SUPERFAMILY 1.75 HMM library and genome assignments server

Please note: Superfamily is currently under maintenance and some functionality may be limited. Please bear with us as we fix these problems.


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 (682) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,313 2,995 9
Proteins 2,309 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) cellular aromatic compound metabolic process 0.00001149 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.00003195 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.00006477 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.000007849 Least Informative Direct
Biological Process (BP) localization 0.00002609 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.00001022 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00003039 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.3951 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.9243 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.05939 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.01212 Least Informative Inherited
Biological Process (BP) response to stimulus 0.3172 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.0000000002249 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.00000000001882 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.000008809 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular localization 0.0000007516 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.0000000009767 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.000000000000001938 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.2858 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.01143 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.02054 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.3365 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.3235 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.3093 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.4642 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.03517 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.0707 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.007767 Moderately Informative Inherited
Biological Process (BP) proteolysis 0.00000000001127 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 0 Informative Direct
Biological Process (BP) nucleoside triphosphate metabolic process 0 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 0 Informative Direct
Biological Process (BP) protein transport 0.00000004694 Informative Direct
Biological Process (BP) cellular membrane organization 0.00003547 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.00004211 Informative Direct
Biological Process (BP) protein catabolic process 0.000000000000003755 Informative Direct
Biological Process (BP) secretion by cell 0.000662 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.00000000008665 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.000000001238 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0 Informative Direct
Biological Process (BP) organophosphate catabolic process 0.0000000003592 Informative Direct
Biological Process (BP) protein modification by small protein conjugation or removal 0.00005026 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 0.000000005848 Informative Direct
Biological Process (BP) organonitrogen compound catabolic process 0.00000004756 Informative Direct
Biological Process (BP) response to DNA damage stimulus 0.1731 Informative Inherited
Biological Process (BP) DNA metabolic process 0.01801 Informative Inherited
Biological Process (BP) double-strand break repair 0.000000003695 Highly Informative Direct
Biological Process (BP) protein glycosylation 0.00000000004473 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 nucleoside triphosphate catabolic process 0 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 0 Highly Informative Direct
Biological Process (BP) purine ribonucleoside monophosphate metabolic process 0 Highly Informative Direct
Biological Process (BP) ribonucleoside triphosphate catabolic process 0 Highly Informative Direct
Biological Process (BP) purine ribonucleoside triphosphate metabolic process 0 Highly Informative Direct
Biological Process (BP) protein ubiquitination 0.0000009855 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 0 Highly Informative Direct
Biological Process (BP) organelle fusion 0.000004584 Highly Informative Direct
Biological Process (BP) membrane fusion 0.0005537 Highly Informative Direct
Biological Process (BP) proteasomal protein catabolic process 0.00549 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.00000007431 Least Informative Direct
Molecular Function (MF) binding 0.003055 Least Informative Inherited
Molecular Function (MF) nucleoside-triphosphatase activity 0 Informative Direct
Molecular Function (MF) protein complex binding 0.00002876 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.001123 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.0457 Least Informative Inherited
Cellular Component (CC) membrane 0.002947 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.001361 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.2394 Least Informative Inherited
Cellular Component (CC) organelle membrane 0.000009474 Moderately Informative Direct
Cellular Component (CC) microbody 0.00001959 Informative Direct
Cellular Component (CC) vacuolar part 0.0001407 Informative Direct
Cellular Component (CC) chromosome 0.003295 Informative Inherited
Cellular Component (CC) lytic vacuole 0.03552 Informative Inherited
Cellular Component (CC) lysosome 0.0000000862 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

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 variant0.00007425Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.00007753Moderately InformativeDirect
Worm Phenotype (WP)cell homeostasis metabolism variant0.00009095Moderately 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 variant0.00000000006947Highly InformativeDirect
Worm Phenotype (WP)nuclear number variant0.0000001782Highly 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
Fly Phenotype (FP)lethal - all die before end of larval stage0InformativeDirect

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)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

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 transport0.0000000000001375Moderately InformativeDirect
Biological processCell cycle0.00000001128Moderately InformativeDirect
Biological processDNA damage0.0006465Moderately InformativeDirect
Biological processER-Golgi transport0.0000001499Highly InformativeDirect
Cellular componentCytoplasm0.000005519Least InformativeDirect
Cellular componentNucleus0.0006827Least InformativeDirect
Cellular componentEndoplasmic reticulum0.00001086Moderately InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionLipid-binding0.00000000004512InformativeDirect
Post-translational modificationHydrolase0.000008773Least InformativeDirect
Post-translational modificationPhosphoprotein0.0000000000004608Least InformativeDirect
Post-translational modificationAcetylation0.00001189Least InformativeDirect
Post-translational modificationUbl conjugation0.00000002159Moderately 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 ]