SUPERFAMILY 1.75 HMM library and genome assignments server

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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 (691) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 2,363 8,696 9
Proteins 2,358 8,686 9


Functional annotation
General category General
Detailed category Small molecule binding

Document:
Function annotation of SCOP domain superfamilies

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)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.003892Least InformativeInherited
Worm Phenotype (WP)cell development variant0.005371Least InformativeInherited
Worm Phenotype (WP)blast cell physiology variant0.01039Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.0104Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.05047Least InformativeInherited
Worm Phenotype (WP)metabolic pathway variant0.00003241Moderately InformativeDirect
Worm Phenotype (WP)cell organization biogenesis variant0.00009209Moderately InformativeDirect
Worm Phenotype (WP)reproductive system development variant0.00009498Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.0001546Moderately InformativeDirect
Worm Phenotype (WP)protein protein interaction variant0.0002391Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0.0003396Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0.0003637Moderately InformativeDirect
Worm Phenotype (WP)cell homeostasis metabolism variant0.0004241Moderately InformativeDirect
Worm Phenotype (WP)germ cell development variant0.0004875Moderately InformativeDirect
Worm Phenotype (WP)level of transgene expression variant0.001265Moderately InformativeInherited
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.00000166InformativeDirect
Worm Phenotype (WP)protein metabolism variant0.0000161InformativeDirect
Worm Phenotype (WP)transgene expression reduced0.0001208InformativeDirect
Worm Phenotype (WP)endoplasmic reticulum morphology variant0.000000000114Highly InformativeDirect
Worm Phenotype (WP)nuclear number variant0.0000002893Highly InformativeDirect
Worm Phenotype (WP)cytoplasmic processing body variant0.0000005345Highly 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

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)nervous system0Least InformativeDirect
Zebrafish Anatomy (ZA)organism subdivision0Least InformativeDirect
Zebrafish Anatomy (ZA)multi-tissue structure0Least InformativeDirect
Zebrafish Anatomy (ZA)cavitated compound organ0Least InformativeDirect
Zebrafish Anatomy (ZA)cell0Least 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)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

Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

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 6 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 6 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 · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]