SUPERFAMILY 1.75 HMM library and genome assignments server

  Home > SCOP hierarchy > Sec1/munc18-like (SM) proteins superfamily


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 (443) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 3,071 2,628 3
Proteins 2,944 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)single-organism cellular process7.153e-079.601e-05Least InformativeDirect
Biological Process (BP)localization00Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis2.953e-060.002128Least InformativeInherited
Biological Process (BP)regulation of cellular process0.77290.951Least InformativeInherited
Biological Process (BP)response to stimulus0.0078830.3682Least InformativeInherited
Biological Process (BP)regulation of localization7.59e-061.057e-06Moderately InformativeDirect
Biological Process (BP)cellular localization00Moderately InformativeDirect
Biological Process (BP)macromolecule localization0.26330.4483Moderately InformativeInherited
Biological Process (BP)organelle organization0.14060.1538Moderately InformativeInherited
Biological Process (BP)organic substance transport0.80020.7406Moderately InformativeInherited
Biological Process (BP)immune system process0.00052860.01231Moderately InformativeInherited
Biological Process (BP)cellular membrane organization1.492e-081.934e-10InformativeDirect
Biological Process (BP)vesicle-mediated transport4.29e-121.025e-12InformativeDirect
Biological Process (BP)regulation of cellular component biogenesis0.00077190.0006204InformativeDirect
Biological Process (BP)secretion4.619e-097.739e-09InformativeDirect
Biological Process (BP)protein localization to organelle0.062650.03296InformativeInherited
Biological Process (BP)protein transport0.00081390.001847InformativeInherited
Biological Process (BP)cytoplasmic transport0.044230.027InformativeInherited
Biological Process (BP)immune effector process0.028820.007466InformativeInherited
Biological Process (BP)immune response0.040870.02517InformativeInherited
Biological Process (BP)cell activation0.0036550.00927InformativeInherited
Biological Process (BP)myeloid leukocyte activation1.149e-085.491e-08Highly InformativeDirect
Biological Process (BP)leukocyte activation involved in immune response1.488e-081.552e-07Highly InformativeDirect
Biological Process (BP)leukocyte mediated immunity1.431e-053.264e-06Highly InformativeDirect
Biological Process (BP)exocytosis7.147e-091.679e-08Highly InformativeDirect
Biological Process (BP)cellular membrane fusion0.00040672.959e-06Highly InformativeDirect
Biological Process (BP)vesicle organization3.248e-091.021e-12Highly InformativeDirect
Biological Process (BP)signal release1.507e-056.419e-06Highly InformativeDirect
Biological Process (BP)Golgi vesicle transport2.407e-058.764e-06Highly InformativeDirect
Biological Process (BP)organelle fusion0.0001726.391e-08Highly InformativeDirect
Biological Process (BP)regulation of vesicle-mediated transport1.534e-101.066e-11Highly InformativeDirect
Molecular Function (MF)binding9.24e-090.001456Least InformativeInherited
Molecular Function (MF)protein binding4.069e-143.294e-08Moderately InformativeDirect
Cellular Component (CC)membrane9.73e-135.503e-09Least InformativeDirect
Cellular Component (CC)cytoplasmic part8.431e-054.773e-07Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.17560.3838Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.065670.05235Least InformativeInherited
Cellular Component (CC)protein complex0.00034190.0193Least InformativeInherited
Cellular Component (CC)organelle membrane0.00051412.003e-05Moderately InformativeDirect
Cellular Component (CC)vesicle1.651e-088.014e-09Moderately InformativeDirect
Cellular Component (CC)plasma membrane0.0012230.002569Moderately InformativeInherited
Cellular Component (CC)endosome0.00016010.0001021InformativeDirect
Cellular Component (CC)vacuole6.447e-084.743e-10InformativeDirect
Cellular Component (CC)Golgi apparatus4.116e-059.402e-05InformativeDirect
Cellular Component (CC)secretory granule0.026060.004972InformativeInherited
Cellular Component (CC)vacuolar membrane0.0007040.0008895Highly InformativeDirect
Cellular Component (CC)apical plasma membrane5.46e-094.58e-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 9.601e-05 Least Informative Direct
Biological Process (BP) localization 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.002128 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.951 Least Informative Inherited
Biological Process (BP) response to stimulus 0.3682 Least Informative Inherited
Biological Process (BP) regulation of localization 1.057e-06 Moderately Informative Direct
Biological Process (BP) cellular localization 0 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.4483 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.1538 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.7406 Moderately Informative Inherited
Biological Process (BP) immune system process 0.01231 Moderately Informative Inherited
Biological Process (BP) cellular membrane organization 1.934e-10 Informative Direct
Biological Process (BP) vesicle-mediated transport 1.025e-12 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.0006204 Informative Direct
Biological Process (BP) secretion 7.739e-09 Informative Direct
Biological Process (BP) protein localization to organelle 0.03296 Informative Inherited
Biological Process (BP) protein transport 0.001847 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.027 Informative Inherited
Biological Process (BP) immune effector process 0.007466 Informative Inherited
Biological Process (BP) immune response 0.02517 Informative Inherited
Biological Process (BP) cell activation 0.00927 Informative Inherited
Biological Process (BP) myeloid leukocyte activation 5.491e-08 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 1.552e-07 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 3.264e-06 Highly Informative Direct
Biological Process (BP) exocytosis 1.679e-08 Highly Informative Direct
Biological Process (BP) cellular membrane fusion 2.959e-06 Highly Informative Direct
Biological Process (BP) vesicle organization 1.021e-12 Highly Informative Direct
Biological Process (BP) signal release 6.419e-06 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 8.764e-06 Highly Informative Direct
Biological Process (BP) organelle fusion 6.391e-08 Highly Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 1.066e-11 Highly Informative Direct
Molecular Function (MF) binding 0.001456 Least Informative Inherited
Molecular Function (MF) protein binding 3.294e-08 Moderately Informative Direct
Cellular Component (CC) membrane 5.503e-09 Least Informative Direct
Cellular Component (CC) cytoplasmic part 4.773e-07 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.3838 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.05235 Least Informative Inherited
Cellular Component (CC) protein complex 0.0193 Least Informative Inherited
Cellular Component (CC) organelle membrane 2.003e-05 Moderately Informative Direct
Cellular Component (CC) vesicle 8.014e-09 Moderately Informative Direct
Cellular Component (CC) plasma membrane 0.002569 Moderately Informative Inherited
Cellular Component (CC) endosome 0.0001021 Informative Direct
Cellular Component (CC) vacuole 4.743e-10 Informative Direct
Cellular Component (CC) Golgi apparatus 9.402e-05 Informative Direct
Cellular Component (CC) secretory granule 0.004972 Informative Inherited
Cellular Component (CC) vacuolar membrane 0.0008895 Highly Informative Direct
Cellular Component (CC) apical plasma membrane 4.58e-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)lethal0Least 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)shoot apex0Least InformativeDirect
Plant ANatomical entity (PAN)shoot internode0Least InformativeDirect
Plant ANatomical entity (PAN)root0Least InformativeDirect
Plant ANatomical entity (PAN)plant embryo0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)vascular leaf0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)sepal0Least InformativeDirect
Plant ANatomical entity (PAN)petal0Least InformativeDirect
Plant ANatomical entity (PAN)stem0Least InformativeDirect
Plant ANatomical entity (PAN)pedicel0Least InformativeDirect
Plant ANatomical entity (PAN)androecium0Least InformativeDirect
Plant ANatomical entity (PAN)gynoecium0Least InformativeDirect
Plant ANatomical entity (PAN)leaf lamina0Least InformativeDirect
Plant ANatomical entity (PAN)collective leaf structure0Least InformativeDirect
Plant ANatomical entity (PAN)stalk0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)phyllome apex0Least InformativeDirect
Plant ANatomical entity (PAN)microgametophyte0Least 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 transport0.0004694Highly InformativeDirect
Cellular componentMembrane1.585e-12Least InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentGolgi apparatus1.218e-12Moderately InformativeDirect
Cellular componentEndoplasmic reticulum8.685e-05Moderately InformativeDirect
Cellular componentLysosome0InformativeDirect
Post-translational modificationPhosphoprotein1.467e-05Least InformativeDirect

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 ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

Please send feedback, comments or questions to superfamily@cs.bris.ac.uk or use the feedback form.

© Copyright 2013 The SUPERFAMILY authors and Julian Gough.