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 (3,166) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 9,355 54,508 3
Proteins 9,341 54,474 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 process0.014170.08259Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.039330.002118Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.040070.002487Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.0890.004409Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.055610.00487Least InformativeInherited
Biological Process (BP)RNA metabolic process0.0061090.03137Moderately InformativeInherited
Biological Process (BP)nucleic acid phosphodiester bond hydrolysis5.698e-060.001062InformativeInherited
Biological Process (BP)RNA phosphodiester bond hydrolysis, endonucleolytic3.491e-081.805e-09Highly InformativeDirect
Molecular Function (MF)hydrolase activity0.010750.007458Least InformativeInherited
Molecular Function (MF)hydrolase activity, acting on ester bonds8.226e-051.291e-06Moderately InformativeDirect
Molecular Function (MF)nuclease activity0.0015620.0009952InformativeInherited
Molecular Function (MF)endoribonuclease activity1.333e-083.463e-10Highly InformativeDirect
Molecular Function (MF)endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomo9.373e-103.267e-11Highly InformativeDirect
Cellular Component (CC)ribonucleoprotein complex0.00014810.0001668Moderately 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) heterocycle metabolic process 0.002118 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.08259 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.002487 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.00487 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.004409 Least Informative Inherited
Biological Process (BP) gene expression 0.1081 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.03137 Moderately Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.001062 Informative Inherited
Biological Process (BP) RNA processing 0.007509 Informative Inherited
Biological Process (BP) ncRNA metabolic process 0.001562 Informative Inherited
Biological Process (BP) RNA phosphodiester bond hydrolysis, endonucleolytic 1.805e-09 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.007458 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 1.291e-06 Moderately Informative Direct
Molecular Function (MF) nuclease activity 0.0009952 Informative Direct
Molecular Function (MF) endoribonuclease activity 3.463e-10 Highly Informative Direct
Molecular Function (MF) endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomo 3.267e-11 Highly Informative Direct
Cellular Component (CC) ribonucleoprotein complex 0.0001668 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)Hydrolases0.4109Least InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.7534Moderately InformativeInherited
Enzyme Commission (EC)DNA-directed DNA polymerase0InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters3.737e-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 processing3.351e-09InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationNuclease1.643e-07Moderately InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0InformativeDirect
Post-translational modificationExonuclease0.0009008InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism3.292e-05Least InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis6.334e-07Moderately InformativeDirect
UniPathway (UP)L-histidine biosynthesis4.718e-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 ]