SUPERFAMILY 1.75 HMM library and genome assignments server


PsbU/PolX domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   SAM domain-like [ 47768] (16)
Superfamily:   PsbU/PolX domain-like [ 81585] (2)
Families:   DNA polymerase beta-like, second domain [ 81584] (3)
  PsbU-like [ 158539]


Superfamily statistics
Genomes (672) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,272 5,208 16
Proteins 1,265 5,194 16


Functional annotation
General category Information
Detailed category DNA replication/repair

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) cellular aromatic compound metabolic process 4.906e-07 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 4.906e-06 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 3.705e-05 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 3.891e-07 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1.323e-06 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.04953 Least Informative Inherited
Biological Process (BP) response to stimulus 0.006081 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.001976 Least Informative Inherited
Biological Process (BP) cellular response to stress 2.198e-08 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 5.163e-05 Moderately Informative Direct
Biological Process (BP) DNA metabolic process 7.318e-15 Informative Direct
Biological Process (BP) response to DNA damage stimulus 3.397e-12 Informative Direct
Biological Process (BP) DNA replication 7.324e-08 Highly Informative Direct
Molecular Function (MF) transferase activity 3.264e-08 Least Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1.842e-11 Moderately Informative Direct
Molecular Function (MF) lyase activity 4.991e-06 Moderately Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) DNA polymerase activity 7.924e-05 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)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0Moderately InformativeDirect
Enzyme Commission (EC)DNA nucleotidylexotransferase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)immune system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)hematopoietic system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)abnormal lymphocyte morphology0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal leukopoiesis0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal hematopoietic cell number0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal lymphocyte cell number0InformativeDirect
Mammalian Phenotype (MP)abnormal B cell differentiation0InformativeDirect
Mammalian Phenotype (MP)abnormal immunoglobulin V(D)J recombination0Highly InformativeDirect

Document: MP 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)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport3.188e-09Least InformativeDirect
Biological processDNA damage8.401e-08Moderately InformativeDirect
Biological processElectron transport0InformativeDirect
Biological processDNA replication0InformativeDirect
Biological processPhotosynthesis0InformativeDirect
Biological processDNA synthesis0Highly InformativeDirect
Cellular componentNucleus9.877e-07Least InformativeDirect
Cellular componentMembrane0.0005313Least InformativeDirect
Cellular componentThylakoid0InformativeDirect
Cellular componentPhotosystem II0Highly InformativeDirect
DomainSignal2.111e-12Least InformativeDirect
Molecular functionMagnesium4.384e-07Moderately InformativeDirect
Molecular functionSodium9.392e-11InformativeDirect
Post-translational modificationTransferase1.318e-10Least InformativeDirect
Post-translational modificationHydrolase0.2431Least InformativeInherited
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationNuclease1.391e-08Moderately InformativeDirect
Post-translational modificationLyase0.0001311Moderately InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0InformativeDirect
Post-translational modificationExonuclease1.105e-15InformativeDirect
Post-translational modificationMethylation1.753e-05Moderately InformativeDirect
Post-translational modificationUbl conjugation2.833e-05Moderately InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · 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 5 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 PsbU/PolX 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 5 hidden Markov models representing the PsbU/PolX 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-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]