SUPERFAMILY 1.75 HMM library and genome assignments server


Peptidylarginine deiminase Pad4, middle domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Common fold of diphtheria toxin/transcription factors/cytochrome f [ 49379] (10)
Superfamily:   Peptidylarginine deiminase Pad4, middle domain [ 110083]
Families:   Peptidylarginine deiminase Pad4, middle domain [ 110084]


Superfamily statistics
Genomes (100) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 307 419 4
Proteins 305 412 4


Functional annotation
General category Metabolism
Detailed category Other enzymes

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) nitrogen compound metabolic process 6.322e-07 Least Informative Direct
Biological Process (BP) biosynthetic process 6.714e-05 Least Informative Direct
Biological Process (BP) protein metabolic process 0.0004758 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 3.339e-06 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0004598 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.5763 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.005312 Least Informative Inherited
Biological Process (BP) cellular protein modification process 1.345e-08 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 2.211e-10 Moderately Informative Direct
Biological Process (BP) organelle organization 0.0001272 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 6.267e-12 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 6.077e-12 Moderately Informative Direct
Biological Process (BP) cellular modified amino acid metabolic process 0 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 2.119e-14 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0 Informative Direct
Biological Process (BP) cellular modified amino acid biosynthetic process 0 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 0 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)In linear amidines0Highly InformativeDirect

Document: EC 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 carbon-nitrogen bonds, other than peptide bonds0Moderately InformativeDirect
Enzyme Commission (EC)In linear amidines0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionCalcium0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR013733 SSF110083 Protein matches
Abstract

This entry represents the central non-catalytic domain of protein-arginine deiminase. This domain has an immunoglobulin-like fold.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · 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 1 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 Peptidylarginine deiminase Pad4, middle domain 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 1 hidden Markov models representing the Peptidylarginine deiminase Pad4, middle domain 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]