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 (496) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 9,595 8,941 5
Proteins 9,523 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 process0.0016430.0009564Least InformativeInherited
Biological Process (BP)multicellular organismal process0.0027010.01773Least InformativeInherited
Biological Process (BP)embryo development ending in birth or egg hatching0.000000085580.0000918InformativeDirect
Biological Process (BP)in utero embryonic development0.000000011840.0000000108Highly 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) regulation of metabolic process 0.00001447 Least Informative Direct
Biological Process (BP) developmental process 0.0009564 Least Informative Direct
Biological Process (BP) positive regulation of biological process 0.000005929 Least Informative Direct
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.3083 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) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.2104 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.01773 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.07473 Least Informative Inherited
Biological Process (BP) localization 0.02092 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.05629 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) signal transduction 0.00007832 Moderately Informative Direct
Biological Process (BP) nervous system development 0.0001293 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0.00000000001143 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.000000001316 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0000006862 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 0 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.0000003606 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.000000000005292 Moderately Informative Direct
Biological Process (BP) regulation of phosphorus metabolic process 0 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 0.00005597 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.4231 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.007401 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.1529 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.1371 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.9008 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.7803 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.6038 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.6818 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) single-organism organelle organization 0.6974 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.234 Moderately Informative Inherited
Biological Process (BP) ion transport 0.04582 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.05476 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.2467 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.04849 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.2129 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.3836 Moderately Informative Inherited
Biological Process (BP) reproductive process 0.08474 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) phospholipid metabolic process 0.0001336 Informative Direct
Biological Process (BP) vitamin metabolic process 0.0000003089 Informative Direct
Biological Process (BP) anion transport 0.00000001677 Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 0 Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 0.0000918 Informative Direct
Biological Process (BP) positive regulation of catabolic process 0.00000000000001246 Informative Direct
Biological Process (BP) lipid localization 0.00000000000008678 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.0005558 Informative Direct
Biological Process (BP) dephosphorylation 0.0005721 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 0.000000000000005526 Informative Direct
Biological Process (BP) intracellular signal transduction 0.00000000000006789 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.000496 Informative Direct
Biological Process (BP) positive regulation of phosphate metabolic process 0.000005928 Informative Direct
Biological Process (BP) glycerolipid metabolic process 0.0003306 Informative Direct
Biological Process (BP) positive regulation of hydrolase activity 0.000001188 Informative Direct
Biological Process (BP) regulation of nervous system development 0.0000000001129 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.001591 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.01395 Informative Inherited
Biological Process (BP) cytoskeleton organization 0.5937 Informative Inherited
Biological Process (BP) synaptic transmission 0.2986 Informative Inherited
Biological Process (BP) regulation of growth 0.002158 Informative Inherited
Biological Process (BP) regulation of lipid metabolic process 0.04296 Informative Inherited
Biological Process (BP) alcohol metabolic process 0.01736 Informative Inherited
Biological Process (BP) organic hydroxy compound biosynthetic process 0.002282 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.008976 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.005169 Informative Inherited
Biological Process (BP) positive regulation of gene expression 0.008456 Informative Inherited
Biological Process (BP) positive regulation of RNA metabolic process 0.2575 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.08934 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.3595 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.111 Informative Inherited
Biological Process (BP) generation of neurons 1 Informative Inherited
Biological Process (BP) regulation of cell development 0.001952 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 1 Informative Inherited
Biological Process (BP) microtubule-based process 0.04533 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.07855 Informative Inherited
Biological Process (BP) growth 0.0549 Informative Inherited
Biological Process (BP) neurological system process 0.04303 Informative Inherited
Biological Process (BP) single-organism behavior 0.005626 Informative Inherited
Biological Process (BP) single-organism intracellular transport 0.8134 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.1595 Informative Inherited
Biological Process (BP) single organism reproductive process 0.1086 Informative Inherited
Biological Process (BP) reproductive structure development 0.02461 Informative Inherited
Biological Process (BP) embryonic organ development 0.1199 Informative Inherited
Biological Process (BP) in utero embryonic development 0.0000000108 Highly Informative Direct
Biological Process (BP) placenta development 0.0001779 Highly Informative Direct
Biological Process (BP) protein dephosphorylation 0.000001979 Highly Informative Direct
Biological Process (BP) lysosome organization 0.0000000000001023 Highly Informative Direct
Biological Process (BP) small GTPase mediated signal transduction 0 Highly Informative Direct
Biological Process (BP) circadian rhythm 0.0001707 Highly Informative Direct
Biological Process (BP) response to heat 0.0003095 Highly Informative Direct
Biological Process (BP) organophosphate ester transport 0 Highly Informative Direct
Biological Process (BP) cell growth 0.00002944 Highly Informative Direct
Biological Process (BP) regulation of cellular amine metabolic process 0.0000007588 Highly Informative Direct
Biological Process (BP) regulation of multicellular organism growth 0.0001649 Highly Informative Direct
Biological Process (BP) positive regulation of GTPase activity 0 Highly Informative Direct
Biological Process (BP) positive regulation of growth 0.0002671 Highly Informative Direct
Biological Process (BP) regulation of developmental growth 0.0001523 Highly Informative Direct
Biological Process (BP) regulation of alcohol biosynthetic process 0.000001062 Highly Informative Direct
Biological Process (BP) negative regulation of nervous system development 0.1105 Highly Informative Inherited
Biological Process (BP) developmental growth 0.00274 Highly Informative Inherited
Biological Process (BP) positive regulation of transcription, DNA-templated 0.001048 Highly Informative Inherited
Biological Process (BP) positive regulation of neurogenesis 0.00666 Highly Informative Inherited
Biological Process (BP) locomotory behavior 0.1215 Highly Informative Inherited
Biological Process (BP) regulation of Rho protein signal transduction 0.001288 Highly Informative Inherited
Biological Process (BP) regulation of Ras GTPase activity 0.02325 Highly Informative Inherited
Biological Process (BP) positive regulation of cyclic nucleotide metabolic process 0.585 Highly Informative Inherited
Biological Process (BP) aging 0.02445 Highly Informative Inherited
Biological Process (BP) learning or memory 0.04077 Highly Informative Inherited
Biological Process (BP) Golgi vesicle transport 0.001249 Highly Informative Inherited
Molecular Function (MF) binding 0.6661 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 0.00000000003913 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.0003603 Moderately Informative Direct
Molecular Function (MF) anion binding 0.0000002943 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.001308 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.1037 Moderately Informative Inherited
Molecular Function (MF) enzyme activator activity 0.000001004 Informative Direct
Molecular Function (MF) lipid binding 0 Informative Direct
Molecular Function (MF) phosphatase activity 0.0004699 Informative Direct
Molecular Function (MF) phosphoprotein phosphatase activity 0.000002483 Highly Informative Direct
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0 Highly Informative Direct
Molecular Function (MF) GTPase activator activity 0.000002298 Highly Informative Direct
Molecular Function (MF) lipid transporter activity 0 Highly Informative Direct
Molecular Function (MF) phosphatidylinositol binding 0.000003515 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.004265 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cell projection 0.000000008389 Moderately Informative Direct
Cellular Component (CC) vesicle 0.01681 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 0.4222 Moderately Informative Inherited
Cellular Component (CC) endosome 0.000004519 Informative Direct
Cellular Component (CC) Golgi apparatus 0.0000003528 Informative Direct
Cellular Component (CC) cell leading edge 0 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.07353 Informative Inherited
Cellular Component (CC) trans-Golgi network 0.00000002202 Highly Informative Direct
Cellular Component (CC) microtubule organizing center 0.0006974 Highly Informative Direct
Cellular Component (CC) spindle 0.0001453 Highly Informative Direct
Cellular Component (CC) coated vesicle 0.00000001498 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

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)alimentary tract and metabolism0Least InformativeDirect
Drugbank ATC_code (DB)other plain vitamin preparations1Moderately InformativeInherited
Drugbank ATC_code (DB)tocopherol (vit e)0.00000001802InformativeDirect

Document: DB 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) · 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 ]