SUPERFAMILY 1.75 HMM library and genome assignments server

  Home > SCOP hierarchy > Rubredoxin-like superfamily


Rubredoxin-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   Rubredoxin-like [ 57769] (17)
Superfamily:   Rubredoxin-like [ 57802] (3)
Families:   Rubredoxin [ 57803] (4)
  Desulforedoxin [ 57813] (2)
  Cytochrome c oxidase Subunit F [ 57818]

 Superfamily statistics
Genomes (1,403) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 3,440 8,621 33
Proteins 3,375 8,339 33

 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)
Molecular Function (MF)electron carrier activity2.589e-083.043e-12InformativeDirect

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) single-organism metabolic process 0.06346 Least Informative Inherited
Biological Process (BP) oxidation-reduction process 4.477e-05 Moderately Informative Direct
Molecular Function (MF) binding 0.6454 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 1.454e-06 Moderately Informative Direct
Molecular Function (MF) cation binding 8.707e-08 Moderately Informative Direct
Molecular Function (MF) electron carrier activity 3.043e-12 Informative Direct
Molecular Function (MF) transition metal ion binding 6.647e-10 Informative Direct
Molecular Function (MF) iron ion binding 1.561e-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)Oxidoreductases5.276e-07Least InformativeDirect
Enzyme Commission (EC)Phosphotransferases with a phosphate group as acce3.824e-07InformativeDirect
Enzyme Commission (EC)Adenylate kinase6.207e-11Highly InformativeDirect

Document: EC annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)vascular leaf0Least InformativeDirect
Plant ANatomical entity (PAN)stalk0Least InformativeDirect
Plant ANatomical entity (PAN)petal0Least InformativeDirect
Plant ANatomical entity (PAN)microgametophyte0Least InformativeDirect
Plant ANatomical entity (PAN)sepal0Least InformativeDirect
Plant ANatomical entity (PAN)pedicel0Least InformativeDirect
Plant ANatomical entity (PAN)collective leaf structure0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)plant embryo0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)phyllome apex0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)gynoecium0Least InformativeDirect
Plant ANatomical entity (PAN)stem0Least InformativeDirect
Plant ANatomical entity (PAN)leaf lamina0Least InformativeDirect
Plant ANatomical entity (PAN)shoot internode0Least InformativeDirect
Plant ANatomical entity (PAN)shoot apex0Least InformativeDirect
Plant ANatomical entity (PAN)androecium0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases5.243e-07Least InformativeDirect
Enzyme Commission (EC)Transferring phosphorous-containing groups0.02676Least InformativeInherited
Enzyme Commission (EC)Phosphotransferases with a phosphate group as acceptor3.504e-07InformativeDirect
Enzyme Commission (EC)Acting on a peroxide as acceptor4.252e-05InformativeDirect
Enzyme Commission (EC)Peroxidases3.336e-08Highly InformativeDirect
Enzyme Commission (EC)Acting on superoxide as acceptor1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processElectron transport0InformativeDirect
Biological processDetoxification0Highly InformativeDirect
Biological processNucleotide biosynthesis0.0001419Highly InformativeDirect
Cellular componentMitochondrion2.638e-06Moderately InformativeDirect
Cellular componentMitochondrion inner membrane3.188e-11InformativeDirect
DomainTransit peptide4.905e-07Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionFlavoprotein0InformativeDirect
Molecular functionFMN0InformativeDirect
Post-translational modificationOxidoreductase4.42e-16Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)aromatic compound metabolism0.8221Least InformativeInherited
UniPathway (UP)nitrogen metabolism0Moderately InformativeDirect
UniPathway (UP)energy metabolism0Moderately InformativeDirect
UniPathway (UP)purine metabolism0.052Moderately InformativeInherited
UniPathway (UP)nucleotide metabolism0.06854Moderately InformativeInherited
UniPathway (UP)nitrate reduction0InformativeDirect
UniPathway (UP)purine biosynthesis via salvage pathway6.215e-05InformativeDirect
UniPathway (UP)hydrocarbon degradation0Highly InformativeDirect
UniPathway (UP)nitric oxide reduction0Highly InformativeDirect
UniPathway (UP)AMP biosynthesis0.0002463Highly InformativeDirect

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) · Arabidopsis Plant Ontology (AP) · 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 18 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 Rubredoxin-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 18 hidden Markov models representing the Rubredoxin-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) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

Please send feedback, comments or questions to superfamily@cs.bris.ac.uk or use the feedback form.

© Copyright 2013 The SUPERFAMILY authors and Julian Gough.