SUPERFAMILY 1.75 HMM library and genome assignments server

  Home > SCOP hierarchy > Saposin superfamily


Saposin superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Saposin-like [ 47861] (2)
Superfamily:   Saposin [ 47862] (4)
Families:   Saposin B [ 81806]
  NKL-like [ 47863] (3)
  Ameobapore A [ 101266]
  Swaposin [ 47866]

 Superfamily statistics
Genomes (206) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 2,679 2,729 9
Proteins 1,520 1,516 9

 Functional annotation
General category Processes_IC
Detailed category Protein modification

Document: Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) response to stimulus 1.253e-05 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0003064 Least Informative Direct
Biological Process (BP) developmental process 0.0008277 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.001789 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.4303 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.4542 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.00978 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) localization 0.003249 Least Informative Inherited
Biological Process (BP) regulation of response to stimulus 1.896e-14 Moderately Informative Direct
Biological Process (BP) cellular lipid metabolic process 2.359e-12 Moderately Informative Direct
Biological Process (BP) regulation of cell communication 2.377e-12 Moderately Informative Direct
Biological Process (BP) reproduction 2.108e-10 Moderately Informative Direct
Biological Process (BP) regulation of signaling 3.124e-09 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 6.029e-09 Moderately Informative Direct
Biological Process (BP) tissue development 1.126e-08 Moderately Informative Direct
Biological Process (BP) cell differentiation 3.081e-07 Moderately Informative Direct
Biological Process (BP) organ development 9.23e-06 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 3.844e-05 Moderately Informative Direct
Biological Process (BP) response to organic substance 9.246e-05 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0.0002084 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 0.0002168 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 0.02578 Moderately Informative Inherited
Biological Process (BP) lipid biosynthetic process 0.01183 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.05496 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.06997 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.001145 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.01034 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.2095 Moderately Informative Inherited
Biological Process (BP) reproductive system development 0 Informative Direct
Biological Process (BP) cellular process involved in reproduction 0 Informative Direct
Biological Process (BP) regulation of intracellular protein kinase cascade 0 Informative Direct
Biological Process (BP) gland development 0 Informative Direct
Biological Process (BP) epithelium development 0 Informative Direct
Biological Process (BP) regulation of lipid metabolic process 0 Informative Direct
Biological Process (BP) growth 0 Informative Direct
Biological Process (BP) developmental process involved in reproduction 2.258e-14 Informative Direct
Biological Process (BP) cellular biogenic amine metabolic process 3.211e-07 Informative Direct
Biological Process (BP) polysaccharide metabolic process 6.246e-07 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 9.491e-07 Informative Direct
Biological Process (BP) cellular amide metabolic process 1.234e-06 Informative Direct
Biological Process (BP) alcohol metabolic process 1.37e-05 Informative Direct
Biological Process (BP) membrane lipid metabolic process 0.000197 Informative Direct
Biological Process (BP) organophosphate catabolic process 0.0005201 Informative Direct
Biological Process (BP) lipid catabolic process 0.0007548 Informative Direct
Biological Process (BP) regulation of response to external stimulus 0.09518 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.07449 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.07047 Informative Inherited
Biological Process (BP) regulation of response to stress 0.9798 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.03491 Informative Inherited
Biological Process (BP) phospholipid metabolic process 0.003261 Informative Inherited
Biological Process (BP) developmental growth 0 Highly Informative Direct
Biological Process (BP) membrane lipid biosynthetic process 1.09e-10 Highly Informative Direct
Biological Process (BP) ethanolamine-containing compound metabolic process 2.52e-10 Highly Informative Direct
Biological Process (BP) regulation of inflammatory response 4.759e-09 Highly Informative Direct
Biological Process (BP) negative regulation of response to external stimulus 1.033e-07 Highly Informative Direct
Biological Process (BP) alcohol catabolic process 1.157e-05 Highly Informative Direct
Biological Process (BP) ceramide metabolic process 0.01524 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.0002259 Least Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 1.785e-07 Moderately Informative Direct
Molecular Function (MF) phosphoric ester hydrolase activity 0.8192 Informative Inherited
Molecular Function (MF) phosphoric diester hydrolase activity 6.229e-09 Highly Informative Direct
Molecular Function (MF) carboxylic ester hydrolase activity 6.179e-05 Highly Informative Direct
Molecular Function (MF) phospholipase activity 0.1479 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 3.167e-08 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0007288 Least Informative Direct
Cellular Component (CC) extracellular region 5.88e-05 Moderately Informative Direct
Cellular Component (CC) extracellular space 1.264e-05 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on ester bonds3.905e-06Least InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases1.042e-07Moderately InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details) Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormal respiratory system morphology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Functional respiratory abnormality0InformativeDirect
Phenotypic Abnormality (PA)Respiratory insufficiency0Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)immune system phenotype0Least InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.01246Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.0556Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.9342Least InformativeInherited
Worm Phenotype (WP)cell death variant0.1155Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.1958Moderately InformativeInherited
Worm Phenotype (WP)transgene expression reduced5.116e-13InformativeDirect
Worm Phenotype (WP)organism pathogen response variant0.0002468InformativeDirect
Worm Phenotype (WP)cell stress response variant0.005831InformativeInherited
Worm Phenotype (WP)egg laying variant0.01396InformativeInherited
Worm Phenotype (WP)genotoxic induced apoptosis variant3.127e-07Highly InformativeDirect
Worm Phenotype (WP)germ cell ionizing radiation response variant2.426e-05Highly InformativeDirect
Worm Phenotype (WP)cell ionizing radiation response variant3.089e-05Highly InformativeDirect

Document: WP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)shoot internode0Least InformativeDirect
Plant ANatomical entity (PAN)vascular leaf0Least InformativeDirect
Plant ANatomical entity (PAN)stem0Least InformativeDirect
Plant ANatomical entity (PAN)collective leaf structure0Least InformativeDirect
Plant ANatomical entity (PAN)phyllome apex0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases1.056e-07InformativeDirect
Enzyme Commission (EC)Carboxylic ester hydrolases0.1508InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processLipid metabolism2.701e-08Moderately InformativeDirect
Biological processSphingolipid metabolism0Highly InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentVacuole2.56e-13InformativeDirect
Cellular componentLysosome1.875e-10InformativeDirect
DomainSignal0Least InformativeDirect
Post-translational modificationHydrolase5.592e-08Least InformativeDirect
Post-translational modificationProtease0.0003133Moderately InformativeDirect
Post-translational modificationAntimicrobial3.826e-11InformativeDirect
Post-translational modificationGlycosidase1.673e-05InformativeDirect
Post-translational modificationAspartyl protease0Highly InformativeDirect
Post-translational modificationAntibiotic1.43e-12Highly InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationGlycoprotein2.347e-13Least InformativeDirect
Post-translational modificationZymogen4.502e-09InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)lipid metabolism0Least InformativeDirect
UniPathway (UP)sphingolipid metabolism0Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR011001 SSF47862 Protein matches
Abstract

The lysosomal degradation of several sphingolipids requires the presence of four small glycoproteins called saposins, generated by proteolytic processing of a common precursor, prosaposin [PubMed9972880]. Saposins have three conserved disulphide bridges, and display a 5-helical, closed, folded leaf topology. Other proteins have been shown to have structures that closely resemble saposin, such as the antimicrobial peptides NK-lysin and granulysin [PubMed8988855, PubMed14499265]. Some proteins contain saposin-like domains, such as prophytepsin, an acid protease from plants, and J3-crystallin, an eye-lens protein from jellyfish, both of which contain circularly permuted saposin motifs called swaposin [PubMed10406799, PubMed11675486]. In some saposins and saposin-like domains, lipid-binding can promote conformational changes and oligomerization.


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-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 6 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 Saposin 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 6 hidden Markov models representing the Saposin 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-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · 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.