SUPERFAMILY 1.75 HMM library and genome assignments server

PHM/PNGase F superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Nucleoplasmin-like/VP (viral coat and capsid proteins) [ 88632] (7)
Superfamily:   PHM/PNGase F [ 49742] (2)
Families:   Glycosyl-asparaginase [ 49743]
  Peptidylglycine alpha-hydroxylating monooxygenase, PHM [ 49746]


Superfamily statistics
Genomes (215) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,625 2,048 16
Proteins 879 1,193 8


Functional annotation
General category Metabolism
Detailed category Redox

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 0.0000000003552 Least Informative Direct
Biological Process (BP) biosynthetic process 0.3595 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.7172 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.6456 Least Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.00003496 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.00007959 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 0.000454 Moderately Informative Direct
Biological Process (BP) peptide metabolic process 0.0000001261 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 0.00000001208 Informative Direct
Biological Process (BP) phenol-containing compound metabolic process 0.0000000004257 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity 8.141e-16 Moderately Informative Direct
Molecular Function (MF) monooxygenase activity 0.00000000001352 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxyge 0.0000000002311 Highly Informative Direct
Cellular Component (CC) membrane 0.001024 Least Informative Inherited
Cellular Component (CC) intrinsic component of membrane 0.000005432 Moderately Informative Direct
Cellular Component (CC) plasma membrane part 0.00001579 Moderately Informative Direct
Cellular Component (CC) integral component of membrane 0.00000341 Informative Direct
Cellular Component (CC) intrinsic component of plasma membrane 0.0000001347 Informative Direct
Cellular Component (CC) integral component of plasma membrane 0.00000007876 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)Oxidoreductases0.00000000000004427Least InformativeDirect
Enzyme Commission (EC)Lyases0.00008747Least InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or red0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-nitrogen lyases0.00000000000005208InformativeDirect
Enzyme Commission (EC)Lyases acting on amides, amidines, etc7.054e-16Highly 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)larval development variant0Least InformativeDirect
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect

Document: FP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0.00000000000005013Least InformativeDirect
Enzyme Commission (EC)Lyases0.0001072Least InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen0InformativeDirect
Enzyme Commission (EC)Carbon-nitrogen lyases0.0000000000008797InformativeDirect
Enzyme Commission (EC)Lyases acting on amides, amidines, etc9.63e-16Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentMembrane0.00000001132Least InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
DomainSignal0.0000002707Least InformativeDirect
DomainTransmembrane0.00002819Least InformativeDirect
DomainSignal-anchor0.0005086InformativeDirect
Molecular functionMetal-binding4.62e-16Least InformativeDirect
Molecular functionCopper0InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationLyase0.0004282Moderately InformativeDirect
Post-translational modificationMonooxygenase0Highly InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationGlycoprotein0.000000000000007038Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)aromatic compound metabolism0Least InformativeDirect
UniPathway (UP)amine and polyamine metabolism0Moderately InformativeDirect
UniPathway (UP)aromatic compound biosynthesis0Moderately InformativeDirect
UniPathway (UP)amine and polyamine biosynthesis0InformativeDirect
UniPathway (UP)catecholamine biosynthesis0Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR008977 SSF49742 Protein matches
Abstract

Peptidylglycine alpha-hydroxylating monooxygenase (PHM) is a copper-containing enzyme that catalyses an oxygen-dependent hydroxylation of peptide-extended glycine residues. Members of this family bind peptide substrates and consists of two domains of this fold packed together. Structurally, this domain consists of a beta-sandwich of 8 strands in 2 beta-sheets, in a jelly-roll topology [PubMed10504734].


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) · Worm Phenotype (WP) · Fly Phenotype (FP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 4 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 PHM/PNGase F 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 4 hidden Markov models representing the PHM/PNGase F 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) · Worm Phenotype (WP) · Fly Phenotype (FP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]