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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 (2,975) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 36,217 219,371 61
Proteins 35,474 214,999 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 process0.0079350Least InformativeInherited
Biological Process (BP)single-organism cellular process0.92380.0000004768Least InformativeInherited
Biological Process (BP)oxidation-reduction process0.00000000076810Moderately InformativeDirect
Biological Process (BP)generation of precursor metabolites and energy0.00022320Moderately InformativeDirect
Molecular Function (MF)binding0.8281Least InformativeInherited
Molecular Function (MF)oxidoreductase activity0.0000000074430Moderately InformativeDirect
Molecular Function (MF)electron carrier activity00InformativeDirect
Molecular Function (MF)iron-sulfur cluster binding10Highly InformativeInherited
Cellular Component (CC)oxidoreductase complex0.00000057810InformativeDirect

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 0.0000004768 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.6368 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.002018 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.4427 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.2503 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.7224 Least Informative Inherited
Biological Process (BP) oxidation-reduction process 0 Moderately Informative Direct
Biological Process (BP) generation of precursor metabolites and energy 0 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0.0000000000004351 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0000000003164 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.00000002297 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0000008777 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.0001204 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.000292 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.0699 Moderately Informative Inherited
Biological Process (BP) protein complex biogenesis 0.2105 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 1 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.3844 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.744 Moderately Informative Inherited
Biological Process (BP) electron transport chain 0 Informative Direct
Biological Process (BP) ATP metabolic process 0 Informative Direct
Biological Process (BP) mitochondrion organization 0.000000009792 Informative Direct
Biological Process (BP) response to oxidative stress 0.00002597 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.00009968 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 0.01514 Informative Inherited
Biological Process (BP) phosphorylation 0.6203 Informative Inherited
Biological Process (BP) cellular protein complex assembly 0.01386 Informative Inherited
Biological Process (BP) cell death 0.06191 Informative Inherited
Biological Process (BP) glycosyl compound metabolic process 0.00662 Informative Inherited
Biological Process (BP) cellular respiration 0.003803 Informative Inherited
Biological Process (BP) xenobiotic metabolic process 0 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound catabolic process 0.000000000000003734 Highly Informative Direct
Biological Process (BP) nucleoside catabolic process 0.00000000004893 Highly Informative Direct
Biological Process (BP) NADH dehydrogenase complex assembly 0.00000002635 Highly Informative Direct
Biological Process (BP) mitochondrial respiratory chain complex I biogenesis 0.00000002826 Highly Informative Direct
Biological Process (BP) regulation of membrane potential 0.000001921 Highly Informative Direct
Biological Process (BP) mitochondrial electron transport, NADH to ubiquinone 0.00001556 Highly Informative Direct
Biological Process (BP) mitochondrial respiratory chain complex assembly 0.0002027 Highly Informative Direct
Biological Process (BP) apoptotic process 0.0003032 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.01678 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.285 Moderately Informative Inherited
Molecular Function (MF) electron carrier activity 0 Informative Direct
Molecular Function (MF) coenzyme binding 0.0322 Informative Inherited
Molecular Function (MF) NADH dehydrogenase activity 0.000000000000009279 Highly Informative Direct
Molecular Function (MF) iron-sulfur cluster binding 0 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on hydrogen as donor 0.00000001524 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on iron-sulfur proteins as donors 0.00003172 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0.2167 Highly Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH group of donors 0.1395 Highly Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on the aldehyde or oxo group of donors 0.1805 Highly Informative Inherited
Cellular Component (CC) protein complex 0.68 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) membrane 0.169 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.6704 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) organelle inner membrane 0 Moderately Informative Direct
Cellular Component (CC) mitochondrial envelope 0 Moderately Informative Direct
Cellular Component (CC) mitochondrial protein complex 0 Moderately Informative Direct
Cellular Component (CC) membrane protein complex 0.0000000000000378 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) oxidoreductase complex 0 Informative Direct
Cellular Component (CC) respiratory chain complex 0.00000000000004454 Informative Direct
Cellular Component (CC) inner mitochondrial membrane protein complex 0.0000000000001339 Informative Direct
Cellular Component (CC) mitochondrial respiratory chain 0.0000000000006134 Informative Direct
Cellular Component (CC) ferredoxin hydrogenase complex 0 Highly Informative Direct
Cellular Component (CC) mitochondrial respiratory chain complex I 0.000000000008025 Highly Informative Direct
Cellular Component (CC) outer membrane-bounded periplasmic space 0.00001002 Highly Informative Direct
Cellular Component (CC) mitochondrial intermembrane space 0.00001341 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processAmino-acid biosynthesis1Moderately InformativeInherited
Biological processPhotosynthesis0InformativeDirect
Biological processElectron transport0InformativeDirect
Biological processNitrogen fixation0InformativeDirect
Biological processMethanogenesis0.000000000001864Highly InformativeDirect
Biological processNitrate assimilation0.00002002Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentCell membrane0.01119Moderately InformativeInherited
Cellular componentMitochondrion0.0125Moderately InformativeInherited
Cellular componentCell inner membrane0InformativeDirect
Cellular componentThylakoid0InformativeDirect
Cellular componentMitochondrion inner membrane0.0002181InformativeDirect
Cellular componentPhotosystem I0Highly InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron-sulfur0Moderately InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionNADP0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular function2Fe-2S0.000000000000003433InformativeDirect
Molecular functionMolybdenum0.0004505InformativeDirect
Molecular functionUbiquinone0Highly InformativeDirect
Molecular function3Fe-4S0Highly InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationQuinone0Highly InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · 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 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) · UniProtKB KeyWords (KW) · Internal database links ]