SUPERFAMILY 1.75 HMM library and genome assignments server


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 (629) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 2,145 2,126 9
Proteins 2,143 2,125 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) cellular component organization or biogenesis 4.48e-06 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 5.15e-06 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 7.594e-06 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1.979e-05 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 2.039e-05 Least Informative Direct
Biological Process (BP) single-organism metabolic process 4.466e-05 Least Informative Direct
Biological Process (BP) localization 5.188e-05 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.5445 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.8202 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.1172 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.01497 Least Informative Inherited
Biological Process (BP) response to stimulus 0.2605 Least Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 3.746e-15 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 3.243e-11 Moderately Informative Direct
Biological Process (BP) organic cyclic compound catabolic process 1.783e-10 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 9.108e-10 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 2.692e-09 Moderately Informative Direct
Biological Process (BP) organonitrogen compound catabolic process 5.498e-08 Moderately Informative Direct
Biological Process (BP) macromolecule catabolic process 2.481e-07 Moderately Informative Direct
Biological Process (BP) cellular localization 2.255e-06 Moderately Informative Direct
Biological Process (BP) cellular response to stress 5.797e-06 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.1455 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.007431 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.008129 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.2421 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.2614 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.2706 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.3911 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.02252 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.0468 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.005399 Moderately Informative Inherited
Biological Process (BP) purine ribonucleoside metabolic process 0 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 0 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 0 Informative Direct
Biological Process (BP) nucleoside triphosphate metabolic process 0 Informative Direct
Biological Process (BP) protein catabolic process 1.854e-13 Informative Direct
Biological Process (BP) proteolysis 2.109e-10 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 3.844e-10 Informative Direct
Biological Process (BP) organophosphate catabolic process 4.033e-10 Informative Direct
Biological Process (BP) glycosyl compound catabolic process 2.455e-09 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 7.093e-09 Informative Direct
Biological Process (BP) protein transport 3.517e-08 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 3.8e-08 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 3.853e-05 Informative Direct
Biological Process (BP) secretion by cell 0.0005617 Informative Direct
Biological Process (BP) membrane organization 0.001707 Informative Inherited
Biological Process (BP) response to DNA damage stimulus 0.1854 Informative Inherited
Biological Process (BP) DNA metabolic process 0.008558 Informative Inherited
Biological Process (BP) purine ribonucleoside triphosphate catabolic process 0 Highly Informative Direct
Biological Process (BP) ATP metabolic process 0 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 0 Highly Informative Direct
Biological Process (BP) ubiquitin-dependent protein catabolic process 0 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate catabolic process 0 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 0 Highly Informative Direct
Biological Process (BP) protein glycosylation 4.583e-11 Highly Informative Direct
Biological Process (BP) double-strand break repair 2.915e-09 Highly Informative Direct
Biological Process (BP) protein ubiquitination 7.634e-07 Highly Informative Direct
Biological Process (BP) organelle fusion 3.076e-06 Highly Informative Direct
Biological Process (BP) cellular membrane fusion 2.06e-05 Highly Informative Direct
Biological Process (BP) proteasomal protein catabolic process 0.002817 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 2.329e-07 Least Informative Direct
Molecular Function (MF) binding 0.007256 Least Informative Inherited
Molecular Function (MF) nucleoside-triphosphatase activity 0 Informative Direct
Molecular Function (MF) protein complex binding 1.995e-05 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.0001804 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.0007072 Least Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.03415 Least Informative Inherited
Cellular Component (CC) membrane 0.001176 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.5978 Least Informative Inherited
Cellular Component (CC) organelle membrane 2.486e-05 Moderately Informative Direct
Cellular Component (CC) microbody 1.409e-05 Informative Direct
Cellular Component (CC) vacuolar part 0.0001109 Informative Direct
Cellular Component (CC) chromosome 0.002197 Informative Inherited
Cellular Component (CC) lytic vacuole 0.05127 Informative Inherited
Cellular Component (CC) lysosome 1.101e-06 Highly Informative Direct
Cellular Component (CC) vacuolar membrane 0.007181 Highly 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

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.004687Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.01832Least InformativeInherited
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect
Worm Phenotype (WP)cell organization biogenesis variant7.425e-05Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal7.753e-05Moderately InformativeDirect
Worm Phenotype (WP)cell homeostasis metabolism variant9.095e-05Moderately InformativeDirect
Worm Phenotype (WP)protein aggregation variant0.000176Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.0002493Moderately InformativeDirect
Worm Phenotype (WP)locomotion variant0.0009551Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.00121Moderately InformativeInherited
Worm Phenotype (WP)endoplasmic reticulum morphology variant6.947e-11Highly InformativeDirect
Worm Phenotype (WP)nuclear number variant1.782e-07Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) 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)organ system0Least InformativeDirect
Fly Anatomy (FA)cell0Least InformativeDirect
Fly Anatomy (FA)anatomical group0Least InformativeDirect
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)head0Moderately InformativeDirect

Document: FA 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 transport1.398e-13Moderately InformativeDirect
Biological processCell cycle1.305e-08Moderately InformativeDirect
Biological processDNA damage0.0006648Moderately InformativeDirect
Biological processER-Golgi transport1.551e-07Highly InformativeDirect
Cellular componentCytoplasm5.285e-06Least InformativeDirect
Cellular componentNucleus0.0006519Least InformativeDirect
Cellular componentEndoplasmic reticulum9.415e-06Moderately InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionLipid-binding2.912e-11InformativeDirect
Post-translational modificationHydrolase8.344e-06Least InformativeDirect
Post-translational modificationPhosphoprotein4.189e-13Least InformativeDirect
Post-translational modificationAcetylation1.171e-05Least InformativeDirect
Post-translational modificationUbl conjugation1.779e-08Moderately InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]