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Rhodanese/Cell cycle control phosphatase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Rhodanese/Cell cycle control phosphatase [ 52820]
Superfamily:   Rhodanese/Cell cycle control phosphatase [ 52821] (4)
Families:   Cell cycle control phosphatase, catalytic domain [ 52822] (4)
  Single-domain sulfurtransferase [ 69509] (3)
  Multidomain sulfurtransferase (rhodanese) [ 52827] (4)
  Ubiquitin carboxyl-terminal hydrolase 8, USP8 [ 117586]


Superfamily statistics
Genomes (3,030) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 24,655 126,045 30
Proteins 20,265 100,147 20


Functional annotation
General category Processes_IC
Detailed category Cell cycle, Apoptosis

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Molecular Function (MF)hydrolase activity0.57690.0000000001051Least InformativeInherited
Molecular Function (MF)transferase activity0.12611Least InformativeInherited
Molecular Function (MF)hydrolase activity, acting on ester bonds0.015760Moderately InformativeInherited
Molecular Function (MF)oxidoreductase activity0.32921Moderately InformativeInherited
Molecular Function (MF)transferase activity, transferring sulfur-containing groups0.0000000000051690InformativeDirect
Molecular Function (MF)phosphatase activity0.00015460InformativeDirect
Molecular Function (MF)sulfurtransferase activity0.0000000000000013860Highly 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) organonitrogen compound metabolic process 0.00003777 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.002471 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.9438 Least Informative Inherited
Biological Process (BP) cellular protein modification process 0.0000408 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0.0001909 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.000000000548 Moderately Informative Direct
Biological Process (BP) regulation of cell communication 0.000000001742 Moderately Informative Direct
Biological Process (BP) regulation of signaling 0.000000001966 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.00005655 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0.0000007915 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.00000000000001763 Moderately Informative Direct
Biological Process (BP) regulation of molecular function 0 Moderately Informative Direct
Biological Process (BP) cellular component assembly 0.7966 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.9891 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.9168 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.6496 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.6577 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.9242 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 0.3366 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.8628 Moderately Informative Inherited
Biological Process (BP) negative regulation of cell communication 0 Informative Direct
Biological Process (BP) cell cycle process 0.00005126 Informative Direct
Biological Process (BP) negative regulation of signaling 0 Informative Direct
Biological Process (BP) regulation of protein modification process 0 Informative Direct
Biological Process (BP) negative regulation of cellular protein metabolic process 0 Informative Direct
Biological Process (BP) regulation of phosphorylation 0 Informative Direct
Biological Process (BP) negative regulation of molecular function 0.0000000008696 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0.00009476 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 0 Informative Direct
Biological Process (BP) regulation of transferase activity 0.00000000001969 Informative Direct
Biological Process (BP) regulation of cell cycle 0.00000003229 Informative Direct
Biological Process (BP) regulation of intracellular signal transduction 0.000000006578 Informative Direct
Biological Process (BP) organelle assembly 0.003293 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.2008 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.6758 Informative Inherited
Biological Process (BP) intracellular transport 0.4754 Informative Inherited
Biological Process (BP) single-organism cellular localization 0.05645 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 1 Informative Inherited
Biological Process (BP) proteolysis 1 Informative Inherited
Biological Process (BP) protein dephosphorylation 0 Highly Informative Direct
Biological Process (BP) mitochondrial transport 0.00006433 Highly Informative Direct
Biological Process (BP) nucleobase-containing compound transport 0.00002319 Highly Informative Direct
Biological Process (BP) cell projection assembly 0.00005977 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 0 Highly Informative Direct
Biological Process (BP) regulation of MAP kinase activity 0.00000008684 Highly Informative Direct
Biological Process (BP) mitotic cell cycle phase transition 0.0004345 Highly Informative Direct
Biological Process (BP) negative regulation of phosphate metabolic process 0 Highly Informative Direct
Biological Process (BP) establishment of RNA localization 0.00002552 Highly Informative Direct
Biological Process (BP) negative regulation of transferase activity 0 Highly Informative Direct
Biological Process (BP) regulation of chromosome segregation 0.0003087 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular signal transduction 0 Highly Informative Direct
Biological Process (BP) regulation of reproductive process 0.00005453 Highly Informative Direct
Biological Process (BP) regulation of chromosome organization 0.02588 Highly Informative Inherited
Biological Process (BP) regulation of mitotic cell cycle phase transition 0.007247 Highly Informative Inherited
Biological Process (BP) negative regulation of mitotic cell cycle 0.09015 Highly Informative Inherited
Biological Process (BP) plasma membrane bounded cell projection organization 0.1621 Highly Informative Inherited
Biological Process (BP) regulation of mitotic nuclear division 0.1602 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.0000000001051 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0 Moderately Informative Direct
Molecular Function (MF) oxidoreductase activity 1 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 1 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring sulfur-containing groups 0 Informative Direct
Molecular Function (MF) phosphatase activity 0 Informative Direct
Molecular Function (MF) RNA binding 0.5206 Informative Inherited
Molecular Function (MF) peptidase activity, acting on L-amino acid peptides 0.07923 Informative Inherited
Molecular Function (MF) phosphoprotein phosphatase activity 0.0000007606 Highly Informative Direct
Molecular Function (MF) sulfurtransferase activity 0 Highly Informative Direct
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.931 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.7358 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0.0466 Moderately Informative Inherited
Cellular Component (CC) cell projection 0.1514 Moderately Informative Inherited
Cellular Component (CC) cilium 0.0008834 Informative Direct
Cellular Component (CC) plastid 0.00005878 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.0002669 Informative Direct
Cellular Component (CC) plasma membrane bounded cell projection part 0.02914 Informative Inherited
Cellular Component (CC) microtubule organizing center 0.00002223 Highly Informative Direct
Cellular Component (CC) thylakoid 0.000006195 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)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0.4896Least InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases0Moderately InformativeDirect
Enzyme Commission (EC)Omega peptidases0.000000001076Moderately InformativeDirect
Enzyme Commission (EC)Protein-tyrosine-phosphatase0InformativeDirect
Enzyme Commission (EC)Sulfurtransferases0InformativeDirect
Enzyme Commission (EC)Phosphoprotein phosphatase0.00002524InformativeDirect
Enzyme Commission (EC)tRNA sulfurtransferase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle0.0000000001709Moderately InformativeDirect
Biological processMitosis0InformativeDirect
Biological processThiamine biosynthesis0Highly InformativeDirect
Biological processCilium biogenesis/degradation0.00000000003185Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentEndosome0.0001607Moderately InformativeDirect
Cellular componentCell projection0.001171Moderately InformativeInherited
Cellular componentCilium0.000000006665InformativeDirect
DiseaseCiliopathy0InformativeDirect
DomainRedox-active center0InformativeDirect
Molecular functionSelenium0Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationHydrolase0.259Least InformativeInherited
Post-translational modificationRNA-binding8.797e-16Moderately InformativeDirect
Post-translational modificationProtease0.7031Moderately InformativeInherited
Post-translational modificationProtein phosphatase0InformativeDirect
Post-translational modificationThiol protease0.0000003974InformativeDirect
Post-translational modificationtRNA-binding0Highly InformativeDirect
Post-translational modificationDisulfide bond0.0000000000002101Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001763 SSF52821 Protein matches
Abstract

Rhodanese, a sulphurtransferase involved in cyanide detoxification (see ) shares evolutionary relationship with a large family of proteins [PubMed9733650], including

  • Cdc25 phosphatase catalytic domain.
  • non-catalytic domains of eukaryotic dual-specificity MAPK-phosphatases.
  • non-catalytic domains of yeast PTP-type MAPK-phosphatases.
  • non-catalytic domains of yeast Ubp4, Ubp5, Ubp7.
  • non-catalytic domains of mammalian Ubp-Y.
  • Drosophila heat shock protein HSP-67BB.
  • several bacterial cold-shock and phage shock proteins.
  • plant senescence associated proteins.
  • catalytic and non-catalytic domains of rhodanese (see ).

Rhodanese has an internal duplication. This domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases [PubMed8702871].


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) · 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 22 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 Rhodanese/Cell cycle control phosphatase 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 22 hidden Markov models representing the Rhodanese/Cell cycle control phosphatase 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) · UniProtKB KeyWords (KW) · Internal database links ]