SUPERFAMILY 1.75 HMM library and genome assignments server

DNA clamp superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   DNA clamp [ 55978]
Superfamily:   DNA clamp [ 55979] (2)
Families:   DNA polymerase III, beta subunit [ 55980]
  DNA polymerase processivity factor [ 55983] (4)


Superfamily statistics
Genomes (3,221) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 11,127 55,526 33
Proteins 4,775 20,507 15


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 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.000000000000007248 Least Informative Direct
Biological Process (BP) biosynthetic process 0.000001125 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.00000003543 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.000002728 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) response to stimulus 0.00000005703 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.2787 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.3955 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.02583 Least Informative Inherited
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00000000009361 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.002273 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.001926 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.06775 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.5184 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.8761 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.01299 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.05878 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.01564 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.002562 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.007208 Moderately Informative Inherited
Biological Process (BP) DNA repair 0 Informative Direct
Biological Process (BP) positive regulation of catabolic process 0.0002347 Informative Direct
Biological Process (BP) cell cycle process 0.000000001187 Informative Direct
Biological Process (BP) positive regulation of hydrolase activity 0.0003033 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 0.001099 Informative Inherited
Biological Process (BP) regulation of mitotic cell cycle 0.07351 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.6063 Informative Inherited
Biological Process (BP) regulation of cell cycle process 0.03952 Informative Inherited
Biological Process (BP) DNA replication 0.000001218 Highly Informative Direct
Biological Process (BP) DNA integrity checkpoint 0 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.0000024 Highly Informative Direct
Biological Process (BP) negative regulation of mitotic cell cycle phase transition 0.00000004547 Highly Informative Direct
Molecular Function (MF) binding 0.004148 Least Informative Inherited
Cellular Component (CC) protein complex 0.00000000000001745 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.000003649 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.002986 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.0074 Least Informative Inherited
Cellular Component (CC) nuclear part 0.000000004324 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.002604 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.00000000729 Informative Direct
Cellular Component (CC) nuclear chromosome part 0.002827 Highly Informative Inherited

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 bonds0.1514Least InformativeInherited
Enzyme Commission (EC)DNA-directed DNA polymerase0Moderately InformativeDirect
Enzyme Commission (EC)Exodeoxyribonuclease III0Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0Least InformativeDirect
Disease Ontology (DO)lung carcinoma0InformativeDirect

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect
Mammalian Phenotype (MP)preweaning lethality0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal embryogenesis/ development1Moderately InformativeInherited
Mammalian Phenotype (MP)embryonic lethality0InformativeDirect
Mammalian Phenotype (MP)embryonic lethality during organogenesis0Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect

Document: AP 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)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0InformativeDirect
Enzyme Commission (EC)Exodeoxyribonucleases producing 5'-phosphomonoesters0.000000002945Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0.0002658Moderately InformativeDirect
Biological processDNA replication0InformativeDirect
Cellular componentNucleus0.0000000000007083Least InformativeDirect
Cellular componentHost nucleus0.00000002778InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Post-translational modificationTransferase0.002422Least InformativeInherited
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationNuclease0.1155Moderately InformativeInherited
Post-translational modificationDNA-directed DNA polymerase0InformativeDirect
Post-translational modificationExonuclease0.0004673InformativeDirect
Post-translational modificationIsopeptide bond0.0000000003234Moderately InformativeDirect
Post-translational modificationUbl conjugation0.000001059Moderately InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 24 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 DNA clamp 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 24 hidden Markov models representing the DNA clamp 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) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]