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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 (684) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,327 2,995 9
Proteins 2,322 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 0.0006398 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.000001825 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.05661 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.5397 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.3718 Least Informative Inherited
Biological Process (BP) response to stimulus 0.05863 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.3561 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.4256 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.2762 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.4331 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.02109 Least Informative Inherited
Biological Process (BP) organelle organization 0.0005367 Moderately Informative Direct
Biological Process (BP) nucleobase-containing compound biosynthetic process 0.0007006 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.00000001678 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.00000004217 Moderately Informative Direct
Biological Process (BP) cellular localization 0.00001398 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative biosynthetic process 0.0001581 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0000001443 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.3432 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.03363 Moderately Informative Inherited
Biological Process (BP) response to stress 0.04729 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.1568 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.02459 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.03439 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.06243 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.08082 Moderately Informative Inherited
Biological Process (BP) system development 0.9927 Moderately Informative Inherited
Biological Process (BP) proteolysis 0.0000000005116 Informative Direct
Biological Process (BP) regulation of catabolic process 0.0000208 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.0001071 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.000000000003976 Informative Direct
Biological Process (BP) single-organism membrane organization 0.000004939 Informative Direct
Biological Process (BP) DNA metabolic process 0.009366 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.02775 Informative Inherited
Biological Process (BP) secretion 0.01667 Informative Inherited
Biological Process (BP) cellular response to DNA damage stimulus 0.2464 Informative Inherited
Biological Process (BP) autophagy 0.00000000000001918 Highly Informative Direct
Biological Process (BP) glycoprotein metabolic process 0.000001594 Highly Informative Direct
Biological Process (BP) modification-dependent protein catabolic process 0.000000000000003692 Highly Informative Direct
Biological Process (BP) cellular component disassembly 0.00002843 Highly Informative Direct
Biological Process (BP) protein modification by small protein conjugation 0.00004558 Highly Informative Direct
Biological Process (BP) response to endoplasmic reticulum stress 0 Highly Informative Direct
Biological Process (BP) regulation of protein catabolic process 0.000003963 Highly Informative Direct
Biological Process (BP) macromolecule glycosylation 0.00000001292 Highly Informative Direct
Biological Process (BP) pigmentation 0.000001071 Highly Informative Direct
Biological Process (BP) single-organism membrane fusion 0.00004284 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 0.0008732 Highly Informative Direct
Biological Process (BP) organelle fusion 0.000000000001962 Highly Informative Direct
Biological Process (BP) proteasomal protein catabolic process 0.004246 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.0000000002823 Least Informative Direct
Molecular Function (MF) binding 0.009948 Least Informative Inherited
Molecular Function (MF) protein binding 0.0003935 Moderately Informative Direct
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 0.005344 Informative Inherited
Cellular Component (CC) intracellular organelle part 0.01232 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.3564 Least Informative Inherited
Cellular Component (CC) membrane 0.001001 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.01642 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.2916 Least Informative Inherited
Cellular Component (CC) vacuole 0.00001274 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0.0004808 Moderately Informative Direct
Cellular Component (CC) whole membrane 0.0001632 Moderately Informative Direct
Cellular Component (CC) microbody 0.0000002325 Informative Direct
Cellular Component (CC) vacuolar part 0.0002709 Informative Direct
Cellular Component (CC) chromosome 0.003619 Informative Inherited
Cellular Component (CC) lytic vacuole 0.01825 Informative Inherited
Cellular Component (CC) lytic vacuole membrane 0.00000001938 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 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 variant0.00198Least InformativeInherited
Worm Phenotype (WP)cell development variant0.004447Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.006974Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.03951Least InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.00007645Moderately InformativeDirect
Worm Phenotype (WP)reproductive system development variant0.00008695Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.0001436Moderately InformativeDirect
Worm Phenotype (WP)cell homeostasis metabolism variant0.0001683Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0.0001821Moderately InformativeDirect
Worm Phenotype (WP)protein protein interaction variant0.0002332Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.0003769Moderately InformativeDirect
Worm Phenotype (WP)cell component morphology variant0.0004564Moderately InformativeDirect
Worm Phenotype (WP)level of transgene expression variant0.0007536Moderately InformativeDirect
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.000001683InformativeDirect
Worm Phenotype (WP)gonad development variant0.00000755InformativeDirect
Worm Phenotype (WP)endoplasmic reticulum morphology variant0.00000000008665Highly InformativeDirect
Worm Phenotype (WP)nuclear number variant0.0000001865Highly InformativeDirect
Worm Phenotype (WP)cytoplasmic processing body variant0.0000005823Highly 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)neuroanatomy defective0Moderately InformativeDirect
Fly Phenotype (FP)lethal - all die before end of P-stage0Moderately 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)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)peripheral nervous system0Moderately 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)eye0InformativeDirect

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 transport0.0000000000002046Moderately InformativeDirect
Biological processCell cycle0.00000002168Moderately InformativeDirect
Biological processDNA damage0.0007231Moderately InformativeDirect
Biological processAutophagy0.00000000000158InformativeDirect
Biological processER-Golgi transport0.0000001477Highly InformativeDirect
Cellular componentCytoplasm0.0000002934Least InformativeDirect
Cellular componentNucleus0.000295Least InformativeDirect
Cellular componentEndoplasmic reticulum0.00001888Moderately InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionLipid-binding0.00000000007126Moderately InformativeDirect
Post-translational modificationHydrolase0.00001244Least InformativeDirect
Post-translational modificationPhosphoprotein0.00000000003684Least InformativeDirect
Post-translational modificationAcetylation0.000008919Least 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 ]