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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 (689) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 2,345 6,995 9
Proteins 2,340 6,986 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 0.0000007808 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.000000009049 Least Informative Direct
Biological Process (BP) biosynthetic process 0.5755 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.6445 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.5121 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.09932 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.2032 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.08963 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.09119 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.4194 Least Informative Inherited
Biological Process (BP) response to stimulus 0.02745 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.5225 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.5025 Least Informative Inherited
Biological Process (BP) cellular response to stress 0.00003627 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.0004158 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.000000002332 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.0000008696 Moderately Informative Direct
Biological Process (BP) cellular localization 0.00000002365 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0000003647 Moderately Informative Direct
Biological Process (BP) single-organism transport 0.03078 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.03324 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 0.04332 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.05567 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.06226 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.004347 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.01118 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.02871 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.001453 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.2201 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.121 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.8299 Moderately Informative Inherited
Biological Process (BP) animal organ development 0.5226 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.005555 Moderately Informative Inherited
Biological Process (BP) proteolysis 0.000000001114 Informative Direct
Biological Process (BP) regulation of catabolic process 0.0003472 Informative Direct
Biological Process (BP) protein transport 0.000000004594 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.00008999 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.0001569 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.00000000003906 Informative Direct
Biological Process (BP) single-organism membrane organization 0.000000227 Informative Direct
Biological Process (BP) intracellular transport 0.00004044 Informative Direct
Biological Process (BP) response to nitrogen compound 0.000007423 Informative Direct
Biological Process (BP) single-organism cellular localization 0.00001763 Informative Direct
Biological Process (BP) cell development 0.1176 Informative Inherited
Biological Process (BP) DNA metabolic process 0.007943 Informative Inherited
Biological Process (BP) cellular response to DNA damage stimulus 0.51 Informative Inherited
Biological Process (BP) double-strand break repair 0.0000001547 Highly Informative Direct
Biological Process (BP) autophagy 0.00000004575 Highly Informative Direct
Biological Process (BP) glycoprotein metabolic process 0.000001958 Highly Informative Direct
Biological Process (BP) cellular component disassembly 0 Highly Informative Direct
Biological Process (BP) protein modification by small protein conjugation 0.00006286 Highly Informative Direct
Biological Process (BP) response to endoplasmic reticulum stress 0.0000000001418 Highly Informative Direct
Biological Process (BP) gliogenesis 0.000006372 Highly Informative Direct
Biological Process (BP) regulation of protein catabolic process 0.000003648 Highly Informative Direct
Biological Process (BP) macromolecule glycosylation 0.00000001518 Highly Informative Direct
Biological Process (BP) pigmentation 0.000000008143 Highly Informative Direct
Biological Process (BP) cellular protein catabolic process 0.00000000000009208 Highly Informative Direct
Biological Process (BP) organelle fusion 0.000004028 Highly Informative Direct
Biological Process (BP) single-organism membrane fusion 0.001252 Highly Informative Inherited
Biological Process (BP) modification-dependent macromolecule catabolic process 0.02818 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.0000000002211 Least Informative Direct
Molecular Function (MF) binding 0.05032 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 0.00000535 Informative Direct
Cellular Component (CC) membrane 0.003165 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.03142 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.4068 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.2809 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.001272 Least Informative Inherited
Cellular Component (CC) vacuole 0.00002744 Moderately Informative Direct
Cellular Component (CC) whole membrane 0.0002385 Moderately Informative Direct
Cellular Component (CC) microbody 0.000000001094 Informative Direct
Cellular Component (CC) vacuolar part 0.0005352 Informative Direct
Cellular Component (CC) chromosome 0.00318 Informative Inherited
Cellular Component (CC) lytic vacuole 0.02348 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processProtein transport0.000000000000188Moderately InformativeDirect
Biological processCell cycle0.00000002178Moderately InformativeDirect
Biological processDNA damage0.0007133Moderately InformativeDirect
Biological processAutophagy0.000000000001734InformativeDirect
Biological processDNA repair0.00007312InformativeDirect
Biological processER-Golgi transport0.0000001406Highly InformativeDirect
Cellular componentCytoplasm0.0000002775Least InformativeDirect
Cellular componentNucleus0.0003207Least InformativeDirect
Cellular componentEndoplasmic reticulum0.00002064Moderately InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionLipid-binding0.0000000004494Moderately InformativeDirect
Post-translational modificationHydrolase0.00001227Least InformativeDirect
Post-translational modificationPhosphoprotein0.00000000003585Least InformativeDirect
Post-translational modificationAcetylation0.00000865Least InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · 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 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) · UniProtKB KeyWords (KW) · Internal database links ]