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 (201) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 1,500 1,545 16
Proteins 809 863 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 3.228e-10 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.03223 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.367 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.6474 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.7178 Least Informative Inherited
Biological Process (BP) system process 8.408e-05 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 3.124e-05 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 7.296e-05 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 0.0003562 Moderately Informative Direct
Biological Process (BP) cellular amide metabolic process 1.457e-08 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 8.385e-09 Informative Direct
Biological Process (BP) phenol-containing compound metabolic process 4.315e-11 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity 7.922e-16 Moderately Informative Direct
Molecular Function (MF) monooxygenase activity 1.044e-11 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxyge 5.35e-10 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.0008588 Least Informative Direct
Cellular Component (CC) membrane 0.003227 Least Informative Inherited
Cellular Component (CC) intrinsic to membrane 4.991e-06 Moderately Informative Direct
Cellular Component (CC) plasma membrane part 1.314e-05 Moderately Informative Direct
Cellular Component (CC) integral to membrane 3.111e-06 Informative Direct
Cellular Component (CC) intrinsic to plasma membrane 1.282e-07 Informative Direct
Cellular Component (CC) integral to plasma membrane 7.548e-08 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)Oxidoreductases4.427e-14Least InformativeDirect
Enzyme Commission (EC)Lyases8.747e-05Least InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or red0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-nitrogen lyases5.208e-14InformativeDirect
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)Oxidoreductases5.727e-14Least InformativeDirect
Enzyme Commission (EC)Lyases0.0001069Least InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen0InformativeDirect
Enzyme Commission (EC)Lyases acting on amides, amidines, etc9.573e-16Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentMembrane1.185e-08Least InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
DomainSignal2.602e-07Least InformativeDirect
DomainTransmembrane2.998e-05Least InformativeDirect
DomainSignal-anchor0.000502InformativeDirect
Molecular functionMetal-binding2.316e-16Least InformativeDirect
Molecular functionCopper0InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationLyase0.0004008Moderately InformativeDirect
Post-translational modificationMonooxygenase0Highly InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationGlycoprotein7.025e-15Least 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)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 ]