SUPERFAMILY 1.75 HMM library and genome assignments server


PHP domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   7-stranded beta/alpha barrel [ 51988] (3)
Superfamily:   PHP domain-like [ 89550] (2)
Families:   PHP domain [ 89551] (2)
  RNase P subunit p30 [ 110442]


Superfamily statistics
Genomes (3,161) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 9,362 0 3
Proteins 9,349 0 3


Functional annotation
General category Metabolism
Detailed category Other enzymes

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)cellular macromolecule metabolic process0.012970.1899Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.035580.009833Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.078910.01565Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.049220.0174Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.034730.008545Least InformativeInherited
Biological Process (BP)RNA metabolic process0.0059660.01604Moderately InformativeInherited
Biological Process (BP)nucleic acid phosphodiester bond hydrolysis5.417e-060.0005812InformativeDirect
Biological Process (BP)RNA phosphodiester bond hydrolysis, endonucleolytic3.134e-082.759e-09Highly InformativeDirect
Molecular Function (MF)hydrolase activity0.011080.009872Least InformativeInherited
Molecular Function (MF)hydrolase activity, acting on ester bonds6.775e-051.77e-06Moderately InformativeDirect
Molecular Function (MF)nuclease activity0.001540.001019InformativeInherited
Molecular Function (MF)endoribonuclease activity1.177e-084.274e-10Highly InformativeDirect
Molecular Function (MF)endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomo8.869e-104.199e-11Highly InformativeDirect
Cellular Component (CC)ribonucleoprotein complex0.00013730.0002207Moderately InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular macromolecule metabolic process 0.1899 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.009833 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.01565 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.0174 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.008545 Least Informative Inherited
Biological Process (BP) gene expression 0.06733 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.01604 Moderately Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.0005812 Informative Direct
Biological Process (BP) RNA processing 0.007285 Informative Inherited
Biological Process (BP) ncRNA metabolic process 0.001463 Informative Inherited
Biological Process (BP) RNA phosphodiester bond hydrolysis, endonucleolytic 2.759e-09 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.009872 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 1.77e-06 Moderately Informative Direct
Molecular Function (MF) nuclease activity 0.001019 Informative Inherited
Molecular Function (MF) endoribonuclease activity 4.274e-10 Highly Informative Direct
Molecular Function (MF) endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomo 4.199e-11 Highly Informative Direct
Cellular Component (CC) ribonucleoprotein complex 0.0002207 Moderately Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds3.611e-13Least InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0Moderately InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters7.16e-12Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.7215Moderately InformativeInherited
Enzyme Commission (EC)Ribonuclease P0Highly InformativeDirect
Enzyme Commission (EC)Histidinol-phosphatase4.182e-14Highly InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Hydrolases0.384Least InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.7547Moderately InformativeInherited
Enzyme Commission (EC)DNA-directed DNA polymerase0InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters3.681e-12InformativeDirect
Enzyme Commission (EC)Ribonuclease P0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Biological processDNA replication0InformativeDirect
Biological processtRNA processing2.721e-09InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationNuclease1.589e-07Moderately InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0InformativeDirect
Post-translational modificationExonuclease0.0009177InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism3.302e-05Least InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis6.384e-07Moderately InformativeDirect
UniPathway (UP)L-histidine biosynthesis4.786e-13InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · 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 3 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 PHP domain-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 3 hidden Markov models representing the PHP domain-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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]