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 process4.982e-080.000866Least InformativeDirect
Biological Process (BP)localization00Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis2.88e-080.0007503Least InformativeDirect
Biological Process (BP)regulation of cellular process0.64010.9822Least InformativeInherited
Biological Process (BP)response to stimulus0.0014790.377Least InformativeInherited
Biological Process (BP)multicellular organismal process0.0010240.5836Least InformativeInherited
Biological Process (BP)regulation of localization1.815e-081.078e-07Moderately InformativeDirect
Biological Process (BP)cellular localization00Moderately InformativeDirect
Biological Process (BP)organelle organization0.032040.0549Moderately InformativeInherited
Biological Process (BP)regulation of cellular component organization0.0056820.01357Moderately InformativeInherited
Biological Process (BP)macromolecule localization0.51210.5795Moderately InformativeInherited
Biological Process (BP)organic substance transport10.8851Moderately InformativeInherited
Biological Process (BP)immune system process5.653e-050.005585Moderately InformativeInherited
Biological Process (BP)system process0.51670.2877Moderately InformativeInherited
Biological Process (BP)protein transport0.00096610.0007124InformativeDirect
Biological Process (BP)cellular membrane organization0.00078331.387e-05InformativeDirect
Biological Process (BP)vesicle-mediated transport1.225e-116.856e-12InformativeDirect
Biological Process (BP)secretion by cell00InformativeDirect
Biological Process (BP)regulation of cellular component biogenesis2.787e-061.131e-05InformativeDirect
Biological Process (BP)organelle localization0.17210.5903InformativeInherited
Biological Process (BP)protein localization to organelle0.057040.07558InformativeInherited
Biological Process (BP)regulation of organelle organization0.0013530.0007589InformativeInherited
Biological Process (BP)cytoplasmic transport0.093230.1088InformativeInherited
Biological Process (BP)immune effector process0.071040.02654InformativeInherited
Biological Process (BP)immune response0.00720.003988InformativeInherited
Biological Process (BP)leukocyte activation0.0077770.01849InformativeInherited
Biological Process (BP)synaptic transmission0.21960.2696InformativeInherited
Biological Process (BP)regulation of neurotransmitter levels0.00030112.4e-05Highly InformativeDirect
Biological Process (BP)myeloid leukocyte activation2.966e-081.691e-07Highly InformativeDirect
Biological Process (BP)leukocyte activation involved in immune response3.21e-086.255e-07Highly InformativeDirect
Biological Process (BP)leukocyte mediated immunity2.138e-057.339e-06Highly InformativeDirect
Biological Process (BP)exocytosis3.487e-097.926e-09Highly InformativeDirect
Biological Process (BP)vesicle organization3.933e-098.46e-13Highly InformativeDirect
Biological Process (BP)regulation of protein complex assembly1.621e-052.161e-06Highly InformativeDirect
Biological Process (BP)Golgi vesicle transport6.648e-052.696e-05Highly InformativeDirect
Biological Process (BP)organelle fusion0.00070514.929e-07Highly InformativeDirect
Biological Process (BP)membrane fusion0.00086452.191e-05Highly InformativeDirect
Biological Process (BP)establishment of synaptic vesicle localization3.992e-071.563e-06Highly InformativeDirect
Biological Process (BP)establishment of protein localization to organelle0.015950.00803Highly InformativeInherited
Molecular Function (MF)binding8.405e-080.04886Least InformativeInherited
Cellular Component (CC)membrane01.696e-10Least InformativeDirect
Cellular Component (CC)cytoplasmic part3.515e-078.059e-08Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.039680.154Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.011420.01159Least InformativeInherited
Cellular Component (CC)protein complex6.754e-060.003365Least InformativeInherited
Cellular Component (CC)organelle membrane8.864e-071.305e-08Moderately InformativeDirect
Cellular Component (CC)vesicle0.00015271.825e-05Moderately InformativeDirect
Cellular Component (CC)plasma membrane0.0033270.007218Moderately InformativeInherited
Cellular Component (CC)endosome1.001e-073.822e-08InformativeDirect
Cellular Component (CC)Golgi apparatus0.00018880.0004225InformativeDirect
Cellular Component (CC)vacuolar part4.769e-111.954e-11InformativeDirect
Cellular Component (CC)secretory granule0.018330.001735InformativeInherited
Cellular Component (CC)apical plasma membrane4.708e-101.268e-07Highly InformativeDirect
Cellular Component (CC)endosomal part7.779e-076.933e-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 0.000866 Least Informative Direct
Biological Process (BP) localization 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0007503 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.9822 Least Informative Inherited
Biological Process (BP) response to stimulus 0.377 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.5836 Least Informative Inherited
Biological Process (BP) regulation of localization 1.078e-07 Moderately Informative Direct
Biological Process (BP) cellular localization 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.01357 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.5795 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.8851 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.0549 Moderately Informative Inherited
Biological Process (BP) immune system process 0.005585 Moderately Informative Inherited
Biological Process (BP) system process 0.2877 Moderately Informative Inherited
Biological Process (BP) protein transport 0.0007124 Informative Direct
Biological Process (BP) cellular membrane organization 1.387e-05 Informative Direct
Biological Process (BP) vesicle-mediated transport 6.856e-12 Informative Direct
Biological Process (BP) secretion by cell 0 Informative Direct
Biological Process (BP) regulation of organelle organization 0.0007589 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 1.131e-05 Informative Direct
Biological Process (BP) organelle localization 0.5903 Informative Inherited
Biological Process (BP) protein localization to organelle 0.07558 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.1088 Informative Inherited
Biological Process (BP) immune effector process 0.02654 Informative Inherited
Biological Process (BP) immune response 0.003988 Informative Inherited
Biological Process (BP) leukocyte activation 0.01849 Informative Inherited
Biological Process (BP) synaptic transmission 0.2696 Informative Inherited
Biological Process (BP) regulation of neurotransmitter levels 2.4e-05 Highly Informative Direct
Biological Process (BP) myeloid leukocyte activation 1.691e-07 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 6.255e-07 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 7.339e-06 Highly Informative Direct
Biological Process (BP) exocytosis 7.926e-09 Highly Informative Direct
Biological Process (BP) vesicle organization 8.46e-13 Highly Informative Direct
Biological Process (BP) regulation of protein complex assembly 2.161e-06 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 2.696e-05 Highly Informative Direct
Biological Process (BP) organelle fusion 4.929e-07 Highly Informative Direct
Biological Process (BP) membrane fusion 2.191e-05 Highly Informative Direct
Biological Process (BP) establishment of synaptic vesicle localization 1.563e-06 Highly Informative Direct
Biological Process (BP) establishment of protein localization to organelle 0.00803 Highly Informative Inherited
Molecular Function (MF) binding 0.04886 Least Informative Inherited
Cellular Component (CC) membrane 1.696e-10 Least Informative Direct
Cellular Component (CC) cytoplasmic part 8.059e-08 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.154 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.01159 Least Informative Inherited
Cellular Component (CC) protein complex 0.003365 Least Informative Inherited
Cellular Component (CC) organelle membrane 1.305e-08 Moderately Informative Direct
Cellular Component (CC) vesicle 1.825e-05 Moderately Informative Direct
Cellular Component (CC) plasma membrane 0.007218 Moderately Informative Inherited
Cellular Component (CC) endosome 3.822e-08 Informative Direct
Cellular Component (CC) Golgi apparatus 0.0004225 Informative Direct
Cellular Component (CC) vacuolar part 1.954e-11 Informative Direct
Cellular Component (CC) secretory granule 0.001735 Informative Inherited
Cellular Component (CC) apical plasma membrane 1.268e-07 Highly Informative Direct
Cellular Component (CC) endosomal part 6.933e-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 ]