SUPERFAMILY 1.75 HMM library and genome assignments server

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C2 domain (Calcium/lipid-binding domain, CaLB) superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   C2 domain-like [ 49561] (5)
Superfamily:   C2 domain (Calcium/lipid-binding domain, CaLB) [ 49562] (2)
Families:   PLC-like (P variant) [ 49563] (11)
  Synaptotagmin-like (S variant) [ 49575] (10)


Superfamily statistics
Genomes (514) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 47,971 127,967 37
Proteins 31,885 86,310 35


Functional annotation
General category Regulation
Detailed category Signal transduction

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases0Moderately InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine kinases0Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases1Moderately InformativeInherited
Enzyme Commission (EC)Carboxylic ester hydrolases1Moderately InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as accep0.005268Moderately InformativeInherited
Enzyme Commission (EC)Phosphoinositide phospholipase C0InformativeDirect
Enzyme Commission (EC)Phosphatidylinositol 3-kinase0Highly InformativeDirect
Enzyme Commission (EC)Phospholipase A(2)0Highly InformativeDirect
Enzyme Commission (EC)Protein kinase C0Highly InformativeDirect
Enzyme Commission (EC)Phosphatidylinositol-4,5-bisphosphate 3-kinase0Highly InformativeDirect
Enzyme Commission (EC)Phosphatidylinositol-4-phosphate 3-kinase2.368e-16Highly InformativeDirect
Enzyme Commission (EC)Lysophospholipase0.000000000002869Highly InformativeDirect
Enzyme Commission (EC)Phospholipase D0.0002652Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the head0.2571Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.8723Least InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.2444Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of immune system physiology0.5305Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.5757Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral cavity morphology1Moderately InformativeInherited
Phenotypic Abnormality (PA)Neoplasm of the endocrine system0.09772InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the thyroid gland0.2113InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.0246Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.1595Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.4772Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.796Least InformativeInherited
Mammalian Phenotype (MP)neoplasm0.1934Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal leukocyte physiology0.5904Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.5917Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.6072Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood coagulation0.004986InformativeInherited
Mammalian Phenotype (MP)abnormal T cell physiology0.8149InformativeInherited
Mammalian Phenotype (MP)increased hamartoma incidence0.001436Highly InformativeInherited
Mammalian Phenotype (MP)abnormal synapse morphology0.001849Highly InformativeInherited
Mammalian Phenotype (MP)increased skin tumor incidence0.002818Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cytotoxic T cell physiology0.3Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell morphology variant0.00001243Least InformativeDirect
Worm Phenotype (WP)blast cell physiology variant0.00001611Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.00001625Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.0001012Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.0001679Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.003041Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.03794Least InformativeInherited
Worm Phenotype (WP)cell development variant0.1024Least InformativeInherited
Worm Phenotype (WP)protein expression variant0.00000002913Moderately InformativeDirect
Worm Phenotype (WP)metabolic pathway variant0.0003778Moderately InformativeDirect
Worm Phenotype (WP)neuron development variant0.006433Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.02578Moderately InformativeInherited
Worm Phenotype (WP)drug response variant0.04013Moderately InformativeInherited
Worm Phenotype (WP)nervous system morphology variant0.1909Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.4258Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.9297Moderately InformativeInherited
Worm Phenotype (WP)locomotion variant1Moderately InformativeInherited
Worm Phenotype (WP)defecation variant0.0000000001889InformativeDirect
Worm Phenotype (WP)body wall muscle sarcomere morphology variant0.00000005944InformativeDirect
Worm Phenotype (WP)muscle cell physiology variant0.00002423InformativeDirect
Worm Phenotype (WP)mitochondria morphology variant0.00003996InformativeDirect
Worm Phenotype (WP)axon outgrowth variant0.0003039InformativeDirect
Worm Phenotype (WP)drug resistant0.0006822InformativeDirect
Worm Phenotype (WP)electrophysiology variant0.0008001InformativeDirect
Worm Phenotype (WP)cell stress response variant0.003002InformativeInherited
Worm Phenotype (WP)male mating variant0.00363InformativeInherited
Worm Phenotype (WP)pattern protein expression variant0.005619InformativeInherited
Worm Phenotype (WP)organism pathogen response variant0.01536InformativeInherited
Worm Phenotype (WP)localized movement variant0.0277InformativeInherited
Worm Phenotype (WP)mechanosensation variant0.1225InformativeInherited
Worm Phenotype (WP)foraging behavior variant0.1662InformativeInherited
Worm Phenotype (WP)neuron morphology variant0.2109InformativeInherited
Worm Phenotype (WP)cell component localization variant0.2792InformativeInherited
Worm Phenotype (WP)oocyte morphology variant0.7156InformativeInherited
Worm Phenotype (WP)defecation contraction variant0Highly InformativeDirect
Worm Phenotype (WP)gonad sheath contractions variant0.000000001462Highly InformativeDirect
Worm Phenotype (WP)drug induced gene expression variant0.000000001654Highly InformativeDirect
Worm Phenotype (WP)response to injury variant0.00000009491Highly InformativeDirect
Worm Phenotype (WP)endomitotic oocytes0.0000004836Highly InformativeDirect
Worm Phenotype (WP)ovulation variant0.000001954Highly InformativeDirect
Worm Phenotype (WP)osmotic stress response variant0.000009621Highly InformativeDirect
Worm Phenotype (WP)growth rate variant0.00005423Highly InformativeDirect
Worm Phenotype (WP)nose touch variant0.00005593Highly InformativeDirect
Worm Phenotype (WP)RNAi response variant0.000265Highly InformativeDirect
Worm Phenotype (WP)male mating defective0.000553Highly InformativeDirect
Worm Phenotype (WP)synaptic transmission variant0.004545Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)neurophysiology defective0.00009318InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)pollen tube cell0.00007221InformativeDirect
Plant structure DEvelopment stage (PDE)pollen development stage0.00003936Moderately InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Aminoacyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine kinases0Moderately InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0.00313Moderately InformativeInherited
Enzyme Commission (EC)Carbon-carbon lyases0.919Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases1Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric diester hydrolases0InformativeDirect
Enzyme Commission (EC)Protein-tyrosine-phosphatase0.00005895InformativeDirect
Enzyme Commission (EC)Protein-tyrosine kinases0.2211InformativeInherited
Enzyme Commission (EC)Carboxy-lyases0.4989InformativeInherited
Enzyme Commission (EC)Carboxylic ester hydrolases1InformativeInherited
Enzyme Commission (EC)HECT-type E3 ubiquitin transferase0Highly InformativeDirect
Enzyme Commission (EC)Phosphoinositide phospholipase C0Highly InformativeDirect
Enzyme Commission (EC)Non-specific protein-tyrosine kinase0.0006417Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR008973 SSF49562 Protein matches
Abstract

The Ca2+-dependent, lipid-binding domain (CaLB) has been identified in a number of proteins, for example the amino-terminal, 138 amino acid C2 domain of cytosolic phospholipase A2 (cPLA2-C2) which mediates an initial step in the production of lipid mediators of inflammation: the Ca2+-dependent translocation of the enzyme to intracellular membranes with subsequent liberation of arachidonic acid. The domain is composed of eight antiparallel beta-strands with six interconnecting loops that fits the "type II" topology for C2 domains. The structure has been identified as a beta-sandwich in the "Greek key" motif [PubMed9665851].


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 · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

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 45 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 C2 domain (Calcium/lipid-binding domain, CaLB) 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 45 hidden Markov models representing the C2 domain (Calcium/lipid-binding domain, CaLB) 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 · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]