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 (442) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 8,254 6,476 5
Proteins 8,205 6,431 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 process0.00046090.000665Least InformativeDirect
Biological Process (BP)multicellular organismal process0.00089460.02921Least InformativeInherited
Biological Process (BP)single-organism developmental process0.0095240.7805Moderately InformativeInherited
Biological Process (BP)chordate embryonic development1.473e-080.5595InformativeInherited

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 0.000665 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0006972 Least Informative Direct
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.07916 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.0744 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.02921 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.4531 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) localization 0.1395 Least Informative Inherited
Biological Process (BP) response to stimulus 0.07944 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.01962 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 signaling 3.327e-07 Moderately Informative Direct
Biological Process (BP) regulation of nitrogen compound metabolic process 3.569e-07 Moderately Informative Direct
Biological Process (BP) regulation of cell communication 1.042e-06 Moderately Informative Direct
Biological Process (BP) cell differentiation 4.519e-06 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 4.634e-05 Moderately Informative Direct
Biological Process (BP) signal transduction 0.0001232 Moderately Informative Direct
Biological Process (BP) nervous system development 0.0003287 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 0.03358 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.5093 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.002233 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.001246 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 0.01785 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.03039 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.8745 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.1364 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.6803 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.3854 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 0.7959 Moderately Informative Inherited
Biological Process (BP) ion transport 0.5041 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.203 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.7805 Moderately Informative Inherited
Biological Process (BP) system process 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.1453 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.7171 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.9975 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.04576 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.2269 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.1555 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) intracellular signal transduction 9.188e-14 Informative Direct
Biological Process (BP) positive regulation of catalytic activity 7.681e-09 Informative Direct
Biological Process (BP) vitamin metabolic process 1.166e-07 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 5.386e-07 Informative Direct
Biological Process (BP) vesicle-mediated transport 2.951e-06 Informative Direct
Biological Process (BP) lipid transport 5.51e-06 Informative Direct
Biological Process (BP) regulation of nervous system development 4.615e-05 Informative Direct
Biological Process (BP) phospholipid metabolic process 9.724e-05 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 0.0002024 Informative Direct
Biological Process (BP) glycerolipid metabolic process 0.000318 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 0.0007426 Informative Direct
Biological Process (BP) positive regulation of gene expression 0.000964 Informative Direct
Biological Process (BP) microtubule-based process 0.0578 Informative Inherited
Biological Process (BP) cytoskeleton organization 0.7229 Informative Inherited
Biological Process (BP) regulation of lipid metabolic process 0.02638 Informative Inherited
Biological Process (BP) alcohol metabolic process 0.003515 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.003626 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.006761 Informative Inherited
Biological Process (BP) regulation of cell development 0.01126 Informative Inherited
Biological Process (BP) generation of neurons 1 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.01801 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.6596 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 1 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 0.1364 Informative Inherited
Biological Process (BP) single-organism behavior 0.7678 Informative Inherited
Biological Process (BP) regulation of growth 0.00746 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.1655 Informative Inherited
Biological Process (BP) dephosphorylation 0.005978 Informative Inherited
Biological Process (BP) negative regulation of cellular metabolic process 1 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 0.005973 Informative Inherited
Biological Process (BP) positive regulation of phosphorus metabolic process 0.4812 Informative Inherited
Biological Process (BP) growth 0.06378 Informative Inherited
Biological Process (BP) anion transport 0.003137 Informative Inherited
Biological Process (BP) cellular membrane organization 0.01454 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.1528 Informative Inherited
Biological Process (BP) chordate embryonic development 0.5595 Informative Inherited
Biological Process (BP) small GTPase mediated signal transduction 0 Highly Informative Direct
Biological Process (BP) lysosome organization 1.202e-13 Highly Informative Direct
Biological Process (BP) organophosphate ester transport 2.179e-08 Highly Informative Direct
Biological Process (BP) regulation of cellular amine metabolic process 3.128e-08 Highly Informative Direct
Biological Process (BP) regulation of neuron differentiation 9.672e-07 Highly Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 2.857e-06 Highly Informative Direct
Biological Process (BP) alcohol biosynthetic process 5.579e-05 Highly Informative Direct
Biological Process (BP) positive regulation of MAPK cascade 5.89e-05 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 6.043e-05 Highly Informative Direct
Biological Process (BP) positive regulation of growth 0.0001389 Highly Informative Direct
Biological Process (BP) regulation of multicellular organism growth 0.0001612 Highly Informative Direct
Biological Process (BP) response to heat 0.000187 Highly Informative Direct
Biological Process (BP) cell growth 0.0002224 Highly Informative Direct
Biological Process (BP) phagocytosis 0.0004743 Highly Informative Direct
Biological Process (BP) protein dephosphorylation 0.0007424 Highly Informative Direct
Biological Process (BP) microtubule cytoskeleton organization 0.001375 Highly Informative Inherited
Biological Process (BP) positive regulation of cell differentiation 0.00184 Highly Informative Inherited
Biological Process (BP) locomotory behavior 0.05296 Highly Informative Inherited
Biological Process (BP) developmental growth 0.001636 Highly Informative Inherited
Biological Process (BP) regulation of purine nucleotide catabolic process 0.8765 Highly Informative Inherited
Biological Process (BP) aging 0.009429 Highly Informative Inherited
Biological Process (BP) learning or memory 0.01281 Highly Informative Inherited
Molecular Function (MF) binding 0.3672 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 1.992e-06 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.0003659 Moderately Informative Direct
Molecular Function (MF) heterocyclic compound binding 1 Moderately Informative Inherited
Molecular Function (MF) organic cyclic compound binding 1 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.1598 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 4.18e-05 Informative Direct
Molecular Function (MF) phosphoric ester hydrolase activity 0.00703 Informative Inherited
Molecular Function (MF) lipid transporter activity 0 Highly Informative Direct
Molecular Function (MF) organic hydroxy compound transmembrane transporter activity 1.368e-11 Highly Informative Direct
Molecular Function (MF) phosphatidylinositol binding 1.06e-05 Highly Informative Direct
Molecular Function (MF) phosphoprotein phosphatase activity 1.975e-05 Highly Informative Direct
Molecular Function (MF) small GTPase regulator activity 0.0001146 Highly Informative Direct
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0.429 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.000189 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 1.679e-09 Moderately Informative Direct
Cellular Component (CC) vesicle 0.009203 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 0.3155 Moderately Informative Inherited
Cellular Component (CC) cell leading edge 0 Informative Direct
Cellular Component (CC) coated vesicle 7.066e-07 Informative Direct
Cellular Component (CC) endosome 1.011e-06 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.05474 Informative Inherited
Cellular Component (CC) lamellipodium 9.246e-10 Highly Informative Direct
Cellular Component (CC) trans-Golgi network 9.329e-09 Highly Informative Direct
Cellular Component (CC) clathrin-coated vesicle 7.45e-08 Highly Informative Direct
Cellular Component (CC) spindle 7.732e-05 Highly Informative Direct
Cellular Component (CC) microtubule organizing center 0.0003469 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 groups8.984e-05Least InformativeDirect
Enzyme Commission (EC)Hydrolases0.1402Least InformativeInherited
Enzyme Commission (EC)Protein-serine/threonine kinases5.231e-11Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases1.751e-05Moderately InformativeDirect
Enzyme Commission (EC)Non-specific serine/threonine protein kinase4.645e-12InformativeDirect
Enzyme Commission (EC)Protein-tyrosine-phosphatase1.262e-08InformativeDirect

Document: EC annotation of SCOP domains

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)vitamins0Least InformativeDirect
Drugbank ATC_code (DB)other plain vitamin preparations1Moderately InformativeInherited
Drugbank ATC_code (DB)tocopherol (vit e)7.377e-09InformativeDirect

Document: DB annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processApoptosis1.774e-09Moderately InformativeDirect
Biological processLipid transport0InformativeDirect
Cellular componentMembrane1.068e-11Least InformativeDirect
Cellular componentCytoplasm3.94e-05Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentGolgi apparatus7.382e-14Moderately InformativeDirect
Cellular componentEndosome6.78e-12Moderately InformativeDirect
Cellular componentCytoplasmic vesicle1.202e-08Moderately InformativeDirect
Cellular componentMicrosome0Highly InformativeDirect
DomainSH3 domain1.257e-10InformativeDirect
DomainImmunoglobulin domain1.541e-05InformativeDirect
Molecular functionLipid-binding0InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationKinase0.4384Moderately InformativeInherited
Post-translational modificationGuanine-nucleotide releasing factor0InformativeDirect
Post-translational modificationGTPase activation5.128e-12InformativeDirect
Post-translational modificationSerine/threonine-protein kinase0.0003993InformativeDirect
Post-translational modificationPhosphoprotein1.816e-05Least 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) · DrugBank ATC (DB) · 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) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · Internal database links ]