SUPERFAMILY 1.75 HMM library and genome assignments server


Frataxin/Nqo15-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   N domain of copper amine oxidase-like [ 55382] (5)
Superfamily:   Frataxin/Nqo15-like [ 55387] (2)
Families:   Frataxin-like [ 55388] (2)
  Nqo15-like [ 143572]


Superfamily statistics
Genomes (1,013) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 1,105 2,609 7
Proteins 1,104 2,609 7


Functional annotation
General category Other
Detailed category Unknown function

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)cellular component organization or biogenesis0.0046694.488e-05Least InformativeInherited
Biological Process (BP)biosynthetic process0.0023892.319e-05Least InformativeInherited
Biological Process (BP)cellular component biogenesis3.075e-054.556e-05Moderately InformativeDirect
Biological Process (BP)iron-sulfur cluster assembly1.897e-100Highly InformativeDirect

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) biosynthetic process 2.319e-05 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 4.488e-05 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.06796 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.1139 Least Informative Inherited
Biological Process (BP) developmental process 0.06856 Least Informative Inherited
Biological Process (BP) response to stimulus 0.003109 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.003886 Least Informative Inherited
Biological Process (BP) homeostatic process 0.0004134 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 4.556e-05 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0.00374 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.2681 Moderately Informative Inherited
Biological Process (BP) response to oxidative stress 2.031e-08 Informative Direct
Biological Process (BP) response to inorganic substance 0.0004956 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 4.887e-10 Informative Direct
Biological Process (BP) phosphorylation 4.366e-05 Informative Direct
Biological Process (BP) regulation of growth 1.412e-06 Informative Direct
Biological Process (BP) cation homeostasis 7.962e-14 Informative Direct
Biological Process (BP) cellular chemical homeostasis 7.325e-14 Informative Direct
Biological Process (BP) oxidative phosphorylation 1.774e-08 Highly Informative Direct
Biological Process (BP) iron-sulfur cluster assembly 0 Highly Informative Direct
Biological Process (BP) transition metal ion homeostasis 0 Highly Informative Direct
Molecular Function (MF) binding 0.2453 Least Informative Inherited
Molecular Function (MF) cation binding 5.78e-07 Moderately Informative Direct
Molecular Function (MF) transition metal ion binding 1.363e-08 Informative Direct
Molecular Function (MF) iron ion binding 3.846e-14 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0006447 Least Informative Direct
Cellular Component (CC) cytoplasmic part 8.698e-06 Least Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Oxidizing metal ions0InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Oxidizing metal ions0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport7.313e-15Least InformativeDirect
Biological processIon transport0Moderately InformativeDirect
Biological processHeme biosynthesis0Highly InformativeDirect
Cellular componentMitochondrion2.705e-14Moderately InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionIron6.827e-15Moderately InformativeDirect
Molecular functionIron transport0Highly InformativeDirect
Post-translational modificationOxidoreductase1.92e-13Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR002908 SSF55387 Protein matches
Abstract

This family is related to the globular C-terminus of frataxin the protein that is mutated in Friedreich's ataxia [PubMed8931268]. Friedreich ataxia is a progressive neurodegenerative disorder caused by loss of function mutations in the gene encoding frataxin (FRDA). Frataxin mRNA is predominantly expressed in tissues with a high metabolic rate (including liver, kidney, brown fat and heart). Mouse and yeast frataxin homologues contain a potential N-terminal mitochondrial targeting sequence, and human frataxin has been observed to co-localise with a mitochondrial protein. Furthermore, disruption of the yeast gene has been shown to result in mitochondrial dysfunction. Friedreich's ataxia is thus believed to be a mitochondrial disease caused by a mutation in the nuclear genome (specifically, expansion of an intronic GAA triplet repeat) [PubMed8596916, PubMed8815938, PubMed9241270].

This family is also found found in a number of bacterial proteins whose functions are currently unknown.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · 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 4 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 Frataxin/Nqo15-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 4 hidden Markov models representing the Frataxin/Nqo15-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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]