SUPERFAMILY 1.75 HMM library and genome assignments server

Toprim domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Toprim domain [ 110454]
Superfamily:   Toprim domain [ 110455]
Families:   Toprim domain [ 110456] (2)


Superfamily statistics
Genomes (680) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 858 10,572 3
Proteins 858 10,572 3


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processRibosome biogenesis0InformativeDirect
Biological processrRNA processing0InformativeDirect
Biological processDNA replication0.000000001859InformativeDirect
Cellular componentPrimosome0Highly InformativeDirect
Cellular componentDNA-directed RNA polymerase0.00000000004761Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionRNA-binding0.000000152Moderately InformativeDirect
Molecular functionrRNA-binding0.000000000000003197InformativeDirect
Post-translational modificationHydrolase0.00000004237Least InformativeDirect
Post-translational modificationTransferase0.4712Least InformativeInherited
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0.0000005607Moderately InformativeDirect
Post-translational modificationEndonuclease0InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · 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 2 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 Toprim domain 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 2 hidden Markov models representing the Toprim domain 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 · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]