SUPERFAMILY 1.75 HMM library and genome assignments server

SNARE-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Profilin-like [ 55769] (10)
Superfamily:   SNARE-like [ 64356] (4)
Families:   Synatpobrevin N-terminal domain [ 64357] (2)
  Sedlin (SEDL) [ 82767]
  Clathrin coat assembly domain [ 75521] (2)
  SRP alpha N-terminal domain-like [ 90019] (2)


Superfamily statistics
Genomes (499) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 11,828 12,400 11
Proteins 11,767 12,365 11


Functional annotation
General category General
Detailed category Protein interaction

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)localization00Least InformativeDirect
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)regulation of cellular process11Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.5681Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.42680.04125Least InformativeInherited
Biological Process (BP)cellular localization0.00000074020Moderately InformativeDirect
Biological Process (BP)macromolecule localization0.26530.0005447Moderately InformativeInherited
Biological Process (BP)regulation of signal transduction0.22071Moderately InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.031331Moderately InformativeInherited
Biological Process (BP)regulation of catalytic activity0.17971Moderately InformativeInherited
Biological Process (BP)regulation of phosphorus metabolic process0.1051Moderately InformativeInherited
Biological Process (BP)organic substance transport10.2025Moderately InformativeInherited
Biological Process (BP)regulation of localization0.40060.3972Moderately InformativeInherited
Biological Process (BP)regulation of biological quality0.59541Moderately InformativeInherited
Biological Process (BP)synaptic transmission0.00066690.0000000005515InformativeDirect
Biological Process (BP)protein transport0.000000000012690InformativeDirect
Biological Process (BP)vesicle-mediated transport0.000000000013960InformativeDirect
Biological Process (BP)organelle localization0.74120.5237InformativeInherited
Biological Process (BP)regulation of nucleoside metabolic process0.0033980.09914InformativeInherited
Biological Process (BP)regulation of cellular catabolic process0.0074720.453InformativeInherited
Biological Process (BP)regulation of purine nucleotide metabolic process0.001460.1896InformativeInherited
Biological Process (BP)secretion by cell0.0030390.0000000000004343InformativeInherited
Biological Process (BP)single-organism intracellular transport0.015350.000000000000001913InformativeInherited
Biological Process (BP)cytoplasmic transport11InformativeInherited
Biological Process (BP)regulation of neurotransmitter levels0.000013920.0000003445Highly InformativeDirect
Biological Process (BP)regulation of lipid storage0.000005120.00000001647Highly InformativeDirect
Biological Process (BP)vesicle organization0.0000070610Highly InformativeDirect
Biological Process (BP)Golgi vesicle transport0.00000064730Highly InformativeDirect
Biological Process (BP)establishment of synaptic vesicle localization0.000001760.6272Highly InformativeInherited
Biological Process (BP)regulation of Ras GTPase activity0.0000041040.01043Highly InformativeInherited
Biological Process (BP)neurotransmitter transport0.0035030.02331Highly InformativeInherited
Biological Process (BP)signal release0.000013250.07621Highly InformativeInherited
Molecular Function (MF)transporter activity0.043730.1432Moderately InformativeInherited
Molecular Function (MF)protein transporter activity0.00000003640.0000000005781Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.00033180.0000000004675Least InformativeDirect
Cellular Component (CC)protein complex0.0000000057530.000000000000003071Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.00076610.0000001615Least InformativeDirect
Cellular Component (CC)membrane0.0096430.00000000000000158Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.0025270Least InformativeInherited
Cellular Component (CC)vesicle0.00000001660Moderately InformativeDirect
Cellular Component (CC)bounding membrane of organelle0.0000000000043170Moderately InformativeDirect
Cellular Component (CC)plasma membrane part0.33510.888Moderately InformativeInherited
Cellular Component (CC)Golgi apparatus00InformativeDirect
Cellular Component (CC)synapse0.0016410.002021InformativeInherited
Cellular Component (CC)Golgi-associated vesicle0.000000012860.00000000000007452Highly InformativeDirect
Cellular Component (CC)trans-Golgi network0.00000023030Highly InformativeDirect
Cellular Component (CC)transport vesicle0.000022050.000004158Highly InformativeDirect
Cellular Component (CC)coated vesicle0.000000000000002780.000000000000006018Highly InformativeDirect
Cellular Component (CC)cytoplasmic vesicle membrane0.00000000000075740.0000000008479Highly InformativeDirect
Cellular Component (CC)endocytic vesicle11Highly InformativeInherited

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) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.04125 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) macromolecule localization 0.0005447 Moderately Informative Direct
Biological Process (BP) cellular localization 0 Moderately Informative Direct
Biological Process (BP) immune system process 0.6593 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 1 Moderately Informative Inherited
Biological Process (BP) regulation of phosphorus metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.2025 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.3972 Moderately Informative Inherited
Biological Process (BP) single-organism organelle organization 0.1093 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) synaptic transmission 0.0000000005515 Informative Direct
Biological Process (BP) protein transport 0 Informative Direct
Biological Process (BP) vesicle-mediated transport 0 Informative Direct
Biological Process (BP) secretion by cell 0.0000000000004343 Informative Direct
Biological Process (BP) single-organism membrane organization 0.000000001407 Informative Direct
Biological Process (BP) single-organism intracellular transport 0.000000000000001913 Informative Direct
Biological Process (BP) protein localization to organelle 1 Informative Inherited
Biological Process (BP) organelle localization 0.5237 Informative Inherited
Biological Process (BP) leukocyte activation 0.02901 Informative Inherited
Biological Process (BP) regulation of nucleoside metabolic process 0.09914 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.453 Informative Inherited
Biological Process (BP) regulation of purine nucleotide metabolic process 0.1896 Informative Inherited
Biological Process (BP) cellular component movement 0.05998 Informative Inherited
Biological Process (BP) cytoplasmic transport 1 Informative Inherited
Biological Process (BP) microtubule-based process 0.001372 Informative Inherited
Biological Process (BP) immune effector process 0.03433 Informative Inherited
Biological Process (BP) immune response 0.3055 Informative Inherited
Biological Process (BP) regulation of neurotransmitter levels 0.0000003445 Highly Informative Direct
Biological Process (BP) myeloid leukocyte activation 0.000004344 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 0.00001741 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 0.0002766 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0.000000009271 Highly Informative Direct
Biological Process (BP) regulation of lipid storage 0.00000001647 Highly Informative Direct
Biological Process (BP) vesicle organization 0 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 0 Highly Informative Direct
Biological Process (BP) organelle fusion 0.0000000000008216 Highly Informative Direct
Biological Process (BP) membrane fusion 0.0007038 Highly Informative Direct
Biological Process (BP) establishment of synaptic vesicle localization 0.6272 Highly Informative Inherited
Biological Process (BP) regulation of Ras GTPase activity 0.01043 Highly Informative Inherited
Biological Process (BP) neurotransmitter transport 0.02331 Highly Informative Inherited
Biological Process (BP) signal release 0.07621 Highly Informative Inherited
Biological Process (BP) phagocytosis 0.03763 Highly Informative Inherited
Biological Process (BP) exocytosis 0.8833 Highly Informative Inherited
Biological Process (BP) post-embryonic development 0.5546 Highly Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transporter activity 0.1432 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0.003554 Informative Inherited
Molecular Function (MF) protein transporter activity 0.0000000005781 Highly Informative Direct
Cellular Component (CC) membrane 0.00000000000000158 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0000000004675 Least Informative Direct
Cellular Component (CC) protein complex 0.000000000000003071 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0000001615 Least Informative Direct
Cellular Component (CC) endoplasmic reticulum 0.000000003273 Moderately Informative Direct
Cellular Component (CC) vesicle 0 Moderately Informative Direct
Cellular Component (CC) bounding membrane of organelle 0 Moderately Informative Direct
Cellular Component (CC) plasma membrane part 0.888 Moderately Informative Inherited
Cellular Component (CC) membrane region 0.0771 Moderately Informative Inherited
Cellular Component (CC) endosome 0.00000001325 Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0.00007145 Informative Direct
Cellular Component (CC) Golgi apparatus 0 Informative Direct
Cellular Component (CC) vacuolar part 0.00000002274 Informative Direct
Cellular Component (CC) synapse 0.002021 Informative Inherited
Cellular Component (CC) lytic vacuole 0.04207 Informative Inherited
Cellular Component (CC) Golgi-associated vesicle 0.00000000000007452 Highly Informative Direct
Cellular Component (CC) trans-Golgi network 0 Highly Informative Direct
Cellular Component (CC) transport vesicle 0.000004158 Highly Informative Direct
Cellular Component (CC) coated vesicle 0.000000000000006018 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 0.0000000008479 Highly Informative Direct
Cellular Component (CC) endosomal part 0.00000028 Highly Informative Direct
Cellular Component (CC) late endosome 0.06007 Highly Informative Inherited
Cellular Component (CC) endocytic vesicle 1 Highly Informative Inherited

Document: GO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0Least InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.00007376Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.004389Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.2382Least InformativeInherited
Worm Phenotype (WP)larval development variant0.3909Least InformativeInherited
Worm Phenotype (WP)growth variant0.7563Least InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant0.00003889Moderately InformativeDirect
Worm Phenotype (WP)organ system development variant0.00008275Moderately InformativeDirect
Worm Phenotype (WP)organism segment morphology variant0.008233Moderately InformativeInherited
Worm Phenotype (WP)chemical response variant0.03482Moderately InformativeInherited
Worm Phenotype (WP)cell organization biogenesis variant0.3587Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.7756Moderately InformativeInherited
Worm Phenotype (WP)germline nuclear positioning variant0.000014InformativeDirect
Worm Phenotype (WP)somatic gonad development variant0.0004648InformativeDirect
Worm Phenotype (WP)sick0.0006275InformativeDirect
Worm Phenotype (WP)pigmentation variant0.001572InformativeInherited
Worm Phenotype (WP)body length variant0.001798InformativeInherited
Worm Phenotype (WP)drug resistant0.001841InformativeInherited
Worm Phenotype (WP)body width variant0.002258InformativeInherited
Worm Phenotype (WP)alimentary system development variant0.09497InformativeInherited
Worm Phenotype (WP)gut granule biogenesis reduced0.0000003662Highly InformativeDirect
Worm Phenotype (WP)cell secretion variant0.00006399Highly InformativeDirect
Worm Phenotype (WP)oocyte septum formation variant0.00006742Highly InformativeDirect
Worm Phenotype (WP)clear0.0001193Highly InformativeDirect
Worm Phenotype (WP)aldicarb resistant0.0002594Highly InformativeDirect
Worm Phenotype (WP)molt variant0.0006612Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)intracellular transport0.02675InformativeInherited
Yeast Phenotype (YP)protein transport0.003887Highly InformativeInherited

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 cell0.00004446InformativeDirect
Plant structure DEvelopment stage (PDE)pollen development stage0.0001194Moderately 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 processEndocytosis0InformativeDirect
Biological processER-Golgi transport0Highly InformativeDirect
Biological processExocytosis0.0000001079Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Cellular componentEndosome0.000000001593Moderately InformativeDirect
Cellular componentCell junction0.001342Moderately InformativeInherited
Cellular componentLysosome0.000000219InformativeDirect
Cellular componentSynapse0.000001332InformativeDirect
Cellular componentCoated pit0Highly InformativeDirect
Cellular componentSynaptosome0.000006642Highly InformativeDirect
DomainTransmembrane0.000009226Least InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
Molecular functionLipid-binding0.0000009165InformativeDirect
Post-translational modificationAcetylation0.000006509Least InformativeDirect
Post-translational modificationPhosphoprotein0.000009611Least InformativeDirect
Post-translational modificationPalmitate0.0000000000000827Moderately InformativeDirect
Post-translational modificationMethylation0.00000000396Moderately InformativeDirect
Post-translational modificationPrenylation0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011012 SSF64356 Protein matches
Abstract

VAMPs (and its homologue synaptobrevins) define a group of SNARE proteins that contain a C-terminal coiled-coil/SNARE motif, in combination with variable N-terminal domains that are used to classify VAMPs: those containing longin N-terminal domains (~150 aa) are referred to as longins, while those with shorter N-termini are referred to as brevins [PubMed12914952]. Longins are the only type of VAMP protein found in all eukaryotes, suggesting that their longin domain is essential. The longin domain is thought to exert a regulatory function. Longin domains have been shown to share the same structural fold, a profilin-like globular domain consisting of a five-stranded antiparallel beta-sheet that is sandwiched by an alpha-helix on one side, and two alpha-helices on the other (beta(2)-alpha-beta(3)-alpha(2)).

Other families have been shown to contain domains that structurally resemble the VAMP longin domain. An example is the eukaryotic conserved protein, SEDL, which is a component of the transport protein particle (TRAPP), critically involved in endoplasmic reticulum-to-Golgi vesicle transport; mutations in the SEDL gene are associated with an X-linked skeletal disorder, spondyloepiphyseal dysplasia tarda [PubMed12361953]. Another example is the assembly domain of clathrin coat proteins, such as Mu2 adaptin (AP50) and Sigma2 adaptin (AP17), which structurally resemble the longin domain. AP50 and AP17 are two of the proteins that make up the core of AP2, a complex that functions in clathrin-mediated endocytosis [PubMed12086608].


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) · Human Phenotype (HP) · 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 7 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 SNARE-like 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 7 hidden Markov models representing the SNARE-like 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) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]