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 (447) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 3,095 2,628 3
Proteins 2,967 2,572 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 process6.985e-080.00159Least InformativeInherited
Biological Process (BP)regulation of cellular process0.71221Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis2.202e-050.01915Least InformativeInherited
Biological Process (BP)response to stimulus0.0011420.3185Least InformativeInherited
Biological Process (BP)regulation of localization6.119e-082.75e-07Moderately InformativeDirect
Biological Process (BP)cellular localization00Moderately InformativeDirect
Biological Process (BP)macromolecule localization0.44470.627Moderately InformativeInherited
Biological Process (BP)organelle organization0.19350.224Moderately InformativeInherited
Biological Process (BP)regulation of cellular component organization0.0044680.01065Moderately InformativeInherited
Biological Process (BP)organic substance transport0.97930.9203Moderately InformativeInherited
Biological Process (BP)immune system process3.536e-050.003626Moderately InformativeInherited
Biological Process (BP)vesicle-mediated transport3.708e-113.667e-12InformativeDirect
Biological Process (BP)secretion by cell00InformativeDirect
Biological Process (BP)regulation of cellular component biogenesis2.246e-067.615e-06InformativeDirect
Biological Process (BP)membrane organization4.644e-061.418e-08InformativeDirect
Biological Process (BP)protein localization to organelle0.06170.03417InformativeInherited
Biological Process (BP)organelle localization0.27550.6924InformativeInherited
Biological Process (BP)regulation of organelle organization0.001020.000583InformativeInherited
Biological Process (BP)protein transport0.00086050.001393InformativeInherited
Biological Process (BP)cytoplasmic transport0.10510.06768InformativeInherited
Biological Process (BP)cell-cell signaling0.00022350.006867InformativeInherited
Biological Process (BP)immune effector process0.085250.0317InformativeInherited
Biological Process (BP)immune response0.0066270.003734InformativeInherited
Biological Process (BP)cell activation0.0043830.01249InformativeInherited
Biological Process (BP)myeloid leukocyte activation2.662e-081.296e-07Highly InformativeDirect
Biological Process (BP)leukocyte activation involved in immune response3.131e-085.655e-07Highly InformativeDirect
Biological Process (BP)leukocyte mediated immunity2.279e-057.253e-06Highly InformativeDirect
Biological Process (BP)exocytosis2.176e-084.336e-08Highly InformativeDirect
Biological Process (BP)vesicle organization3.197e-091.172e-12Highly InformativeDirect
Biological Process (BP)regulation of protein complex assembly1.749e-051.856e-06Highly InformativeDirect
Biological Process (BP)Golgi vesicle transport5.632e-051.768e-05Highly InformativeDirect
Biological Process (BP)organelle fusion0.0001635.447e-08Highly InformativeDirect
Biological Process (BP)regulation of vesicle-mediated transport5.139e-141.773e-14Highly InformativeDirect
Molecular Function (MF)binding8.133e-080.03703Least InformativeInherited
Cellular Component (CC)membrane06.539e-12Least InformativeDirect
Cellular Component (CC)cytoplasmic part1.301e-065.866e-08Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.023080.09224Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.019660.01538Least InformativeInherited
Cellular Component (CC)protein complex5.192e-060.0024Least InformativeInherited
Cellular Component (CC)organelle membrane1.31e-061.459e-08Moderately InformativeDirect
Cellular Component (CC)vesicle1.11e-052.192e-06Moderately InformativeDirect
Cellular Component (CC)plasma membrane part0.033130.226Moderately InformativeInherited
Cellular Component (CC)endosome9.755e-073.798e-07InformativeDirect
Cellular Component (CC)Golgi apparatus0.0001790.0002964InformativeDirect
Cellular Component (CC)vacuolar part5.199e-112.734e-11InformativeDirect
Cellular Component (CC)secretory granule0.021240.001853InformativeInherited
Cellular Component (CC)vacuolar membrane3.212e-071.68e-06Highly InformativeDirect
Cellular Component (CC)apical plasma membrane4.016e-101.004e-07Highly InformativeDirect
Cellular Component (CC)endosomal part6.085e-077.395e-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) localization 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.01915 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.00159 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.3185 Least Informative Inherited
Biological Process (BP) regulation of localization 2.75e-07 Moderately Informative Direct
Biological Process (BP) cellular localization 0 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.627 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.01065 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.224 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.9203 Moderately Informative Inherited
Biological Process (BP) immune system process 0.003626 Moderately Informative Inherited
Biological Process (BP) vesicle-mediated transport 3.667e-12 Informative Direct
Biological Process (BP) secretion by cell 0 Informative Direct
Biological Process (BP) regulation of organelle organization 0.000583 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 7.615e-06 Informative Direct
Biological Process (BP) membrane organization 1.418e-08 Informative Direct
Biological Process (BP) protein localization to organelle 0.03417 Informative Inherited
Biological Process (BP) organelle localization 0.6924 Informative Inherited
Biological Process (BP) protein transport 0.001393 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.06768 Informative Inherited
Biological Process (BP) cell-cell signaling 0.006867 Informative Inherited
Biological Process (BP) immune effector process 0.0317 Informative Inherited
Biological Process (BP) immune response 0.003734 Informative Inherited
Biological Process (BP) cell activation 0.01249 Informative Inherited
Biological Process (BP) myeloid leukocyte activation 1.296e-07 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 5.655e-07 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 7.253e-06 Highly Informative Direct
Biological Process (BP) exocytosis 4.336e-08 Highly Informative Direct
Biological Process (BP) cellular membrane fusion 0.0002825 Highly Informative Direct
Biological Process (BP) vesicle organization 1.172e-12 Highly Informative Direct
Biological Process (BP) regulation of protein complex assembly 1.856e-06 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 1.768e-05 Highly Informative Direct
Biological Process (BP) organelle fusion 5.447e-08 Highly Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 1.773e-14 Highly Informative Direct
Molecular Function (MF) binding 0.03703 Least Informative Inherited
Cellular Component (CC) membrane 6.539e-12 Least Informative Direct
Cellular Component (CC) cytoplasmic part 5.866e-08 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.09224 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.01538 Least Informative Inherited
Cellular Component (CC) protein complex 0.0024 Least Informative Inherited
Cellular Component (CC) organelle membrane 1.459e-08 Moderately Informative Direct
Cellular Component (CC) vesicle 2.192e-06 Moderately Informative Direct
Cellular Component (CC) plasma membrane part 0.226 Moderately Informative Inherited
Cellular Component (CC) endosome 3.798e-07 Informative Direct
Cellular Component (CC) Golgi apparatus 0.0002964 Informative Direct
Cellular Component (CC) vacuolar part 2.734e-11 Informative Direct
Cellular Component (CC) secretory granule 0.001853 Informative Inherited
Cellular Component (CC) vacuolar membrane 1.68e-06 Highly Informative Direct
Cellular Component (CC) apical plasma membrane 1.004e-07 Highly Informative Direct
Cellular Component (CC) endosomal part 7.395e-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

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 transport0.0004252Highly InformativeDirect
Cellular componentMembrane2.347e-13Least InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentGolgi apparatus1.731e-12Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.0001085Moderately 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 ]