiotic cell cycle 0.0001281 Highly Informative Direct
Biological Process (BP) establishment of synaptic vesicle localization 0.01864 Highly Informative Inherited
Biological Process (BP) female pregnancy 0.001886 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) channel regulator activity 0.0000006035 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000256 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) protein complex 0.00000000002044 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.01334 Least Informative Inherited
Cellular Component (CC) bounding membrane of organelle 0 Moderately Informative Direct
Cellular Component (CC) vesicle 0.000000002104 Moderately Informative Direct
Cellular Component (CC) cell projection 0.07405 Moderately Informative Inherited
Cellular Component (CC) cytosol 1 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 0 Informative Direct
Cellular Component (CC) endosome 0.00000000001182 Informative Direct
Cellular Component (CC) vacuolar part 0.000000002175 Informative Direct
Cellular Component (CC) neuron projection 0.00003939 Informative Direct
Cellular Component (CC) synapse 0.00006282 Informative Direct
Cellular Component (CC) trans-Golgi network 0.000000000000006018 Highly Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.00000006733 Highly Informative Direct
Cellular Component (CC) endosomal part 0.0004351 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 variant0.000002487Least InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.0000000003985Moderately 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

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 cell0.00002754InformativeDirect
Plant structure DEvelopment stage (PDE)pollen development stage0.0001036Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)M germinated pollen stage0.00004764InformativeDirect

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 processExocytosis0.000000001234Highly InformativeDirect
Biological processAutophagy0.0000003398Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0.00000000001229Moderately InformativeDirect
Cellular componentCell junction0.0001111Moderately InformativeDirect
Cellular componentSynapse0.0000002119InformativeDirect
Cellular componentSynaptosome0.00003864Highly InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect
Post-translational modificationPhosphoprotein0.00000003132Least 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 ]