SUPERFAMILY 1.75 HMM library and genome assignments server


CRAL/TRIO domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   SpoIIaa-like [ 52086] (2)
Superfamily:   CRAL/TRIO domain [ 52087]
Families:   CRAL/TRIO domain [ 52088] (3)


Superfamily statistics
Genomes (495) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 9,529 8,941 5
Proteins 9,462 8,878 5


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)developmental process0.0016290.0009624Least InformativeInherited
Biological Process (BP)multicellular organismal process0.0029870.03585Least InformativeInherited
Biological Process (BP)single-organism developmental process0.010510.9135Moderately InformativeInherited
Biological Process (BP)embryo development ending in birth or egg hatching8.267e-089.433e-05InformativeDirect

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) developmental process 0.0009624 Least Informative Direct
Biological Process (BP) single-organism cellular process 5.797e-05 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.01863 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.7767 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.05383 Least Informative Inherited
Biological Process (BP) localization 0.01429 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.03585 Least Informative Inherited
Biological Process (BP) response to stimulus 0.302 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.3597 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of phosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 0 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 1.021e-09 Moderately Informative Direct
Biological Process (BP) cell differentiation 5.089e-07 Moderately Informative Direct
Biological Process (BP) signal transduction 8.944e-05 Moderately Informative Direct
Biological Process (BP) nervous system development 9.394e-05 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.0003133 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.4834 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.00688 Moderately Informative Inherited
Biological Process (BP) system process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.8307 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.2269 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.9135 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.7553 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.09388 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.1215 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.7756 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.8875 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.06802 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.05504 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) ion transport 0.05606 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.2427 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.3561 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.07497 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.2818 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.05723 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.1572 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.343 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.6749 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 9.433e-05 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 0 Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 0 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0 Informative Direct
Biological Process (BP) intracellular signal transduction 7.318e-15 Informative Direct
Biological Process (BP) lipid localization 6.379e-14 Informative Direct
Biological Process (BP) regulation of nervous system development 9.272e-11 Informative Direct
Biological Process (BP) anion transport 1.215e-08 Informative Direct
Biological Process (BP) vitamin metabolic process 2.955e-07 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 1.487e-06 Informative Direct
Biological Process (BP) positive regulation of hydrolase activity 1.778e-06 Informative Direct
Biological Process (BP) phospholipid metabolic process 0.0001313 Informative Direct
Biological Process (BP) regulation of cell development 0.0001329 Informative Direct
Biological Process (BP) glycerolipid metabolic process 0.0003253 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.0003776 Informative Direct
Biological Process (BP) dephosphorylation 0.0008467 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.0008675 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.06589 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.00511 Informative Inherited
Biological Process (BP) microtubule-based process 0.1058 Informative Inherited
Biological Process (BP) cytoskeleton organization 0.6638 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 1 Informative Inherited
Biological Process (BP) synaptic transmission 0.03816 Informative Inherited
Biological Process (BP) regulation of growth 0.002546 Informative Inherited
Biological Process (BP) regulation of lipid metabolic process 0.05208 Informative Inherited
Biological Process (BP) organic hydroxy compound biosynthetic process 0.001585 Informative Inherited
Biological Process (BP) alcohol metabolic process 0.01553 Informative Inherited
Biological Process (BP) positive regulation of gene expression 0.001888 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.006408 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.007684 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.03211 Informative Inherited
Biological Process (BP) generation of neurons 1 Informative Inherited
Biological Process (BP) single-organism behavior 0.8292 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.2439 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 1 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.02744 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 1 Informative Inherited
Biological Process (BP) growth 0.05505 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.5852 Informative Inherited
Biological Process (BP) embryonic organ development 0.05141 Informative Inherited
Biological Process (BP) organophosphate ester transport 0 Highly Informative Direct
Biological Process (BP) small GTPase mediated signal transduction 0 Highly Informative Direct
Biological Process (BP) regulation of Rho GTPase activity 0 Highly Informative Direct
Biological Process (BP) lysosome organization 1.08e-13 Highly Informative Direct
Biological Process (BP) regulation of cellular amine metabolic process 2.966e-07 Highly Informative Direct
Biological Process (BP) protein dephosphorylation 1.941e-06 Highly Informative Direct
Biological Process (BP) regulation of striated muscle tissue development 1.762e-05 Highly Informative Direct
Biological Process (BP) positive regulation of growth 4.413e-05 Highly Informative Direct
Biological Process (BP) placenta development 6.136e-05 Highly Informative Direct
Biological Process (BP) alcohol biosynthetic process 8.348e-05 Highly Informative Direct
Biological Process (BP) cell growth 0.000128 Highly Informative Direct
Biological Process (BP) regulation of developmental growth 0.0001546 Highly Informative Direct
Biological Process (BP) circadian rhythm 0.0001642 Highly Informative Direct
Biological Process (BP) regulation of multicellular organism growth 0.0002316 Highly Informative Direct
Biological Process (BP) response to heat 0.0003125 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 0.0006207 Highly Informative Direct
Biological Process (BP) developmental growth 0.0006677 Highly Informative Direct
Biological Process (BP) positive regulation of Ras GTPase activity 0.0009315 Highly Informative Direct
Biological Process (BP) positive regulation of transcription, DNA-dependent 0.009981 Highly Informative Inherited
Biological Process (BP) locomotory behavior 0.04602 Highly Informative Inherited
Biological Process (BP) regulation of cyclic nucleotide metabolic process 0.8625 Highly Informative Inherited
Biological Process (BP) aging 0.009416 Highly Informative Inherited
Biological Process (BP) learning or memory 0.01228 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) binding 0.6279 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 2.785e-07 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.001342 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.1007 Moderately Informative Inherited
Molecular Function (MF) GTPase regulator activity 0 Informative Direct
Molecular Function (MF) lipid binding 0 Informative Direct
Molecular Function (MF) anion transmembrane transporter activity 6.935e-05 Informative Direct
Molecular Function (MF) phosphoric ester hydrolase activity 0.002669 Informative Inherited
Molecular Function (MF) lipid transporter activity 0 Highly Informative Direct
Molecular Function (MF) organic cation transmembrane transporter activity 2.262e-11 Highly Informative Direct
Molecular Function (MF) organic hydroxy compound transmembrane transporter activity 3.757e-11 Highly Informative Direct
Molecular Function (MF) phosphoprotein phosphatase activity 2.316e-06 Highly Informative Direct
Molecular Function (MF) phosphatidylinositol binding 2.943e-06 Highly Informative Direct
Molecular Function (MF) small GTPase regulator activity 0.000775 Highly Informative Direct
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0.444 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.0008218 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cell projection 1.538e-09 Moderately Informative Direct
Cellular Component (CC) vesicle 0.01563 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 0.382 Moderately Informative Inherited
Cellular Component (CC) cell leading edge 0 Informative Direct
Cellular Component (CC) coated vesicle 1.825e-06 Informative Direct
Cellular Component (CC) endosome 4.358e-06 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.07112 Informative Inherited
Cellular Component (CC) trans-Golgi network 2.028e-08 Highly Informative Direct
Cellular Component (CC) clathrin-coated vesicle 1.45e-07 Highly Informative Direct
Cellular Component (CC) centrosome 8.134e-05 Highly Informative Direct
Cellular Component (CC) spindle 0.0001378 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)Protein-serine/threonine kinases5.505e-11Moderately InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0Least InformativeDirect

Document: FA 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)Transferring phosphorous-containing groups8.533e-05Least InformativeDirect
Enzyme Commission (EC)Hydrolases0.1365Least InformativeInherited
Enzyme Commission (EC)Protein-serine/threonine kinases4.62e-11Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases1.758e-05Moderately InformativeDirect
Enzyme Commission (EC)Non-specific serine/threonine protein kinase4.136e-12InformativeDirect
Enzyme Commission (EC)Protein-tyrosine-phosphatase1.212e-08InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processApoptosis7.209e-09Moderately InformativeDirect
Biological processLipid transport0InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentEndosome9.858e-11Moderately InformativeDirect
Cellular componentCytoplasmic vesicle5.97e-08Moderately InformativeDirect
Cellular componentMicrosome0Highly InformativeDirect
DomainCoiled coil2.729e-11Moderately InformativeDirect
DomainSH3 domain2.878e-10InformativeDirect
DomainImmunoglobulin domain2.774e-05InformativeDirect
Molecular functionLipid-binding0InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationKinase0.5666Moderately InformativeInherited
Post-translational modificationGuanine-nucleotide releasing factor0InformativeDirect
Post-translational modificationGTPase activation1.564e-11InformativeDirect
Post-translational modificationSerine/threonine-protein kinase0.000718InformativeDirect
Post-translational modificationPhosphoprotein0.0001399Least InformativeDirect
Post-translational modificationAcetylation0.000487Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001251 SSF52087 Protein matches
Abstract This entry defines the C-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes [PubMed1715867]. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains [PubMed8643598]. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth.

Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.


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) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · 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 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 CRAL/TRIO domain 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 CRAL/TRIO domain 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) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]