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 (487) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,303 3,831 3
Proteins 3,155 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)localization00Least InformativeDirect
Biological Process (BP)single-organism cellular process0.000000083650.004756Least InformativeInherited
Biological Process (BP)regulation of cellular process0.71061Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.000038310.04078Least InformativeInherited
Biological Process (BP)response to stimulus0.0019530.4663Least InformativeInherited
Biological Process (BP)regulation of localization0.000000093950.0000009806Moderately InformativeDirect
Biological Process (BP)cellular localization00Moderately InformativeDirect
Biological Process (BP)organelle organization0.19560.2523Moderately InformativeInherited
Biological Process (BP)regulation of cellular component organization0.0040430.01763Moderately InformativeInherited
Biological Process (BP)macromolecule localization0.46680.522Moderately InformativeInherited
Biological Process (BP)organic substance transport0.98340.8454Moderately InformativeInherited
Biological Process (BP)immune system process0.000071330.007527Moderately InformativeInherited
Biological Process (BP)protein transport0.00096140.0007164InformativeDirect
Biological Process (BP)cellular membrane organization0.00060050.00001044InformativeDirect
Biological Process (BP)vesicle-mediated transport0.000000000029310.00000000001595InformativeDirect
Biological Process (BP)secretion by cell00InformativeDirect
Biological Process (BP)regulation of organelle organization0.00087810.0009561InformativeDirect
Biological Process (BP)regulation of cellular component biogenesis0.0000018940.00001542InformativeDirect
Biological Process (BP)protein localization to organelle0.057590.0808InformativeInherited
Biological Process (BP)organelle localization0.27790.7292InformativeInherited
Biological Process (BP)cytoplasmic transport0.094890.1085InformativeInherited
Biological Process (BP)cell-cell signaling0.00024450.01046InformativeInherited
Biological Process (BP)immune effector process0.071570.02668InformativeInherited
Biological Process (BP)immune response0.0074360.003934InformativeInherited
Biological Process (BP)leukocyte activation0.0079240.0184InformativeInherited
Biological Process (BP)myeloid leukocyte activation0.000000034540.0000002164Highly InformativeDirect
Biological Process (BP)leukocyte activation involved in immune response0.00000003740.000000743Highly InformativeDirect
Biological Process (BP)leukocyte mediated immunity0.000024810.000009509Highly InformativeDirect
Biological Process (BP)exocytosis0.000000016940.00000003321Highly InformativeDirect
Biological Process (BP)vesicle organization0.0000000054820.000000000001333Highly InformativeDirect
Biological Process (BP)regulation of protein complex assembly0.000017160.000002106Highly InformativeDirect
Biological Process (BP)Golgi vesicle transport0.000053590.00002195Highly InformativeDirect
Biological Process (BP)organelle fusion0.00018330.0000000673Highly InformativeDirect
Biological Process (BP)establishment of protein localization to organelle0.016420.008113Highly InformativeInherited
Molecular Function (MF)binding0.0000008160.1697Least InformativeInherited
Cellular Component (CC)membrane00.0000000004322Least InformativeDirect
Cellular Component (CC)cytoplasmic part0.00000045140.000000944Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.030540.1274Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.014740.04015Least InformativeInherited
Cellular Component (CC)protein complex0.0000095310.005502Least InformativeInherited
Cellular Component (CC)organelle membrane0.00000076940.00000001042Moderately InformativeDirect
Cellular Component (CC)vesicle0.000069150.000007815Moderately InformativeDirect
Cellular Component (CC)plasma membrane0.0012050.003796Moderately InformativeInherited
Cellular Component (CC)endosome0.0000006840.0000002716InformativeDirect
Cellular Component (CC)Golgi apparatus0.00016780.0003726InformativeDirect
Cellular Component (CC)vacuolar part0.000000000036170.00000000001464InformativeDirect
Cellular Component (CC)secretory granule0.018280.001723InformativeInherited
Cellular Component (CC)apical plasma membrane0.00000000059660.0000001795Highly InformativeDirect
Cellular Component (CC)endosomal part0.00000056870.0000005639Highly 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) localization 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.04078 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.004756 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.4663 Least Informative Inherited
Biological Process (BP) regulation of localization 0.0000009806 Moderately Informative Direct
Biological Process (BP) cellular localization 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.01763 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.522 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.8454 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.2523 Moderately Informative Inherited
Biological Process (BP) immune system process 0.007527 Moderately Informative Inherited
Biological Process (BP) protein transport 0.0007164 Informative Direct
Biological Process (BP) cellular membrane organization 0.00001044 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.00000000001595 Informative Direct
Biological Process (BP) secretion by cell 0 Informative Direct
Biological Process (BP) regulation of organelle organization 0.0009561 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.00001542 Informative Direct
Biological Process (BP) protein localization to organelle 0.0808 Informative Inherited
Biological Process (BP) organelle localization 0.7292 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.1085 Informative Inherited
Biological Process (BP) cell-cell signaling 0.01046 Informative Inherited
Biological Process (BP) immune effector process 0.02668 Informative Inherited
Biological Process (BP) immune response 0.003934 Informative Inherited
Biological Process (BP) leukocyte activation 0.0184 Informative Inherited
Biological Process (BP) myeloid leukocyte activation 0.0000002164 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 0.000000743 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 0.000009509 Highly Informative Direct
Biological Process (BP) exocytosis 0.00000003321 Highly Informative Direct
Biological Process (BP) cellular membrane fusion 0.0003134 Highly Informative Direct
Biological Process (BP) vesicle organization 0.000000000001333 Highly Informative Direct
Biological Process (BP) regulation of protein complex assembly 0.000002106 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 0.00002195 Highly Informative Direct
Biological Process (BP) organelle fusion 0.0000000673 Highly Informative Direct
Biological Process (BP) establishment of protein localization to organelle 0.008113 Highly Informative Inherited
Molecular Function (MF) binding 0.1697 Least Informative Inherited
Cellular Component (CC) membrane 0.0000000004322 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.000000944 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.1274 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.04015 Least Informative Inherited
Cellular Component (CC) protein complex 0.005502 Least Informative Inherited
Cellular Component (CC) organelle membrane 0.00000001042 Moderately Informative Direct
Cellular Component (CC) vesicle 0.000007815 Moderately Informative Direct
Cellular Component (CC) plasma membrane 0.003796 Moderately Informative Inherited
Cellular Component (CC) endosome 0.0000002716 Informative Direct
Cellular Component (CC) Golgi apparatus 0.0003726 Informative Direct
Cellular Component (CC) vacuolar part 0.00000000001464 Informative Direct
Cellular Component (CC) secretory granule 0.001723 Informative Inherited
Cellular Component (CC) apical plasma membrane 0.0000001795 Highly Informative Direct
Cellular Component (CC) endosomal part 0.0000005639 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 defect0.00004944Moderately InformativeDirect
Worm Phenotype (WP)protein aggregation variant0.00008919Moderately 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 variant0.00001124InformativeDirect
Worm Phenotype (WP)accumulated germline cell corpses0.000004394Highly 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

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 transport0.0004214Highly InformativeDirect
Cellular componentMembrane0.0000000000002258Least InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentGolgi apparatus0.000000000001828Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.0001182Moderately 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 ]