SUPERFAMILY 1.75 HMM library and genome assignments server

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 (3,023) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 24,524 121,336 30
Proteins 20,146 99,293 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)
Biological Process (BP)protein metabolic process0.88980.0000000002321Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.94680.0000002532Least InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process0.31770.0000000001565Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.35950.0000002652Moderately InformativeInherited
Biological Process (BP)dephosphorylation0.00081710InformativeDirect
Biological Process (BP)protein dephosphorylation0.00043360Highly InformativeDirect
Molecular Function (MF)hydrolase activity0.65140.00000000002947Least InformativeInherited
Molecular Function (MF)transferase activity0.10011Least InformativeInherited
Molecular Function (MF)oxidoreductase activity0.22481Moderately InformativeInherited
Molecular Function (MF)hydrolase activity, acting on ester bonds0.031910Moderately InformativeInherited
Molecular Function (MF)phosphoric ester hydrolase activity0.0014380InformativeInherited
Molecular Function (MF)sulfurtransferase activity0.000000000000002620Highly 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) protein metabolic process 0.0000000002321 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0000002532 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.2107 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.0253 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.0000000001565 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.0000002652 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.00000000000007043 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.000000007805 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0.000001522 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.000009535 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0002198 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.6006 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.396 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.9953 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.8161 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.8609 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) dephosphorylation 0 Informative Direct
Biological Process (BP) negative regulation of signaling 0 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 0 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 0 Informative Direct
Biological Process (BP) negative regulation of cell communication 0 Informative Direct
Biological Process (BP) regulation of intracellular protein kinase cascade 0.000000000000643 Informative Direct
Biological Process (BP) negative regulation of catalytic activity 0.00000000004021 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0.0000008008 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 0.000005211 Informative Direct
Biological Process (BP) cell cycle process 0.0000097 Informative Direct
Biological Process (BP) regulation of kinase activity 0.0001923 Informative Direct
Biological Process (BP) organelle assembly 0.0005245 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.5942 Informative Inherited
Biological Process (BP) cell projection organization 0.293 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.153 Informative Inherited
Biological Process (BP) nitrogen compound transport 0.1193 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 1 Informative Inherited
Biological Process (BP) protein modification by small protein conjugation or removal 1 Informative Inherited
Biological Process (BP) regulation of mitotic cell cycle 0.002733 Informative Inherited
Biological Process (BP) regulation of cell cycle process 0.05945 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.008019 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.4508 Informative Inherited
Biological Process (BP) protein dephosphorylation 0 Highly Informative Direct
Biological Process (BP) negative regulation of phosphorylation 0.000000000000003755 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 0.0000000000001209 Highly Informative Direct
Biological Process (BP) regulation of MAP kinase activity 0.00000002995 Highly Informative Direct
Biological Process (BP) cilium organization 0.00000005353 Highly Informative Direct
Biological Process (BP) cell projection assembly 0.000005597 Highly Informative Direct
Biological Process (BP) cellular component assembly involved in morphogenesis 0.00008418 Highly Informative Direct
Biological Process (BP) stress-activated protein kinase signaling cascade 0.00008674 Highly Informative Direct
Biological Process (BP) establishment of RNA localization 0.0001217 Highly Informative Direct
Biological Process (BP) regulation of reproductive process 0.0004289 Highly Informative Direct
Biological Process (BP) mitochondrial transport 0.0004622 Highly Informative Direct
Biological Process (BP) mitotic cell cycle phase transition 0.0007368 Highly Informative Direct
Biological Process (BP) nucleobase-containing compound transport 0.0009136 Highly Informative Direct
Biological Process (BP) negative regulation of cell cycle 0.003977 Highly Informative Inherited
Biological Process (BP) cell part morphogenesis 0.0951 Highly Informative Inherited
Biological Process (BP) small GTPase mediated signal transduction 0.07944 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.00000000002947 Least Informative Direct
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) binding 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) phosphoric ester hydrolase activity 0 Informative Direct
Molecular Function (MF) peptidase activity 0.9685 Informative Inherited
Molecular Function (MF) RNA binding 0.3949 Informative Inherited
Molecular Function (MF) sulfurtransferase activity 0 Highly Informative Direct
Molecular Function (MF) phosphoprotein phosphatase activity 0.000000366 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.9399 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.01072 Least Informative Inherited
Cellular Component (CC) cell projection 0.05153 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 0.3925 Moderately Informative Inherited
Cellular Component (CC) vesicle 1 Moderately Informative Inherited
Cellular Component (CC) plastid 0.00009662 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.01673 Informative Inherited
Cellular Component (CC) secretory granule 0.002077 Informative Inherited
Cellular Component (CC) cilium part 0.00000007364 Highly Informative Direct
Cellular Component (CC) centrosome 0.0000005282 Highly Informative Direct
Cellular Component (CC) midbody 0.000009234 Highly Informative Direct
Cellular Component (CC) sperm part 0.00003136 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

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.3002Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.4009Least InformativeInherited
Mammalian Phenotype (MP)abnormal cell death0.009557Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.04552Moderately InformativeInherited
Mammalian Phenotype (MP)digestive/alimentary phenotype0.3256Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.341Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal intestine morphology0.04137InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system physiology0.08182InformativeInherited
Mammalian Phenotype (MP)increased apoptosis0.1667InformativeInherited
Mammalian Phenotype (MP)abnormal cell differentiation0.1737InformativeInherited
Mammalian Phenotype (MP)abnormal cell proliferation0.2857InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system development0.0004762Highly InformativeDirect
Mammalian Phenotype (MP)abnormal intestinal mucosa morphology0.005485Highly InformativeInherited
Mammalian Phenotype (MP)abnormal tumor necrosis factor secretion0.06124Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism environmental stimulus response variant0.3406Least InformativeInherited
Worm Phenotype (WP)organism pathogen response variant0.001217InformativeInherited
Worm Phenotype (WP)pathogen susceptibility increased0.00004183Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)adult0Least InformativeDirect
Fly Anatomy (FA)organ system0Least InformativeDirect
Fly Anatomy (FA)cell0Least InformativeDirect
Fly Anatomy (FA)multi-tissue structure0Least InformativeDirect
Fly Anatomy (FA)anatomical group0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)thoracic segment0Moderately InformativeDirect
Fly Anatomy (FA)adult segment0Moderately InformativeDirect
Fly Anatomy (FA)adult thorax0Moderately InformativeDirect
Fly Anatomy (FA)adult sense organ0Moderately InformativeDirect
Fly Anatomy (FA)external sensory organ0Moderately InformativeDirect
Fly Anatomy (FA)adult integumentary system0Moderately InformativeDirect
Fly Anatomy (FA)sensillum0Moderately InformativeDirect
Fly Anatomy (FA)tagmatic subdivision of integument0Moderately InformativeDirect
Fly Anatomy (FA)sensory organ cell0InformativeDirect
Fly Anatomy (FA)extended germ band embryo0InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.4507Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue0.8568Least InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.1275Moderately InformativeInherited
Xenopus ANatomical entity (XAN)neural plate0.0002145InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0.05167Least InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0.512Moderately InformativeInherited
Enzyme Commission (EC)Protein-tyrosine-phosphatase0InformativeDirect
Enzyme Commission (EC)Omega peptidases0.000000001995InformativeDirect
Enzyme Commission (EC)Sulfurtransferases0Highly InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine phosphatase0.000002441Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle0.0000000000936Moderately InformativeDirect
Biological processMitosis0InformativeDirect
Biological processThiamine biosynthesis0Highly InformativeDirect
Biological processCilium biogenesis/degradation0.000000000001691Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentEndosome0.00004239Moderately InformativeDirect
Cellular componentCell projection0.00007237Moderately InformativeDirect
Cellular componentCilium0.000000001584Highly InformativeDirect
DiseaseCiliopathy0InformativeDirect
DomainRedox-active center0InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functiontRNA-binding0InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationHydrolase0.3328Least InformativeInherited
Post-translational modificationProtease0.7063Moderately InformativeInherited
Post-translational modificationProtein phosphatase0InformativeDirect
Post-translational modificationThiol protease0.0000002936InformativeDirect
Post-translational modificationDisulfide bond0.00000000000001183Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)cofactor metabolism0Least InformativeDirect
UniPathway (UP)thiamine metabolism0InformativeDirect

Document: UP 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]