SUPERFAMILY 1.75 HMM library and genome assignments server


Sec1/munc18-like (SM) proteins superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Multi-domain proteins (alpha and beta) [ 56572] (66)
Fold:   Sec1/munc18-like (SM) proteins [ 56814]
Superfamily:   Sec1/munc18-like (SM) proteins [ 56815]
Families:   Sec1/munc18-like (SM) proteins [ 56816] (2)


Superfamily statistics
Genomes (498) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,404 3,831 3
Proteins 3,253 3,737 3


Functional annotation
General category coiled coil
Detailed category This is a complex coiled arrangement. The details of which will appear on this page shortly (some coiled coil details are being checked before they are included on the site). If you want to see examples of the states please click here here. If you require further details urgently please contact Owen Rackham

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 process4.365e-080.0004134Least InformativeDirect
Biological Process (BP)localization00Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis2.075e-080.0004738Least InformativeDirect
Biological Process (BP)regulation of cellular process0.63650.9407Least InformativeInherited
Biological Process (BP)response to stimulus0.0012440.3251Least InformativeInherited
Biological Process (BP)multicellular organismal process0.00079270.5172Least InformativeInherited
Biological Process (BP)regulation of localization1.895e-087.341e-08Moderately InformativeDirect
Biological Process (BP)cellular localization00Moderately InformativeDirect
Biological Process (BP)macromolecule localization0.51840.5807Moderately InformativeInherited
Biological Process (BP)organelle organization0.031020.05405Moderately InformativeInherited
Biological Process (BP)regulation of cellular component organization0.0053580.01149Moderately InformativeInherited
Biological Process (BP)organic substance transport10.8848Moderately InformativeInherited
Biological Process (BP)immune system process4.706e-050.00447Moderately InformativeInherited
Biological Process (BP)system process0.51760.2876Moderately InformativeInherited
Biological Process (BP)regulation of biological quality0.01280.0307Moderately InformativeInherited
Biological Process (BP)cellular membrane organization0.00073961.385e-05InformativeDirect
Biological Process (BP)vesicle-mediated transport1.253e-118.238e-12InformativeDirect
Biological Process (BP)secretion by cell00InformativeDirect
Biological Process (BP)regulation of cellular component biogenesis2.931e-061.074e-05InformativeDirect
Biological Process (BP)regulation of vesicle-mediated transport1.684e-150InformativeDirect
Biological Process (BP)organelle localization0.17790.5844InformativeInherited
Biological Process (BP)protein localization to organelle0.054840.07424InformativeInherited
Biological Process (BP)regulation of organelle organization0.0012830.0006956InformativeInherited
Biological Process (BP)protein transport0.001040.0007607InformativeInherited
Biological Process (BP)cytoplasmic transport0.095280.1096InformativeInherited
Biological Process (BP)immune effector process0.071120.02603InformativeInherited
Biological Process (BP)immune response0.0067740.003848InformativeInherited
Biological Process (BP)leukocyte activation0.0077580.01854InformativeInherited
Biological Process (BP)synaptic transmission0.21980.2714InformativeInherited
Biological Process (BP)regulation of neurotransmitter levels0.00028532.343e-05Highly InformativeDirect
Biological Process (BP)myeloid leukocyte activation2.625e-081.42e-07Highly InformativeDirect
Biological Process (BP)leukocyte activation involved in immune response2.841e-085.261e-07Highly InformativeDirect
Biological Process (BP)leukocyte mediated immunity1.914e-056.208e-06Highly InformativeDirect
Biological Process (BP)exocytosis4.212e-098.595e-09Highly InformativeDirect
Biological Process (BP)vesicle organization3.812e-099.371e-13Highly InformativeDirect
Biological Process (BP)regulation of protein complex assembly1.79e-052.258e-06Highly InformativeDirect
Biological Process (BP)Golgi vesicle transport6.774e-052.862e-05Highly InformativeDirect
Biological Process (BP)organelle fusion0.0006975.31e-07Highly InformativeDirect
Biological Process (BP)membrane fusion0.0008822.273e-05Highly InformativeDirect
Biological Process (BP)establishment of synaptic vesicle localization4.257e-071.405e-06Highly InformativeDirect
Biological Process (BP)establishment of protein localization to organelle0.014620.007845Highly InformativeInherited
Molecular Function (MF)binding3.892e-080.02451Least InformativeInherited
Cellular Component (CC)membrane04.747e-11Least InformativeDirect
Cellular Component (CC)cytoplasmic part3.636e-072.583e-08Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.039910.151Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.011560.01091Least InformativeInherited
Cellular Component (CC)protein complex5.261e-060.00241Least InformativeInherited
Cellular Component (CC)organelle membrane8.737e-071.314e-08Moderately InformativeDirect
Cellular Component (CC)vesicle0.00015671.935e-05Moderately InformativeDirect
Cellular Component (CC)plasma membrane0.0034480.007485Moderately InformativeInherited
Cellular Component (CC)endosome1.157e-074.347e-08InformativeDirect
Cellular Component (CC)Golgi apparatus0.00018890.0004196InformativeDirect
Cellular Component (CC)vacuolar part5.003e-112.013e-11InformativeDirect
Cellular Component (CC)secretory granule0.018130.001678InformativeInherited
Cellular Component (CC)apical plasma membrane3.995e-101.093e-07Highly InformativeDirect
Cellular Component (CC)endosomal part7.784e-076.881e-07Highly InformativeDirect

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 0.0004134 Least Informative Direct
Biological Process (BP) localization 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0004738 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.9407 Least Informative Inherited
Biological Process (BP) response to stimulus 0.3251 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.5172 Least Informative Inherited
Biological Process (BP) regulation of localization 7.341e-08 Moderately Informative Direct
Biological Process (BP) cellular localization 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.01149 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.5807 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.8848 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.05405 Moderately Informative Inherited
Biological Process (BP) immune system process 0.00447 Moderately Informative Inherited
Biological Process (BP) system process 0.2876 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.0307 Moderately Informative Inherited
Biological Process (BP) protein transport 0.0007607 Informative Direct
Biological Process (BP) cellular membrane organization 1.385e-05 Informative Direct
Biological Process (BP) vesicle-mediated transport 8.238e-12 Informative Direct
Biological Process (BP) secretion by cell 0 Informative Direct
Biological Process (BP) regulation of organelle organization 0.0006956 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 1.074e-05 Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 0 Informative Direct
Biological Process (BP) organelle localization 0.5844 Informative Inherited
Biological Process (BP) protein localization to organelle 0.07424 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.1096 Informative Inherited
Biological Process (BP) immune effector process 0.02603 Informative Inherited
Biological Process (BP) immune response 0.003848 Informative Inherited
Biological Process (BP) leukocyte activation 0.01854 Informative Inherited
Biological Process (BP) synaptic transmission 0.2714 Informative Inherited
Biological Process (BP) regulation of neurotransmitter levels 2.343e-05 Highly Informative Direct
Biological Process (BP) myeloid leukocyte activation 1.42e-07 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 5.261e-07 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 6.208e-06 Highly Informative Direct
Biological Process (BP) exocytosis 8.595e-09 Highly Informative Direct
Biological Process (BP) vesicle organization 9.371e-13 Highly Informative Direct
Biological Process (BP) regulation of protein complex assembly 2.258e-06 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 2.862e-05 Highly Informative Direct
Biological Process (BP) organelle fusion 5.31e-07 Highly Informative Direct
Biological Process (BP) membrane fusion 2.273e-05 Highly Informative Direct
Biological Process (BP) establishment of synaptic vesicle localization 1.405e-06 Highly Informative Direct
Biological Process (BP) establishment of protein localization to organelle 0.007845 Highly Informative Inherited
Molecular Function (MF) binding 0.02451 Least Informative Inherited
Cellular Component (CC) membrane 4.747e-11 Least Informative Direct
Cellular Component (CC) cytoplasmic part 2.583e-08 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.151 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.01091 Least Informative Inherited
Cellular Component (CC) protein complex 0.00241 Least Informative Inherited
Cellular Component (CC) organelle membrane 1.314e-08 Moderately Informative Direct
Cellular Component (CC) vesicle 1.935e-05 Moderately Informative Direct
Cellular Component (CC) plasma membrane 0.007485 Moderately Informative Inherited
Cellular Component (CC) endosome 4.347e-08 Informative Direct
Cellular Component (CC) Golgi apparatus 0.0004196 Informative Direct
Cellular Component (CC) vacuolar part 2.013e-11 Informative Direct
Cellular Component (CC) secretory granule 0.001678 Informative Inherited
Cellular Component (CC) apical plasma membrane 1.093e-07 Highly Informative Direct
Cellular Component (CC) endosomal part 6.881e-07 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)growth variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.0002382Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.00193Least InformativeInherited
Worm Phenotype (WP)endocytic transport defect4.944e-05Moderately InformativeDirect
Worm Phenotype (WP)protein aggregation variant8.919e-05Moderately InformativeDirect
Worm Phenotype (WP)organ system development variant0.0003446Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.0009528Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.00286Moderately InformativeInherited
Worm Phenotype (WP)cell death variant0.05475Moderately InformativeInherited
Worm Phenotype (WP)cell corpse number variant1.124e-05InformativeDirect
Worm Phenotype (WP)accumulated germline cell corpses4.394e-06Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0Least InformativeDirect
Fly Phenotype (FP)lethal - all die before end of P-stage0Moderately InformativeDirect
Fly Phenotype (FP)lethal - all die before end of larval stage0InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0Least InformativeDirect
Fly Anatomy (FA)multi-tissue structure0Least InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least 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 processER-Golgi transport0.0004185Highly InformativeDirect
Cellular componentMembrane2.311e-13Least InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentGolgi apparatus1.8e-12Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.0001174Moderately InformativeDirect
Cellular componentLysosome0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001619 SSF56815 Protein matches
Abstract

Sec1-like molecules have been implicated in a variety of eukaryotic vesicle transport processes including neurotransmitter release by exocytosis [PubMed8769846]. They regulate vesicle transport by binding to a t-SNARE from the syntaxin family. This process is thought to prevent SNARE complex formation, a protein complex required for membrane fusion. Whereas Sec1 molecules are essential for neurotransmitter release and other secretory events, their interaction with syntaxin molecules seems to represent a negative regulatory step in secretion [PubMed10903948].


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 Phenotype (FP) · 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 3 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 Sec1/munc18-like (SM) 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 3 hidden Markov models representing the Sec1/munc18-like (SM) 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 Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]