SUPERFAMILY 1.75 HMM library and genome assignments server

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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 process0.0016460.0009686Least InformativeInherited
Biological Process (BP)multicellular organismal process0.0030110.0363Least InformativeInherited
Biological Process (BP)embryo development ending in birth or egg hatching0.000000082470.00009118InformativeDirect

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 0.0009686 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.00006098 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.01968 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.7735 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 0.055 Least Informative Inherited
Biological Process (BP) localization 0.01535 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.0363 Least Informative Inherited
Biological Process (BP) response to stimulus 0.3088 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.3727 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 0.0000000008732 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0000005243 Moderately Informative Direct
Biological Process (BP) signal transduction 0.00007953 Moderately Informative Direct
Biological Process (BP) nervous system development 0.00009828 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.0003714 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.4903 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.007407 Moderately Informative Inherited
Biological Process (BP) system process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.8274 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.235 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.759 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.09044 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.1213 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.792 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.8791 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.06453 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.0579 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) ion transport 0.05506 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.2443 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.3562 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.07255 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.2712 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.04865 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.1559 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.345 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.678 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.00009118 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 0.00000000000001086 Informative Direct
Biological Process (BP) lipid localization 0.00000000000006238 Informative Direct
Biological Process (BP) regulation of nervous system development 0.0000000001078 Informative Direct
Biological Process (BP) anion transport 0.00000001198 Informative Direct
Biological Process (BP) vitamin metabolic process 0.0000003133 Informative Direct
Biological Process (BP) positive regulation of hydrolase activity 0.0000008922 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 0.000001694 Informative Direct
Biological Process (BP) phospholipid metabolic process 0.0001312 Informative Direct
Biological Process (BP) regulation of cell development 0.00015 Informative Direct
Biological Process (BP) glycerolipid metabolic process 0.0003268 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.000381 Informative Direct
Biological Process (BP) dephosphorylation 0.0007641 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.0008026 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.06774 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.005243 Informative Inherited
Biological Process (BP) microtubule-based process 0.1045 Informative Inherited
Biological Process (BP) cytoskeleton organization 0.6606 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 1 Informative Inherited
Biological Process (BP) synaptic transmission 0.03868 Informative Inherited
Biological Process (BP) regulation of growth 0.002586 Informative Inherited
Biological Process (BP) regulation of lipid metabolic process 0.05067 Informative Inherited
Biological Process (BP) organic hydroxy compound biosynthetic process 0.001612 Informative Inherited
Biological Process (BP) alcohol metabolic process 0.01563 Informative Inherited
Biological Process (BP) positive regulation of gene expression 0.001952 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.006509 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.008503 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.03226 Informative Inherited
Biological Process (BP) generation of neurons 1 Informative Inherited
Biological Process (BP) single-organism behavior 0.8214 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.2372 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 1 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 1 Informative Inherited
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0.01847 Informative Inherited
Biological Process (BP) growth 0.05602 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.5842 Informative Inherited
Biological Process (BP) embryonic organ development 0.05104 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) positive regulation of GTPase activity 0 Highly Informative Direct
Biological Process (BP) lysosome organization 0.0000000000001052 Highly Informative Direct
Biological Process (BP) regulation of cellular amine metabolic process 0.0000002776 Highly Informative Direct
Biological Process (BP) protein dephosphorylation 0.000001983 Highly Informative Direct
Biological Process (BP) regulation of striated muscle tissue development 0.00002445 Highly Informative Direct
Biological Process (BP) positive regulation of growth 0.00004609 Highly Informative Direct
Biological Process (BP) placenta development 0.00005747 Highly Informative Direct
Biological Process (BP) cell growth 0.0001327 Highly Informative Direct
Biological Process (BP) regulation of developmental growth 0.0001471 Highly Informative Direct
Biological Process (BP) circadian rhythm 0.0001721 Highly Informative Direct
Biological Process (BP) regulation of multicellular organism growth 0.0002219 Highly Informative Direct
Biological Process (BP) response to heat 0.0003097 Highly Informative Direct
Biological Process (BP) developmental growth 0.0006024 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 0.0006681 Highly Informative Direct
Biological Process (BP) positive regulation of transcription, DNA-dependent 0.009842 Highly Informative Inherited
Biological Process (BP) locomotory behavior 0.04415 Highly Informative Inherited
Biological Process (BP) regulation of Rho protein signal transduction 0.001284 Highly Informative Inherited
Biological Process (BP) regulation of Ras GTPase activity 0.02301 Highly Informative Inherited
Biological Process (BP) regulation of cyclic nucleotide metabolic process 0.9213 Highly Informative Inherited
Biological Process (BP) regulation of striated muscle cell differentiation 0.3645 Highly Informative Inherited
Biological Process (BP) aging 0.009762 Highly Informative Inherited
Biological Process (BP) learning or memory 0.0133 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) binding 0.6426 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.0000002948 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.001314 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.09844 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 0.00006909 Informative Direct
Molecular Function (MF) phosphoric ester hydrolase activity 0.002524 Informative Inherited
Molecular Function (MF) lipid transporter activity 0 Highly Informative Direct
Molecular Function (MF) organic cation transmembrane transporter activity 0.00000000002233 Highly Informative Direct
Molecular Function (MF) organic hydroxy compound transmembrane transporter activity 0.00000000003709 Highly Informative Direct
Molecular Function (MF) phosphoprotein phosphatase activity 0.000002334 Highly Informative Direct
Molecular Function (MF) phosphatidylinositol binding 0.000003462 Highly Informative Direct
Molecular Function (MF) small GTPase regulator activity 0.0007665 Highly Informative Direct
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0.4443 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.0008646 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 0.000000005004 Moderately Informative Direct
Cellular Component (CC) vesicle 0.01568 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 0.3837 Moderately Informative Inherited
Cellular Component (CC) cell leading edge 0 Informative Direct
Cellular Component (CC) coated vesicle 0.000001924 Informative Direct
Cellular Component (CC) endosome 0.000004438 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.07063 Informative Inherited
Cellular Component (CC) trans-Golgi network 0.00000002102 Highly Informative Direct
Cellular Component (CC) clathrin-coated vesicle 0.000000153 Highly Informative Direct
Cellular Component (CC) centrosome 0.00008125 Highly Informative Direct
Cellular Component (CC) spindle 0.0001375 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 kinases0.00000000005505Moderately 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 groups0.00008453Least InformativeDirect
Enzyme Commission (EC)Hydrolases0.1363Least InformativeInherited
Enzyme Commission (EC)Protein-serine/threonine kinases0.00000000004588Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.00001755Moderately InformativeDirect
Enzyme Commission (EC)Non-specific serine/threonine protein kinase0.000000000004154InformativeDirect
Enzyme Commission (EC)Protein-tyrosine-phosphatase0.00000001205InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processApoptosis0.000000007253Moderately InformativeDirect
Biological processLipid transport0InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentEndosome0.0000000001068Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0.00000006267Moderately InformativeDirect
Cellular componentMicrosome0Highly InformativeDirect
DomainCoiled coil0.00000000002844Moderately InformativeDirect
DomainSH3 domain0.0000000002843InformativeDirect
DomainImmunoglobulin domain0.00002759InformativeDirect
Molecular functionLipid-binding0InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationKinase0.5671Moderately InformativeInherited
Post-translational modificationGuanine-nucleotide releasing factor0InformativeDirect
Post-translational modificationGTPase activation0.00000000001399InformativeDirect
Post-translational modificationSerine/threonine-protein kinase0.0007199InformativeDirect
Post-translational modificationPhosphoprotein0.000143Least InformativeDirect
Post-translational modificationAcetylation0.0004894Least 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 ]