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  Home > SCOP hierarchy > Cysteine proteinases superfamily


Cysteine proteinases superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Cysteine proteinases [ 54000]
Superfamily:   Cysteine proteinases [ 54001] (22)
Families:   Papain-like [ 54002] (25)
  Avirulence protein Avrpph3 [ 102723]
  FMDV leader protease [ 54037]
  Calpain large subunit, catalytic domain (domain II) [ 54040]
  Transglutaminase core [ 54044] (2)
  Arylamine N-acetyltransferase [ 54047]
  Ubiquitin carboxyl-terminal hydrolase UCH-L [ 54050] (2)
  Ubiquitin carboxyl-terminal hydrolase, UCH [ 82568] (5)
  Adenain-like [ 54054] (5)
  Microbial transglutaminase [ 75336]
  Ubiquitin thiolesterase protein OTUB2 (Otubain-2) [ 110773]
  IgG-specific endopeptidase IdeS (Sib38) [ 117762]
  Lpg0564-like [ 142864]
  Phytochelatin synthase [ 142867]
  CHAP domain [ 142870]
  NlpC/P60 [ 142873]
  PMT C-terminal domain like [ 159843]
  MOA C-terminal domain-like [ 159846]
  Atu2299-like [ 159849]
  M48USP-like [ 159852]
  YiiX-like [ 159855]
  Autophagin-like [ 159858] (2)

Superfamily statistics
Genomes (3,041) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 65,580 287,676 132
Proteins 64,550 284,432 132

 Functional annotation
General category Processes_IC
Detailed category Proteases

Document: Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds1Least InformativeInherited
Enzyme Commission (EC)Cysteine endopeptidases0Moderately InformativeDirect
Enzyme Commission (EC)Omega peptidases0Moderately InformativeDirect
Enzyme Commission (EC)In linear amides0.000001738Moderately InformativeDirect
Enzyme Commission (EC)Transferring groups other than amino-acyl groups1Moderately InformativeInherited
Enzyme Commission (EC)Aminoacyltransferases0InformativeDirect
Enzyme Commission (EC)Dipeptidyl-peptidases and tripeptidyl-peptidases1InformativeInherited
Enzyme Commission (EC)Protein-glutamine gamma-glutamyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Poly(A)-specific ribonuclease0Highly InformativeDirect
Enzyme Commission (EC)Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagin0Highly InformativeDirect
Enzyme Commission (EC)N-acetylmuramoyl-L-alanine amidase0.00000006359Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)skin disease0.01121Moderately InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.5345Moderately InformativeInherited
Disease Ontology (DO)bullous skin disease0.01667InformativeInherited

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.6794Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of central motor function0.01269Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of movement0.3651Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reflex0.06763InformativeInherited
Phenotypic Abnormality (PA)Upper motor neuron dysfunction0.5192InformativeInherited
Phenotypic Abnormality (PA)Abnormal pyramidal sign0.005869Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype1Least InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.00000003358Least InformativeDirect
Worm Phenotype (WP)cell development variant0.0477Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.3955Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.7697Least InformativeInherited
Worm Phenotype (WP)protein interaction variant0.00000000000001252Moderately InformativeDirect
Worm Phenotype (WP)pericellular component development variant0.0000000000007876Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.0000003667Moderately InformativeDirect
Worm Phenotype (WP)organism stress response variant0.9585Moderately InformativeInherited
Worm Phenotype (WP)basement membrane remodeling variant0.000000000000005821InformativeDirect
Worm Phenotype (WP)neuron migration variant0.0000008075InformativeDirect
Worm Phenotype (WP)pigmentation variant0.003535InformativeInherited
Worm Phenotype (WP)pesticide response variant0.06893InformativeInherited
Worm Phenotype (WP)chemical hypersensitive0.09476InformativeInherited
Worm Phenotype (WP)osmotic integrity variant0.000001174Highly InformativeDirect
Worm Phenotype (WP)developmental pigmentation variant0.0009337Highly InformativeDirect
Worm Phenotype (WP)non apoptotic cell death variant0.01635Highly InformativeInherited
Worm Phenotype (WP)paraquat response variant0.04153Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)behavior defective0.000126Moderately InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)organism subdivision0.0007718Least InformativeDirect
Zebrafish Anatomy (ZA)multi-tissue structure0.3224Least InformativeInherited
Zebrafish Anatomy (ZA)compound organ0.9955Least InformativeInherited
Zebrafish Anatomy (ZA)anatomical cluster0.2541Moderately InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.4554Moderately InformativeInherited
Zebrafish Anatomy (ZA)head0.7954Moderately InformativeInherited
Zebrafish Anatomy (ZA)post-vent region0.00001216InformativeDirect
Zebrafish Anatomy (ZA)pharyngeal arch0.0008339InformativeDirect
Zebrafish Anatomy (ZA)skeletal system0.0008848InformativeDirect
Zebrafish Anatomy (ZA)pericardial region0.002645InformativeInherited
Zebrafish Anatomy (ZA)trunk0.00555InformativeInherited
Zebrafish Anatomy (ZA)surface structure1InformativeInherited
Zebrafish Anatomy (ZA)olfactory region0.000000002228Highly InformativeDirect
Zebrafish Anatomy (ZA)pharyngeal arch cartilage0.0000001621Highly InformativeDirect
Zebrafish Anatomy (ZA)mandibular arch skeleton0.000007876Highly InformativeDirect
Zebrafish Anatomy (ZA)oral region0.0003708Highly InformativeDirect
Zebrafish Anatomy (ZA)median fin0.295Highly InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Transferring phosphorus-containing groups1Least InformativeInherited
Enzyme Commission (EC)Acting on peptide bonds (peptidases)0Moderately InformativeDirect
Enzyme Commission (EC)Aminoacyltransferases0.0000000012Moderately InformativeDirect
Enzyme Commission (EC)Transferring groups other than amino-acyl groups1Moderately InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds1Moderately InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides1Moderately InformativeInherited
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)Omega peptidases0InformativeDirect
Enzyme Commission (EC)Cysteine endopeptidases0InformativeDirect
Enzyme Commission (EC)RNA-directed RNA polymerase0.0000005313InformativeDirect
Enzyme Commission (EC)In linear amides0.00005035InformativeDirect
Enzyme Commission (EC)In phosphorus-containing anhydrides0.8764InformativeInherited
Enzyme Commission (EC)Poly(A)-specific ribonuclease0Highly InformativeDirect
Enzyme Commission (EC)N-acetylmuramoyl-L-alanine amidase0.00000000000005377Highly InformativeDirect
Enzyme Commission (EC)Nucleoside-triphosphate phosphatase0.0000006691Highly InformativeDirect
Enzyme Commission (EC)Dipeptidyl-peptidases and tripeptidyl-peptidases1Highly InformativeInherited

Document: EC annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) ]

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 116 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 Cysteine proteinases 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 116 hidden Markov models representing the Cysteine proteinases 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 · Functional annotation · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

Please send feedback, comments or questions to superfamily@cs.bris.ac.uk or use the feedback form.

© Copyright 2013 The SUPERFAMILY authors and Julian Gough.