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 (499) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,415 3,831 3
Proteins 3,264 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)cellular component organization or biogenesis0.0000000003730.00008492Least InformativeDirect
Biological Process (BP)regulation of cellular process0.70330.9337Least InformativeInherited
Biological Process (BP)response to stimulus0.00076460.3012Least InformativeInherited
Biological Process (BP)single-organism cellular process0.0023410.07699Least InformativeInherited
Biological Process (BP)regulation of localization0.0000000061470.00000003094Moderately InformativeDirect
Biological Process (BP)cellular localization0.000000000093740.0000000000775Moderately InformativeDirect
Biological Process (BP)regulation of cellular component organization0.011140.01923Moderately InformativeInherited
Biological Process (BP)immune system process0.000058210.005638Moderately InformativeInherited
Biological Process (BP)macromolecule localization0.53560.5909Moderately InformativeInherited
Biological Process (BP)organic substance transport10.908Moderately InformativeInherited
Biological Process (BP)regulation of biological quality0.018050.03692Moderately InformativeInherited
Biological Process (BP)protein transport0.00022110.00003008InformativeDirect
Biological Process (BP)vesicle-mediated transport0.0000000000099220.000000000005866InformativeDirect
Biological Process (BP)secretion by cell00InformativeDirect
Biological Process (BP)regulation of cellular component biogenesis0.0000056360.00001806InformativeDirect
Biological Process (BP)single-organism membrane organization0.0002060.000006428InformativeDirect
Biological Process (BP)regulation of vesicle-mediated transport00InformativeDirect
Biological Process (BP)organelle localization0.22080.6384InformativeInherited
Biological Process (BP)regulation of organelle organization0.0021490.001373InformativeInherited
Biological Process (BP)single-organism intracellular transport0.023190.1043InformativeInherited
Biological Process (BP)protein localization to organelle0.059480.0739InformativeInherited
Biological Process (BP)cytoplasmic transport0.20520.242InformativeInherited
Biological Process (BP)single-organism cellular localization0.44520.7139InformativeInherited
Biological Process (BP)immune effector process0.070830.02634InformativeInherited
Biological Process (BP)immune response0.0084520.00486InformativeInherited
Biological Process (BP)leukocyte activation0.0076940.01831InformativeInherited
Biological Process (BP)synaptic transmission0.00053190.005469InformativeInherited
Biological Process (BP)regulation of neurotransmitter levels0.0002870.00002544Highly InformativeDirect
Biological Process (BP)myeloid leukocyte activation0.000000030030.0000001751Highly InformativeDirect
Biological Process (BP)leukocyte activation involved in immune response0.000000032490.000000612Highly InformativeDirect
Biological Process (BP)leukocyte mediated immunity0.000021660.000007848Highly InformativeDirect
Biological Process (BP)exocytosis0.0000000066840.0000000165Highly InformativeDirect
Biological Process (BP)vesicle organization0.0000000032180.000000000001077Highly InformativeDirect
Biological Process (BP)regulation of protein complex assembly0.000011590.000001814Highly InformativeDirect
Biological Process (BP)organelle fusion0.000088550.00000003006Highly InformativeDirect
Biological Process (BP)membrane fusion0.00011330.000002518Highly InformativeDirect
Biological Process (BP)establishment of synaptic vesicle localization0.0000005130.000001741Highly InformativeDirect
Molecular Function (MF)binding0.000000046230.02849Least InformativeInherited
Cellular Component (CC)membrane00.00000000004139Least InformativeDirect
Cellular Component (CC)cytoplasmic part0.00000060090.0000002628Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.18240.4003Least InformativeInherited
Cellular Component (CC)protein complex0.0000017070.001286Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.007360.01228Least InformativeInherited
Cellular Component (CC)vesicle0.000022460.000002584Moderately InformativeDirect
Cellular Component (CC)bounding membrane of organelle0.00000010950.000001663Moderately InformativeDirect
Cellular Component (CC)plasma membrane part0.040820.2861Moderately InformativeInherited
Cellular Component (CC)membrane region0.12870.2846Moderately InformativeInherited
Cellular Component (CC)endosome0.000000097360.00000004013InformativeDirect
Cellular Component (CC)Golgi apparatus0.000014240.00003684InformativeDirect
Cellular Component (CC)secretory granule0.00064880.00005977InformativeDirect
Cellular Component (CC)vacuolar part0.0008220.0002954InformativeDirect
Cellular Component (CC)plasma membrane region0.0020250.0109InformativeInherited
Cellular Component (CC)apical plasma membrane0.000012350.0001501Highly InformativeDirect
Cellular Component (CC)endosomal part0.00000073090.0000006127Highly 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 0.00008492 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.9337 Least Informative Inherited
Biological Process (BP) response to stimulus 0.3012 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.07699 Least Informative Inherited
Biological Process (BP) regulation of localization 0.00000003094 Moderately Informative Direct
Biological Process (BP) cellular localization 0.0000000000775 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.01923 Moderately Informative Inherited
Biological Process (BP) immune system process 0.005638 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.5909 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.908 Moderately Informative Inherited
Biological Process (BP) single-organism organelle organization 0.06624 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.03692 Moderately Informative Inherited
Biological Process (BP) protein transport 0.00003008 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.000000000005866 Informative Direct
Biological Process (BP) secretion by cell 0 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.00001806 Informative Direct
Biological Process (BP) single-organism membrane organization 0.000006428 Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 0 Informative Direct
Biological Process (BP) organelle localization 0.6384 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.001373 Informative Inherited
Biological Process (BP) single-organism intracellular transport 0.1043 Informative Inherited
Biological Process (BP) protein localization to organelle 0.0739 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.242 Informative Inherited
Biological Process (BP) single-organism cellular localization 0.7139 Informative Inherited
Biological Process (BP) immune effector process 0.02634 Informative Inherited
Biological Process (BP) immune response 0.00486 Informative Inherited
Biological Process (BP) leukocyte activation 0.01831 Informative Inherited
Biological Process (BP) synaptic transmission 0.005469 Informative Inherited
Biological Process (BP) regulation of neurotransmitter levels 0.00002544 Highly Informative Direct
Biological Process (BP) myeloid leukocyte activation 0.0000001751 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 0.000000612 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 0.000007848 Highly Informative Direct
Biological Process (BP) exocytosis 0.0000000165 Highly Informative Direct
Biological Process (BP) vesicle organization 0.000000000001077 Highly Informative Direct
Biological Process (BP) regulation of protein complex assembly 0.000001814 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 0.0007117 Highly Informative Direct
Biological Process (BP) organelle fusion 0.00000003006 Highly Informative Direct
Biological Process (BP) membrane fusion 0.000002518 Highly Informative Direct
Biological Process (BP) establishment of synaptic vesicle localization 0.000001741 Highly Informative Direct
Molecular Function (MF) binding 0.02849 Least Informative Inherited
Cellular Component (CC) membrane 0.00000000004139 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.0000002628 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.4003 Least Informative Inherited
Cellular Component (CC) protein complex 0.001286 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.01228 Least Informative Inherited
Cellular Component (CC) vesicle 0.000002584 Moderately Informative Direct
Cellular Component (CC) bounding membrane of organelle 0.000001663 Moderately Informative Direct
Cellular Component (CC) plasma membrane part 0.2861 Moderately Informative Inherited
Cellular Component (CC) membrane region 0.2846 Moderately Informative Inherited
Cellular Component (CC) endosome 0.00000004013 Informative Direct
Cellular Component (CC) Golgi apparatus 0.00003684 Informative Direct
Cellular Component (CC) secretory granule 0.00005977 Informative Direct
Cellular Component (CC) vacuolar part 0.0002954 Informative Direct
Cellular Component (CC) plasma membrane region 0.0109 Informative Inherited
Cellular Component (CC) apical plasma membrane 0.0001501 Highly Informative Direct
Cellular Component (CC) endosomal part 0.0000006127 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
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 transport0.0004159Highly InformativeDirect
Cellular componentMembrane0.0000000000002405Least InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentGolgi apparatus0.000000000001879Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.0001222Moderately 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 ]