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 (673) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,280 5,208 16
Proteins 1,271 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 0.0000009203 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.000008906 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.00005802 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0000007299 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000002412 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.00731 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.1594 Least Informative Inherited
Biological Process (BP) response to stimulus 0.008592 Least Informative Inherited
Biological Process (BP) cellular response to stress 0.00000003483 Moderately Informative Direct
Biological Process (BP) DNA repair 0.00000000000007575 Informative Direct
Molecular Function (MF) transferase activity 0.0000001878 Least Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.00000000002966 Moderately Informative Direct
Molecular Function (MF) lyase activity 0.000005408 Moderately Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) DNA polymerase activity 0.00007822 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 leukopoiesis0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0Moderately 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 processTransport0.000000003248Least InformativeDirect
Biological processDNA damage0.00000008384Moderately InformativeDirect
Biological processElectron transport0InformativeDirect
Biological processDNA replication0InformativeDirect
Biological processPhotosynthesis0InformativeDirect
Biological processDNA synthesis0Highly InformativeDirect
Cellular componentNucleus0.000001012Least InformativeDirect
Cellular componentMembrane0.0005421Least InformativeDirect
Cellular componentThylakoid0InformativeDirect
Cellular componentPhotosystem II0Highly InformativeDirect
DomainSignal0.000000000002086Least InformativeDirect
Molecular functionMagnesium0.0000006306Moderately InformativeDirect
Molecular functionSodium0.00000000009325InformativeDirect
Post-translational modificationTransferase0.000000000132Least InformativeDirect
Post-translational modificationHydrolase0.2465Least InformativeInherited
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationNuclease0.00000001397Moderately InformativeDirect
Post-translational modificationLyase0.000136Moderately InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0InformativeDirect
Post-translational modificationExonuclease0.000000000000001107InformativeDirect
Post-translational modificationMethylation0.00001744Moderately InformativeDirect
Post-translational modificationUbl conjugation0.0000296Moderately 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 ]