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 (504) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 9,900 22,997 5
Proteins 9,791 22,607 5


Functional annotation
General category Processes_IC
Detailed category Phospholipid metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) multicellular organismal process 0.0002554 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biological regulation 0.1508 Least Informative Inherited
Biological Process (BP) response to stimulus 0.8775 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.2117 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.3197 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cell communication 0.0000003185 Moderately Informative Direct
Biological Process (BP) regulation of signaling 0.00000005836 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.000004295 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0.0001456 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.005637 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.2377 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.412 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.7925 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.1349 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.001114 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.1095 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.0121 Moderately Informative Inherited
Biological Process (BP) cell communication 0.03491 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.1918 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.9701 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.3378 Moderately Informative Inherited
Biological Process (BP) ion transport 0.3394 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.004171 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) reproduction 0.03957 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.9683 Moderately Informative Inherited
Biological Process (BP) single organism signaling 0.04501 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.3262 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.1992 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.06074 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.04873 Moderately Informative Inherited
Biological Process (BP) phospholipid metabolic process 0.0002164 Informative Direct
Biological Process (BP) response to oxidative stress 0.0006964 Informative Direct
Biological Process (BP) behavior 0.000000000008378 Informative Direct
Biological Process (BP) lipid localization 0.000000435 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.0004923 Informative Direct
Biological Process (BP) intracellular signal transduction 0.000001624 Informative Direct
Biological Process (BP) regulation of growth 0.00003233 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.00001461 Informative Direct
Biological Process (BP) cell development 0.0007476 Informative Direct
Biological Process (BP) positive regulation of developmental process 0.0005241 Informative Direct
Biological Process (BP) regulation of nervous system development 0.0000000008218 Informative Direct
Biological Process (BP) regulation of intracellular signal transduction 0.0000000000007927 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.007899 Informative Inherited
Biological Process (BP) system process 0.01442 Informative Inherited
Biological Process (BP) regulation of lipid metabolic process 0.005255 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.1661 Informative Inherited
Biological Process (BP) growth 0.001735 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.008847 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 1 Informative Inherited
Biological Process (BP) positive regulation of catalytic activity 0.003149 Informative Inherited
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0.09049 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.03156 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.3744 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.06621 Informative Inherited
Biological Process (BP) phosphorylation 0.8861 Informative Inherited
Biological Process (BP) anion transport 0.06048 Informative Inherited
Biological Process (BP) response to temperature stimulus 0.0236 Informative Inherited
Biological Process (BP) response to radiation 0.4436 Informative Inherited
Biological Process (BP) localization of cell 0.1612 Informative Inherited
Biological Process (BP) single organism reproductive process 0.01382 Informative Inherited
Biological Process (BP) multi-organism reproductive process 0.07011 Informative Inherited
Biological Process (BP) movement of cell or subcellular component 0.2173 Informative Inherited
Biological Process (BP) locomotion 0.16 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.02571 Informative Inherited
Biological Process (BP) multicellular organism reproduction 0.3148 Informative Inherited
Biological Process (BP) epithelium development 0.5292 Informative Inherited
Biological Process (BP) protein dephosphorylation 0.0000229 Highly Informative Direct
Biological Process (BP) phagocytosis 0.0005655 Highly Informative Direct
Biological Process (BP) lysosome organization 0.00000000000003269 Highly Informative Direct
Biological Process (BP) small GTPase mediated signal transduction 0.000000000007246 Highly Informative Direct
Biological Process (BP) circadian rhythm 0.0000006279 Highly Informative Direct
Biological Process (BP) response to heat 0.00001164 Highly Informative Direct
Biological Process (BP) regulation of cellular ketone metabolic process 0.0001151 Highly Informative Direct
Biological Process (BP) organophosphate ester transport 0.00003007 Highly Informative Direct
Biological Process (BP) cell growth 0.00000004553 Highly Informative Direct
Biological Process (BP) regulation of cyclic nucleotide metabolic process 0.000000008931 Highly Informative Direct
Biological Process (BP) gliogenesis 0.0000002226 Highly Informative Direct
Biological Process (BP) single-organism behavior 0.000000000003229 Highly Informative Direct
Biological Process (BP) negative regulation of growth 0.0002675 Highly Informative Direct
Biological Process (BP) positive regulation of growth 0.00000001151 Highly Informative Direct
Biological Process (BP) positive regulation of nucleotide metabolic process 0.00000002108 Highly Informative Direct
Biological Process (BP) regulation of developmental growth 0.00003006 Highly Informative Direct
Biological Process (BP) nervous system process 0.0000004765 Highly Informative Direct
Biological Process (BP) protein localization to membrane 0.0006608 Highly Informative Direct
Biological Process (BP) negative regulation of nervous system development 0.01215 Highly Informative Inherited
Biological Process (BP) locomotory behavior 0.1824 Highly Informative Inherited
Biological Process (BP) second-messenger-mediated signaling 0.005121 Highly Informative Inherited
Biological Process (BP) aging 0.001188 Highly Informative Inherited
Biological Process (BP) germ cell development 0.5509 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.01506 Highly Informative Inherited
Biological Process (BP) epithelial cell differentiation 0.4328 Highly Informative Inherited
Molecular Function (MF) binding 0.5835 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) anion binding 0.000134 Moderately Informative Direct
Molecular Function (MF) molecular function regulator 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.1216 Moderately Informative Inherited
Molecular Function (MF) transporter activity 0.0169 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.06767 Moderately Informative Inherited
Molecular Function (MF) phospholipid binding 0.00000000323 Informative Direct
Molecular Function (MF) enzyme activator activity 0.000001841 Informative Direct
Molecular Function (MF) phosphatase activity 0.0001925 Informative Direct
Molecular Function (MF) enzyme binding 0.003116 Informative Inherited
Molecular Function (MF) phosphoprotein phosphatase activity 0.000000574 Highly Informative Direct
Molecular Function (MF) lipid transporter activity 0 Highly Informative Direct
Molecular Function (MF) vitamin binding 0.0000005146 Highly Informative Direct
Molecular Function (MF) GTPase regulator activity 0 Highly Informative Direct
Molecular Function (MF) small GTPase binding 0.000006319 Highly Informative Direct
Molecular Function (MF) phosphatidylinositol phosphate binding 0.1699 Highly Informative Inherited
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0.08206 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.00000694 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.4159 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) endomembrane system 0.0000001969 Moderately Informative Direct
Cellular Component (CC) vesicle 0.0007826 Moderately Informative Direct
Cellular Component (CC) Golgi apparatus 0.0000002949 Informative Direct
Cellular Component (CC) coated vesicle 0.000009034 Highly Informative Direct
Cellular Component (CC) Golgi subcompartment 0.0001219 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processApoptosis0.00000001126Moderately InformativeDirect
Biological processLipid transport0InformativeDirect
Biological processSensory transduction0.00007437InformativeDirect
Biological processVision0.00000009673Highly InformativeDirect
Cellular componentMembrane6.573e-16Least InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentEndosome0.0000000007089Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0.0000003826Moderately InformativeDirect
Cellular componentMicrosome0Highly InformativeDirect
DomainCoiled coil0.0000000001116Moderately InformativeDirect
DomainSH3 domain0.00000000001659InformativeDirect
DomainImmunoglobulin domain0.000003723InformativeDirect
Molecular functionLipid-binding0Moderately InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationKinase0.4407Moderately InformativeInherited
Post-translational modificationGuanine-nucleotide releasing factor0InformativeDirect
Post-translational modificationGTPase activation0.00000000003547InformativeDirect
Post-translational modificationSerine/threonine-protein kinase0.0001953InformativeDirect
Post-translational modificationPhosphoprotein0.000000402Least 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-coverage) · 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-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]