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 (447) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 10,698 8,674 11
Proteins 10,654 8,660 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)single-organism cellular process0.00021092.184e-11Least InformativeDirect
Biological Process (BP)localization00Least InformativeDirect
Biological Process (BP)regulation of cellular process11Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.4931Least InformativeInherited
Biological Process (BP)multicellular organismal process0.64151Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.51940.1163Least InformativeInherited
Biological Process (BP)cellular localization1.335e-120Moderately InformativeDirect
Biological Process (BP)regulation of signal transduction0.18351Moderately InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.027771Moderately InformativeInherited
Biological Process (BP)regulation of phosphate metabolic process10.9603Moderately InformativeInherited
Biological Process (BP)regulation of catalytic activity0.18161Moderately InformativeInherited
Biological Process (BP)macromolecule localization0.46230.007424Moderately InformativeInherited
Biological Process (BP)organic substance transport10.4318Moderately InformativeInherited
Biological Process (BP)regulation of localization0.33950.549Moderately InformativeInherited
Biological Process (BP)system process0.10580.001621Moderately InformativeInherited
Biological Process (BP)organelle organization0.990.286Moderately InformativeInherited
Biological Process (BP)protein transport1.038e-080InformativeDirect
Biological Process (BP)vesicle-mediated transport7.719e-120InformativeDirect
Biological Process (BP)membrane organization0.00077540InformativeDirect
Biological Process (BP)regulation of nucleoside metabolic process0.0039510.08496InformativeInherited
Biological Process (BP)regulation of nucleotide catabolic process0.00046480.07748InformativeInherited
Biological Process (BP)regulation of purine nucleotide metabolic process0.0015650.1671InformativeInherited
Biological Process (BP)organelle localization0.53860.2354InformativeInherited
Biological Process (BP)secretion by cell0.0064332.291e-12InformativeInherited
Biological Process (BP)transmission of nerve impulse0.0014084.13e-09InformativeInherited
Biological Process (BP)cell-cell signaling0.0051012.12e-07InformativeInherited
Biological Process (BP)regulation of neurotransmitter levels1.423e-052.053e-07Highly InformativeDirect
Biological Process (BP)regulation of lipid storage4.795e-061.33e-08Highly InformativeDirect
Biological Process (BP)vesicle organization4.403e-060Highly InformativeDirect
Biological Process (BP)Golgi vesicle transport1.768e-080Highly InformativeDirect
Biological Process (BP)synaptic vesicle localization1.357e-060.4443Highly InformativeInherited
Biological Process (BP)regulation of Ras GTPase activity5.998e-060.009779Highly InformativeInherited
Biological Process (BP)establishment of vesicle localization0.062568.632e-06Highly InformativeInherited
Biological Process (BP)neurotransmitter transport0.0039050.0179Highly InformativeInherited
Biological Process (BP)signal release1.164e-050.8105Highly InformativeInherited
Molecular Function (MF)transporter activity0.043080.1249Moderately InformativeInherited
Molecular Function (MF)protein transporter activity4.365e-086.163e-10Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.00035895.332e-08Least InformativeDirect
Cellular Component (CC)protein complex4.07e-091.701e-13Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.014750.00513Least InformativeInherited
Cellular Component (CC)membrane0.0034427.268e-15Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.054363.009e-13Least InformativeInherited
Cellular Component (CC)endomembrane system3.323e-120Moderately InformativeDirect
Cellular Component (CC)organelle membrane3.126e-070Moderately InformativeDirect
Cellular Component (CC)vesicle2.884e-100Moderately InformativeDirect
Cellular Component (CC)plasma membrane part0.2850.9417Moderately InformativeInherited
Cellular Component (CC)Golgi apparatus2.598e-110InformativeDirect
Cellular Component (CC)coated vesicle5.507e-097.164e-07InformativeDirect
Cellular Component (CC)synapse part0.00010395.774e-06InformativeDirect
Cellular Component (CC)endosome0.025532.324e-08InformativeInherited
Cellular Component (CC)Golgi membrane1.091e-102.764e-09Highly InformativeDirect
Cellular Component (CC)Golgi-associated vesicle1.51e-091.521e-15Highly InformativeDirect
Cellular Component (CC)trans-Golgi network3.205e-060Highly InformativeDirect
Cellular Component (CC)coated pit8.885e-094.697e-09Highly InformativeDirect
Cellular Component (CC)TRAPP complex2.676e-150Highly InformativeDirect
Cellular Component (CC)cytoplasmic vesicle membrane2.655e-123.35e-07Highly InformativeDirect
Cellular Component (CC)endosomal part0.00095713.738e-07Highly InformativeDirect
Cellular Component (CC)endocytic vesicle11Highly InformativeInherited
Cellular Component (CC)clathrin-coated vesicle11Highly InformativeInherited
Cellular Component (CC)transport vesicle0.003060.0337Highly 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) single-organism cellular process 2.184e-11 Least Informative Direct
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) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.1163 Least Informative Inherited
Biological Process (BP) response to stimulus 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) system process 0.001621 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 phosphate metabolic process 0.9603 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.007424 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.4318 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.549 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.286 Moderately Informative Inherited
Biological Process (BP) immune system process 0.7061 Moderately Informative Inherited
Biological Process (BP) cell-cell signaling 2.12e-07 Informative Direct
Biological Process (BP) protein transport 0 Informative Direct
Biological Process (BP) vesicle-mediated transport 0 Informative Direct
Biological Process (BP) transmission of nerve impulse 4.13e-09 Informative Direct
Biological Process (BP) secretion by cell 2.291e-12 Informative Direct
Biological Process (BP) membrane organization 0 Informative Direct
Biological Process (BP) protein localization to organelle 1 Informative Inherited
Biological Process (BP) regulation of nucleoside metabolic process 0.08496 Informative Inherited
Biological Process (BP) regulation of nucleotide catabolic process 0.07748 Informative Inherited
Biological Process (BP) regulation of purine nucleotide metabolic process 0.1671 Informative Inherited
Biological Process (BP) organelle localization 0.2354 Informative Inherited
Biological Process (BP) cytoplasmic transport 1 Informative Inherited
Biological Process (BP) cellular component movement 0.6273 Informative Inherited
Biological Process (BP) microtubule-based process 0.03562 Informative Inherited
Biological Process (BP) immune effector process 0.03179 Informative Inherited
Biological Process (BP) immune response 0.4272 Informative Inherited
Biological Process (BP) cell activation 0.3922 Informative Inherited
Biological Process (BP) regulation of neurotransmitter levels 2.053e-07 Highly Informative Direct
Biological Process (BP) myeloid leukocyte activation 3.155e-06 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 1.615e-05 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 0.0002571 Highly Informative Direct
Biological Process (BP) cellular membrane fusion 9.767e-05 Highly Informative Direct
Biological Process (BP) microtubule-based movement 4.2e-09 Highly Informative Direct
Biological Process (BP) regulation of lipid storage 1.33e-08 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 5.023e-10 Highly Informative Direct
Biological Process (BP) establishment of vesicle localization 8.632e-06 Highly Informative Direct
Biological Process (BP) synaptic vesicle localization 0.4443 Highly Informative Inherited
Biological Process (BP) regulation of Ras GTPase activity 0.009779 Highly Informative Inherited
Biological Process (BP) neurotransmitter transport 0.0179 Highly Informative Inherited
Biological Process (BP) signal release 0.8105 Highly Informative Inherited
Biological Process (BP) phagocytosis 0.04896 Highly Informative Inherited
Biological Process (BP) exocytosis 0.7648 Highly Informative Inherited
Biological Process (BP) post-embryonic development 0.4875 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transporter activity 0.1249 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0.002715 Informative Inherited
Molecular Function (MF) protein transporter activity 6.163e-10 Highly Informative Direct
Cellular Component (CC) membrane 7.268e-15 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 5.332e-08 Least Informative Direct
Cellular Component (CC) protein complex 1.701e-13 Least Informative Direct
Cellular Component (CC) cytoplasmic part 3.009e-13 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.00513 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 3.65e-08 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0 Moderately Informative Direct
Cellular Component (CC) vesicle 0 Moderately Informative Direct
Cellular Component (CC) plasma membrane part 0.9417 Moderately Informative Inherited
Cellular Component (CC) endosome 2.324e-08 Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 8.561e-05 Informative Direct
Cellular Component (CC) Golgi apparatus 0 Informative Direct
Cellular Component (CC) coated vesicle 7.164e-07 Informative Direct
Cellular Component (CC) vacuolar part 3.587e-09 Informative Direct
Cellular Component (CC) synapse part 5.774e-06 Informative Direct
Cellular Component (CC) lytic vacuole 0.03302 Informative Inherited
Cellular Component (CC) Golgi membrane 2.764e-09 Highly Informative Direct
Cellular Component (CC) Golgi-associated vesicle 1.521e-15 Highly Informative Direct
Cellular Component (CC) trans-Golgi network 0 Highly Informative Direct
Cellular Component (CC) coated pit 4.697e-09 Highly Informative Direct
Cellular Component (CC) TRAPP complex 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 3.35e-07 Highly Informative Direct
Cellular Component (CC) SNARE complex 0 Highly Informative Direct
Cellular Component (CC) endosomal part 3.738e-07 Highly Informative Direct
Cellular Component (CC) late endosome 0.09837 Highly Informative Inherited
Cellular Component (CC) endocytic vesicle 1 Highly Informative Inherited
Cellular Component (CC) clathrin-coated vesicle 1 Highly Informative Inherited
Cellular Component (CC) transport vesicle 0.0337 Highly Informative Inherited
Cellular Component (CC) lysosome 0.2858 Highly Informative Inherited
Cellular Component (CC) vacuolar membrane 0.0114 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 the skeletal system0Least 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 variant7.376e-05Least 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 variant3.889e-05Moderately InformativeDirect
Worm Phenotype (WP)organ system development variant8.275e-05Moderately 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 variant1.4e-05InformativeDirect
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 reduced3.662e-07Highly InformativeDirect
Worm Phenotype (WP)cell secretion variant6.399e-05Highly InformativeDirect
Worm Phenotype (WP)oocyte septum formation variant6.742e-05Highly 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 transport0.02244InformativeInherited
Yeast Phenotype (YP)protein transport0.002125Highly 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 cell4.446e-05InformativeDirect
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 processExocytosis1.12e-07Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Cellular componentEndosome1.448e-09Moderately InformativeDirect
Cellular componentCell junction0.001252Moderately InformativeInherited
Cellular componentLysosome2.263e-07InformativeDirect
Cellular componentSynapse1.123e-06InformativeDirect
Cellular componentCoated pit0Highly InformativeDirect
Cellular componentSynaptosome6.639e-06Highly InformativeDirect
DomainTransmembrane9.561e-06Least InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
Molecular functionLipid-binding5.879e-07InformativeDirect
Post-translational modificationAcetylation6.345e-06Least InformativeDirect
Post-translational modificationPhosphoprotein9.534e-06Least InformativeDirect
Post-translational modificationPalmitate7.418e-14Moderately InformativeDirect
Post-translational modificationMethylation4.247e-09Moderately 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 ]