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PLC-like phosphodiesterases superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   TIM beta/alpha-barrel [ 51350] (33)
Superfamily:   PLC-like phosphodiesterases [ 51695] (3)
Families:   Mammalian PLC [ 51696] (2)
  Bacterial PLC [ 51699]
  Glycerophosphoryl diester phosphodiesterase [ 89508] (4)

Superfamily statistics
Genomes (1,965) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 10,817 21,255 17
Proteins 10,483 21,023 17

 Functional annotation
General category Processes_IC
Detailed category Phospholipid metabolism and transport

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 metabolic process0.1142.362e-10Least InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process0.021050Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.0020970Moderately InformativeInherited
Biological Process (BP)cellular lipid metabolic process0.0013730Moderately InformativeInherited
Biological Process (BP)phospholipid metabolic process1.145e-060InformativeDirect
Molecular Function (MF)hydrolase activity1.384e-060Least InformativeDirect
Molecular Function (MF)hydrolase activity, acting on ester bonds4.572e-120Moderately InformativeDirect
Molecular Function (MF)phosphoric ester hydrolase activity0.0037023.82e-15InformativeInherited
Molecular Function (MF)phospholipase activity1.872e-110Highly InformativeDirect
Molecular Function (MF)phosphoric diester hydrolase activity00Highly 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 metabolic process 2.362e-10 Least Informative Direct
Biological Process (BP) localization 0.003329 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.14 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.6711 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.1261 Least Informative Inherited
Biological Process (BP) response to stimulus 0.02709 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.04972 Least Informative Inherited
Biological Process (BP) developmental process 0.5907 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) ion transport 3.346e-05 Moderately Informative Direct
Biological Process (BP) signal transduction 0.0007164 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of localization 2.394e-06 Moderately Informative Direct
Biological Process (BP) homeostatic process 0.0002195 Moderately Informative Direct
Biological Process (BP) cellular lipid metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular localization 0.0004088 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 8.16e-11 Moderately Informative Direct
Biological Process (BP) organ development 0.335 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.004688 Moderately Informative Inherited
Biological Process (BP) lipid biosynthetic process 0.001855 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.6901 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.7683 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.05145 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.4716 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.2866 Moderately Informative Inherited
Biological Process (BP) reproduction 0.01583 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.357 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.2759 Moderately Informative Inherited
Biological Process (BP) system process 0.1924 Moderately Informative Inherited
Biological Process (BP) immune system process 0.1029 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.7969 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.9252 Moderately Informative Inherited
Biological Process (BP) alcohol metabolic process 4.008e-15 Informative Direct
Biological Process (BP) phospholipid metabolic process 0 Informative Direct
Biological Process (BP) metal ion transport 3.724e-09 Informative Direct
Biological Process (BP) regulation of locomotion 1.171e-05 Informative Direct
Biological Process (BP) chordate embryonic development 9.836e-05 Informative Direct
Biological Process (BP) glycerolipid metabolic process 9.818e-08 Informative Direct
Biological Process (BP) metal ion homeostasis 1.36e-11 Informative Direct
Biological Process (BP) cellular cation homeostasis 0.003682 Informative Inherited
Biological Process (BP) embryonic organ development 0.008773 Informative Inherited
Biological Process (BP) cardiovascular system development 0.04391 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.008584 Informative Inherited
Biological Process (BP) regulation of growth 0.02097 Informative Inherited
Biological Process (BP) response to organic nitrogen 0.00593 Informative Inherited
Biological Process (BP) response to hormone stimulus 0.1304 Informative Inherited
Biological Process (BP) regulation of cellular component movement 0.002604 Informative Inherited
Biological Process (BP) cellular component movement 0.02675 Informative Inherited
Biological Process (BP) actin filament-based process 0.0195 Informative Inherited
Biological Process (BP) lipid catabolic process 0.001592 Informative Inherited
Biological Process (BP) organophosphate catabolic process 0.3396 Informative Inherited
Biological Process (BP) cell activation 0.00355 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 0.003454 Informative Inherited
Biological Process (BP) sexual reproduction 0.02988 Informative Inherited
Biological Process (BP) single organism reproductive process 0.01958 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.0114 Informative Inherited
Biological Process (BP) regulation of immune response 0.1257 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.3939 Informative Inherited
Biological Process (BP) angiogenesis 0.0002774 Highly Informative Direct
Biological Process (BP) activation of immune response 9.164e-05 Highly Informative Direct
Biological Process (BP) calcium ion transport 2.258e-14 Highly Informative Direct
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 8.175e-08 Highly Informative Direct
Biological Process (BP) fertilization 2.316e-07 Highly Informative Direct
Biological Process (BP) polyol metabolic process 2.473e-09 Highly Informative Direct
Biological Process (BP) actin filament-based movement 2.038e-07 Highly Informative Direct
Biological Process (BP) positive regulation of growth 0.0008126 Highly Informative Direct
Biological Process (BP) regulation of ion homeostasis 2.357e-13 Highly Informative Direct
Biological Process (BP) embryonic placenta development 0.003433 Highly Informative Inherited
Biological Process (BP) cellular calcium ion homeostasis 0.002743 Highly Informative Inherited
Biological Process (BP) organelle localization 0.0598 Highly Informative Inherited
Biological Process (BP) sensory perception 0.08224 Highly Informative Inherited
Biological Process (BP) immune response-regulating signaling pathway 0.002216 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0 Moderately Informative Direct
Molecular Function (MF) phosphoric ester hydrolase activity 3.82e-15 Informative Direct
Molecular Function (MF) phospholipase activity 0 Highly Informative Direct
Molecular Function (MF) phosphoric diester hydrolase activity 0 Highly Informative Direct
Cellular Component (CC) membrane 2.519e-07 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.2613 Least Informative Inherited
Cellular Component (CC) cytosol 3.042e-06 Moderately Informative Direct
Cellular Component (CC) plasma membrane 4.183e-07 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.05328 Moderately Informative Inherited
Cellular Component (CC) anchored to membrane 3.265e-06 Highly 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 bonds0Least InformativeDirect
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Phosphoric diester hydrolases0Moderately InformativeDirect
Enzyme Commission (EC)Phosphoinositide phospholipase C1.001e-07InformativeDirect
Enzyme Commission (EC)Phosphorus-oxygen lyases1InformativeInherited

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details) Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal homeostasis0.4953Least InformativeInherited
Mammalian Phenotype (MP)abnormal ion homeostasis0.000596InformativeDirect
Mammalian Phenotype (MP)abnormal blood coagulation0.0084InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic system physiology0.03211InformativeInherited
Mammalian Phenotype (MP)abnormal calcium ion homeostasis6.735e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal platelet physiology0.0006401Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism environmental stimulus response variant0.007523Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.02032Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.1195Least InformativeInherited
Worm Phenotype (WP)germ cell morphology variant3.637e-05Moderately InformativeDirect
Worm Phenotype (WP)cell homeostasis metabolism variant4.553e-05Moderately InformativeDirect
Worm Phenotype (WP)cell stress response variant1.767e-08InformativeDirect
Worm Phenotype (WP)organism pathogen response variant2.22e-08InformativeDirect
Worm Phenotype (WP)copulation variant0.001263InformativeInherited
Worm Phenotype (WP)protein expression variant0.01288InformativeInherited
Worm Phenotype (WP)male behavior variant1InformativeInherited
Worm Phenotype (WP)osmotic stress response variant0Highly InformativeDirect
Worm Phenotype (WP)gonad sheath contractions variant7.484e-16Highly InformativeDirect
Worm Phenotype (WP)defecation contraction variant1.045e-14Highly InformativeDirect
Worm Phenotype (WP)endomitotic oocytes6.858e-14Highly InformativeDirect
Worm Phenotype (WP)ovulation variant7.006e-11Highly InformativeDirect
Worm Phenotype (WP)post hermaphrodite contact variant9.643e-06Highly InformativeDirect
Worm Phenotype (WP)male mating defective1.068e-05Highly InformativeDirect
Worm Phenotype (WP)response to injury variant0.0002097Highly InformativeDirect
Worm Phenotype (WP)protein subcellular localization variant0.0009183Highly 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)viable0Least InformativeDirect
Fly Phenotype (FP)fertile0Least InformativeDirect

Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)head0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) 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)Lyases1Least InformativeInherited
Enzyme Commission (EC)Phosphoric diester hydrolases0InformativeDirect
Enzyme Commission (EC)Phosphoinositide phospholipase C5.252e-08Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processLipid metabolism0Moderately InformativeDirect
Biological processCytolysis0InformativeDirect
Biological processVirulence0.0005839InformativeDirect
Biological processHemolysis0Highly InformativeDirect
Biological processLipid degradation0Highly InformativeDirect
Biological processFertilization9.846e-13Highly InformativeDirect
Biological processGlycerol metabolism5.831e-12Highly InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
DomainSignal0.0003781Least InformativeDirect
DomainSH2 domain9.394e-08InformativeDirect
DomainSH3 domain2.765e-05InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionCalcium0Moderately InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationToxin0InformativeDirect
Post-translational modificationTransducer0InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · 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 8 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 PLC-like phosphodiesterases 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 8 hidden Markov models representing the PLC-like phosphodiesterases 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 · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · 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.