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Cdc48 domain 2-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Cdc48 domain 2-like [ 54584]
Superfamily:   Cdc48 domain 2-like [ 54585]
Families:   Cdc48 domain 2-like [ 54586] (4)


Superfamily statistics
Genomes (688) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,342 2,995 9
Proteins 2,337 2,992 9


Functional annotation
General category General
Detailed category Small molecule binding

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) single-organism cellular process 0.000006795 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.00000009289 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.6478 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.421 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.508 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.5279 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.5744 Least Informative Inherited
Biological Process (BP) biological regulation 0.9811 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.06326 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.04275 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.05565 Least Informative Inherited
Biological Process (BP) response to stimulus 0.03642 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.5071 Least Informative Inherited
Biological Process (BP) cellular response to stress 0.00003768 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0000000008154 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.0000009823 Moderately Informative Direct
Biological Process (BP) cellular localization 0.0000003167 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0009223 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0000001647 Moderately Informative Direct
Biological Process (BP) organelle organization 0.0208 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.01417 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 0.1444 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.03975 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.02203 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.06705 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.443 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.2368 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.03259 Moderately Informative Inherited
Biological Process (BP) system development 0.9816 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.003167 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.008228 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.004064 Moderately Informative Inherited
Biological Process (BP) proteolysis 0.0000000005768 Informative Direct
Biological Process (BP) regulation of catabolic process 0.0002142 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.0000689 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.0001008 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.00000000003855 Informative Direct
Biological Process (BP) response to nitrogen compound 0.000002168 Informative Direct
Biological Process (BP) single-organism intracellular transport 0.00004883 Informative Direct
Biological Process (BP) membrane organization 0.002357 Informative Inherited
Biological Process (BP) cellular response to DNA damage stimulus 0.4225 Informative Inherited
Biological Process (BP) sensory organ development 0.006106 Informative Inherited
Biological Process (BP) DNA metabolic process 0.008506 Informative Inherited
Biological Process (BP) double-strand break repair 0.0000001017 Highly Informative Direct
Biological Process (BP) autophagy 0.00000004199 Highly Informative Direct
Biological Process (BP) glycoprotein metabolic process 0.000001453 Highly Informative Direct
Biological Process (BP) cellular component disassembly 0.000000001146 Highly Informative Direct
Biological Process (BP) protein modification by small protein conjugation 0.00004146 Highly Informative Direct
Biological Process (BP) response to endoplasmic reticulum stress 0.00000000001505 Highly Informative Direct
Biological Process (BP) macromolecule glycosylation 0.000000008912 Highly Informative Direct
Biological Process (BP) pigmentation 0.000001922 Highly Informative Direct
Biological Process (BP) single-organism membrane fusion 0.0001248 Highly Informative Direct
Biological Process (BP) organelle fusion 0.0000000000004879 Highly Informative Direct
Biological Process (BP) proteolysis involved in cellular protein catabolic process 0.00000000000001439 Highly Informative Direct
Biological Process (BP) modification-dependent macromolecule catabolic process 0.03016 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.00000000003792 Least Informative Direct
Molecular Function (MF) binding 0.01259 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0 Moderately Informative Direct
Molecular Function (MF) ATPase activity 0 Informative Direct
Molecular Function (MF) macromolecular complex binding 0.0000063 Informative Direct
Cellular Component (CC) membrane 0.001462 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.3144 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.01592 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.3346 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.002897 Least Informative Inherited
Cellular Component (CC) whole membrane 0.0002782 Moderately Informative Direct
Cellular Component (CC) microbody 0.0000002855 Informative Direct
Cellular Component (CC) vacuolar part 0.0004547 Informative Direct
Cellular Component (CC) chromosome 0.003573 Informative Inherited
Cellular Component (CC) lytic vacuole 0.02222 Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on acid anhydrides0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)general pace of development variant0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.002431Least InformativeInherited
Worm Phenotype (WP)cell development variant0.004501Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.008191Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.0436Least InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.00007393Moderately InformativeDirect
Worm Phenotype (WP)reproductive system development variant0.00008801Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.0001424Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0.0002092Moderately InformativeDirect
Worm Phenotype (WP)cell homeostasis metabolism variant0.0002356Moderately InformativeDirect
Worm Phenotype (WP)protein protein interaction variant0.0002384Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.0003758Moderately InformativeDirect
Worm Phenotype (WP)cell component morphology variant0.0006349Moderately InformativeDirect
Worm Phenotype (WP)level of transgene expression variant0.0009538Moderately InformativeDirect
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.000001706InformativeDirect
Worm Phenotype (WP)gonad development variant0.000007486InformativeDirect
Worm Phenotype (WP)endoplasmic reticulum morphology variant0.00000000008814Highly InformativeDirect
Worm Phenotype (WP)multiple nuclei0.0000001149Highly InformativeDirect
Worm Phenotype (WP)cytoplasmic processing body variant0.0000005676Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)morphology0Moderately InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0Least InformativeDirect
Fly Phenotype (FP)behavior defective0Moderately InformativeDirect
Fly Phenotype (FP)neuroanatomy defective0Moderately InformativeDirect
Fly Phenotype (FP)lethal - all die before end of P-stage0Moderately InformativeDirect
Fly Phenotype (FP)locomotor behavior defective0Highly InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0Least InformativeDirect
Fly Anatomy (FA)nervous system0Least InformativeDirect
Fly Anatomy (FA)multi-tissue structure0Least InformativeDirect
Fly Anatomy (FA)anatomical group0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)somatic cell0Least InformativeDirect
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)peripheral nervous system0Moderately InformativeDirect
Fly Anatomy (FA)late embryo0Moderately InformativeDirect

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)nervous system0Least InformativeDirect
Zebrafish Anatomy (ZA)compound organ0Least InformativeDirect
Zebrafish Anatomy (ZA)organism subdivision0Least InformativeDirect
Zebrafish Anatomy (ZA)multi-tissue structure0Least InformativeDirect
Zebrafish Anatomy (ZA)sensory system0Moderately InformativeDirect
Zebrafish Anatomy (ZA)head0Moderately InformativeDirect
Zebrafish Anatomy (ZA)portion of tissue0Moderately InformativeDirect
Zebrafish Anatomy (ZA)anatomical cluster0Moderately InformativeDirect
Zebrafish Anatomy (ZA)cell0Moderately InformativeDirect
Zebrafish Anatomy (ZA)retina0InformativeDirect

Document: ZA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect

Document: AP 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)Acting on acid anhydrides0Moderately InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processProtein transport0.0000000000001972Moderately InformativeDirect
Biological processCell cycle0.00000002134Moderately InformativeDirect
Biological processDNA damage0.0007193Moderately InformativeDirect
Biological processAutophagy0.00000000000176InformativeDirect
Biological processER-Golgi transport0.0000001447Highly InformativeDirect
Cellular componentCytoplasm0.0000003003Least InformativeDirect
Cellular componentNucleus0.0003157Least InformativeDirect
Cellular componentEndoplasmic reticulum0.00002081Moderately InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionLipid-binding0.0000000004422Moderately InformativeDirect
Post-translational modificationHydrolase0.00001245Least InformativeDirect
Post-translational modificationPhosphoprotein0.00000000003624Least InformativeDirect
Post-translational modificationAcetylation0.000009226Least InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Arabidopsis Plant Ontology (AP) · 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 5 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 Cdc48 domain 2-like 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 5 hidden Markov models representing the Cdc48 domain 2-like 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 · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]