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4Fe-4S ferredoxins superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ferredoxin-like [ 54861] (59)
Superfamily:   4Fe-4S ferredoxins [ 54862] (6)
Families:   Short-chain ferredoxins [ 54863]
  7-Fe ferredoxin [ 54870] (2)
  Archaeal ferredoxins [ 54874]
  Single 4Fe-4S cluster ferredoxin [ 54877] (4)
  Ferredoxin domains from multidomain proteins [ 54884] (13)
  ETF-QO domain-like [ 143256]


Superfamily statistics
Genomes (2,968) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 36,149 215,019 61
Proteins 35,406 212,005 61


Functional annotation
General category Metabolism
Detailed category Redox

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)single-organism metabolic process0.0012520Least InformativeInherited
Biological Process (BP)single-organism cellular process0.8230.000002478Least InformativeInherited
Biological Process (BP)generation of precursor metabolites and energy0.000085990Moderately InformativeDirect
Biological Process (BP)oxidation-reduction process0.00000000077750Moderately InformativeDirect
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)oxidoreductase activity0.0000000042880Moderately InformativeDirect
Molecular Function (MF)electron carrier activity00InformativeDirect
Molecular Function (MF)metal cluster binding0.0000011350Highly InformativeDirect
Cellular Component (CC)oxidoreductase complex0.00000017290InformativeDirect

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 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000002478 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.00000001154 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.225 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.7467 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.4146 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.002309 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) generation of precursor metabolites and energy 0 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.000082 Moderately Informative Direct
Biological Process (BP) ribose phosphate metabolic process 0.000000002496 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.00000004216 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.0001154 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0.000000000308 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0000000003153 Moderately Informative Direct
Biological Process (BP) glycosyl compound metabolic process 0.00000001984 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.05832 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.5809 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.3749 Moderately Informative Inherited
Biological Process (BP) response to stress 1 Moderately Informative Inherited
Biological Process (BP) response to oxidative stress 0.00001139 Informative Direct
Biological Process (BP) mitochondrion organization 0.0000003011 Informative Direct
Biological Process (BP) electron transport chain 0 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.00009459 Informative Direct
Biological Process (BP) ATP metabolic process 0 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0.0000000000000208 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 0.01517 Informative Inherited
Biological Process (BP) cellular respiration 0.007123 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.07847 Informative Inherited
Biological Process (BP) cell death 0.02645 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.05268 Informative Inherited
Biological Process (BP) phosphorylation 0.6429 Informative Inherited
Biological Process (BP) mitochondrial electron transport, NADH to ubiquinone 0.00001677 Highly Informative Direct
Biological Process (BP) apoptotic process 0.000186 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0.000000000000007239 Highly Informative Direct
Biological Process (BP) mitochondrial respiratory chain complex assembly 0.00002365 Highly Informative Direct
Biological Process (BP) regulation of membrane potential 0.000001009 Highly Informative Direct
Biological Process (BP) cellular response to xenobiotic stimulus 0 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound catabolic process 0.0000000000004539 Highly Informative Direct
Biological Process (BP) reactive oxygen species metabolic process 0.000000292 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.1933 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.005957 Moderately Informative Inherited
Molecular Function (MF) electron carrier activity 0 Informative Direct
Molecular Function (MF) coenzyme binding 0.02659 Informative Inherited
Molecular Function (MF) NADH dehydrogenase activity 0.000000000000003237 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on iron-sulfur proteins as donors 0.00003722 Highly Informative Direct
Molecular Function (MF) metal cluster binding 0 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH group of donors 0.1239 Highly Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0.2257 Highly Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on the aldehyde or oxo group of donors 0.2207 Highly Informative Inherited
Cellular Component (CC) protein complex 0.6701 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) membrane 0.2274 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.34 Least Informative Inherited
Cellular Component (CC) organelle membrane 0.0000000257 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.000000000001501 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.0000000000001973 Moderately Informative Direct
Cellular Component (CC) membrane protein complex 0.00000000000002585 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) mitochondrial respiratory chain 0.0000000000001858 Informative Direct
Cellular Component (CC) inner mitochondrial membrane protein complex 0.00000000000003133 Informative Direct
Cellular Component (CC) respiratory chain complex 0 Informative Direct
Cellular Component (CC) oxidoreductase complex 0 Informative Direct
Cellular Component (CC) mitochondrial respiratory chain complex I 0 Highly Informative Direct
Cellular Component (CC) ferredoxin hydrogenase complex 0 Highly Informative Direct
Cellular Component (CC) organelle envelope lumen 0.00000000001312 Highly Informative Direct
Cellular Component (CC) periplasmic space 0 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)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Acting on NADH or NADPH0Moderately InformativeDirect
Enzyme Commission (EC)Acting on a sulfur group of donors1Moderately InformativeInherited
Enzyme Commission (EC)Acting on the CH-NH group of donors1Moderately InformativeInherited
Enzyme Commission (EC)Acting on the CH-CH group of donors1Moderately InformativeInherited
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors1Moderately InformativeInherited
Enzyme Commission (EC)NADH:ubiquinone reductase (H(+)-translocating)0InformativeDirect
Enzyme Commission (EC)With other acceptors0InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor1InformativeInherited
Enzyme Commission (EC)Dihydropyrimidine dehydrogenase (NADP(+))0Highly InformativeDirect
Enzyme Commission (EC)With a quinone or similar compound as acceptor0Highly InformativeDirect
Enzyme Commission (EC)Other oxidoreductases0Highly InformativeDirect
Enzyme Commission (EC)Formate dehydrogenase0.000000000000001404Highly InformativeDirect
Enzyme Commission (EC)With an iron-sulfur protein as acceptor0.0000000000000543Highly InformativeDirect
Enzyme Commission (EC)With other acceptors0.000000000007567Highly InformativeDirect
Enzyme Commission (EC)With other, known, acceptors0.000000000009104Highly InformativeDirect
Enzyme Commission (EC)Nitrate reductase0.000002992Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details) Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the eye0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the musculature0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the skull0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of higher mental function0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of muscle physiology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of forebrain morphology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of skull size0InformativeDirect
Phenotypic Abnormality (PA)Muscular hypotonia0InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)anatomical cluster0Least InformativeDirect
Xenopus ANatomical entity (XAN)brain0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)female genitalia0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)heart0InformativeDirect
Xenopus ANatomical entity (XAN)intestine0InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect

Document: AP 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)Acting on NADH or NADPH0InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.000008871InformativeDirect
Enzyme Commission (EC)Acting on CH or CH(2) groups1InformativeInherited
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors1InformativeInherited
Enzyme Commission (EC)Acting on the CH-NH(2) group of donors1InformativeInherited
Enzyme Commission (EC)Acting on the CH-NH group of donors1InformativeInherited
Enzyme Commission (EC)Acting on other nitrogenous compounds as donors1InformativeInherited
Enzyme Commission (EC)Acting on a sulfur group of donors1InformativeInherited
Enzyme Commission (EC)With other acceptors0Highly InformativeDirect
Enzyme Commission (EC)With a quinone or similar compound as acceptor0Highly InformativeDirect
Enzyme Commission (EC)NADH dehydrogenase0Highly InformativeDirect
Enzyme Commission (EC)Formate dehydrogenase0.00000000000000146Highly InformativeDirect
Enzyme Commission (EC)With an iron-sulfur protein as acceptor0.00000000000003284Highly InformativeDirect
Enzyme Commission (EC)With other, known, acceptors0.000000000004083Highly InformativeDirect
Enzyme Commission (EC)NADH dehydrogenase (quinone)0.000000004211Highly InformativeDirect
Enzyme Commission (EC)With other acceptors0.00001654Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.00004524Highly InformativeDirect
Enzyme Commission (EC)Acting on hydrogen as donors0.0002084Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processAmino-acid biosynthesis1Moderately InformativeInherited
Biological processElectron transport0InformativeDirect
Biological processNitrogen fixation0InformativeDirect
Biological processPhotosynthesis0InformativeDirect
Biological processMethanogenesis0.000000000001963Highly InformativeDirect
Biological processNitrate assimilation0.0000177Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentCell membrane0.006884Moderately InformativeInherited
Cellular componentMitochondrion0.01207Moderately InformativeInherited
Cellular componentThylakoid0InformativeDirect
Cellular componentCell inner membrane0InformativeDirect
Cellular componentMitochondrion inner membrane0.0002401InformativeDirect
Cellular componentPhotosystem I0Highly InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionIron-sulfur0InformativeDirect
Molecular functionNADP0InformativeDirect
Molecular function2Fe-2S0.000000000000005984InformativeDirect
Molecular functionMolybdenum0.00009496InformativeDirect
Molecular function3Fe-4S0Highly InformativeDirect
Molecular functionUbiquinone0Highly InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationQuinone0Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0.0002059Least InformativeDirect
UniPathway (UP)cofactor metabolism0.0841Least InformativeInherited
UniPathway (UP)amino-acid metabolism0.5931Least InformativeInherited
UniPathway (UP)one-carbon metabolism0Moderately InformativeDirect
UniPathway (UP)tRNA modification0.000000000003687InformativeDirect
UniPathway (UP)nonprotein amino-acid biosynthesis0.00000000003927InformativeDirect
UniPathway (UP)methanogenesis0.00003668InformativeDirect
UniPathway (UP)beta-alanine biosynthesis0Highly InformativeDirect
UniPathway (UP)tRNA-queuosine biosynthesis0Highly InformativeDirect
UniPathway (UP)coenzyme M-coenzyme B heterodisulfide reduction0Highly InformativeDirect
UniPathway (UP)methylamine degradation0.000000000775Highly 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) · Disease Ontology (DO) · Human Phenotype (HP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · 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 32 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 4Fe-4S ferredoxins 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 32 hidden Markov models representing the 4Fe-4S ferredoxins 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) · Disease Ontology (DO) · Human Phenotype (HP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]