SUPERFAMILY 1.75 HMM library and genome assignments server

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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 (507) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 12,025 32,381 11
Proteins 11,964 32,260 11


Functional annotation
General category General
Detailed category Protein interaction

Document:
Function annotation of SCOP domain superfamilies

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell morphology variant0.0000007031Least InformativeDirect
Worm Phenotype (WP)blast cell physiology variant0.00001413Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.00001419Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.00003185Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.00009922Least InformativeDirect
Worm Phenotype (WP)cell development variant0.0002632Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.2783Least InformativeInherited
Worm Phenotype (WP)larval development variant0.3873Least InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant0.00000001272Moderately InformativeDirect
Worm Phenotype (WP)body region morphology variant0.00006663Moderately InformativeDirect
Worm Phenotype (WP)organism segment morphology variant0.00006663Moderately InformativeDirect
Worm Phenotype (WP)developmental morphology variant0.00006703Moderately InformativeDirect
Worm Phenotype (WP)adult body morphology variant0.00006742Moderately InformativeDirect
Worm Phenotype (WP)body morphology variant0.0000777Moderately InformativeDirect
Worm Phenotype (WP)germ cell differentiation variant0.0004697Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.0006555Moderately InformativeDirect
Worm Phenotype (WP)germ cell development variant0.006994Moderately InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.0249Moderately InformativeInherited
Worm Phenotype (WP)drug response variant0.03281Moderately InformativeInherited
Worm Phenotype (WP)metabolic pathway variant0.06444Moderately InformativeInherited
Worm Phenotype (WP)nervous system morphology variant0.2434Moderately InformativeInherited
Worm Phenotype (WP)cell organization biogenesis variant0.3193Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.4996Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.6344Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.7015Moderately InformativeInherited
Worm Phenotype (WP)vesicle morphology variant0.00007571InformativeDirect
Worm Phenotype (WP)sick0.00009997InformativeDirect
Worm Phenotype (WP)tail morphology variant0.0001649InformativeDirect
Worm Phenotype (WP)sensillum morphology variant0.0003697InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant0.0006386InformativeDirect
Worm Phenotype (WP)protein metabolism variant0.0008983InformativeDirect
Worm Phenotype (WP)nuclear positioning variant0.0009048InformativeDirect
Worm Phenotype (WP)aldicarb response variant0.001092InformativeInherited
Worm Phenotype (WP)somatic gonad development variant0.002282InformativeInherited
Worm Phenotype (WP)pigmentation variant0.002684InformativeInherited
Worm Phenotype (WP)drug resistant0.003826InformativeInherited
Worm Phenotype (WP)mitosis variant0.006388InformativeInherited
Worm Phenotype (WP)alimentary system development variant0.08053InformativeInherited
Worm Phenotype (WP)meiotic chromosome organization variant0.08896InformativeInherited
Worm Phenotype (WP)gut granule development variant0.00001279Highly InformativeDirect
Worm Phenotype (WP)molt variant0.00004254Highly InformativeDirect
Worm Phenotype (WP)oocyte septum formation variant0.00008028Highly InformativeDirect
Worm Phenotype (WP)lysosome organization biogenesis variant0.0000982Highly InformativeDirect
Worm Phenotype (WP)clear0.0001729Highly InformativeDirect
Worm Phenotype (WP)dumpy0.0001791Highly InformativeDirect
Worm Phenotype (WP)chromosome condensation variant0.0002372Highly InformativeDirect
Worm Phenotype (WP)aldicarb resistant0.0003854Highly InformativeDirect
Worm Phenotype (WP)cell secretion variant0.000388Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)intracellular transport0.03124InformativeInherited
Yeast Phenotype (YP)protein transport0.004068Highly InformativeInherited

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0Least InformativeDirect

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)organism subdivision0Least InformativeDirect

Document: ZA 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 cell0.00004523InformativeDirect
Plant structure DEvelopment stage (PDE)pollen development stage0.0001202Moderately InformativeDirect

Document: AP 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 · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) ]

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 8 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 8 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 · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Internal database links ]