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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 (2,973) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 36,181 219,371 61
Proteins 35,438 214,999 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 process0.0097350Least InformativeInherited
Biological Process (BP)single-organism cellular process0.93440.0000005594Least InformativeInherited
Biological Process (BP)oxidation-reduction process0.00000000069460Moderately InformativeDirect
Biological Process (BP)generation of precursor metabolites and energy0.00023840Moderately InformativeDirect
Molecular Function (MF)binding0.77621Least InformativeInherited
Molecular Function (MF)oxidoreductase activity0.0000000092910Moderately InformativeDirect
Molecular Function (MF)electron carrier activity00InformativeDirect
Molecular Function (MF)iron-sulfur cluster binding10Highly InformativeInherited
Cellular Component (CC)macromolecular complex0.37180.00002211Least InformativeInherited
Cellular Component (CC)oxidoreductase complex0.00000049340InformativeDirect

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 0.0000005594 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.002108 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.6474 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.2618 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.7104 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.4552 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 0.0000000000007187 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0000000004029 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.00000001946 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0000009774 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.0001331 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.0003545 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) protein complex biogenesis 0.2138 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.3802 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.7522 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.06561 Moderately Informative Inherited
Biological Process (BP) ATP metabolic process 0 Informative Direct
Biological Process (BP) electron transport chain 0 Informative Direct
Biological Process (BP) mitochondrion organization 0.00000001489 Informative Direct
Biological Process (BP) response to oxidative stress 0.00002895 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.0001061 Informative Direct
Biological Process (BP) cellular protein complex assembly 0.01357 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.01596 Informative Inherited
Biological Process (BP) glycosyl compound metabolic process 0.006675 Informative Inherited
Biological Process (BP) cell death 0.06498 Informative Inherited
Biological Process (BP) cellular respiration 0.00505 Informative Inherited
Biological Process (BP) phosphorylation 0.6143 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 0.000000000000003764 Highly Informative Direct
Biological Process (BP) nucleoside catabolic process 0.00000000006039 Highly Informative Direct
Biological Process (BP) regulation of membrane potential 0.000002353 Highly Informative Direct
Biological Process (BP) mitochondrial electron transport, NADH to ubiquinone 0.0000166 Highly Informative Direct
Biological Process (BP) mitochondrial respiratory chain complex assembly 0.00005578 Highly Informative Direct
Biological Process (BP) apoptotic process 0.000348 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 0.02013 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.3049 Moderately Informative Inherited
Molecular Function (MF) electron carrier activity 0 Informative Direct
Molecular Function (MF) coenzyme binding 0.03062 Informative Inherited
Molecular Function (MF) NADH dehydrogenase activity 0.00000000000001547 Highly Informative Direct
Molecular Function (MF) iron-sulfur cluster binding 0 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on hydrogen as donor 0.00000001804 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on iron-sulfur proteins as donors 0.00003631 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH group of donors 0.1432 Highly Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0.2305 Highly Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on the aldehyde or oxo group of donors 0.1709 Highly Informative Inherited
Cellular Component (CC) macromolecular complex 0.00002211 Least Informative Direct
Cellular Component (CC) membrane 0.2321 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.7187 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) membrane protein complex 0.00000000000004603 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.000000000002471 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.00000000001652 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 0.00000000000004324 Informative Direct
Cellular Component (CC) inner mitochondrial membrane protein complex 0.00000000000008125 Informative Direct
Cellular Component (CC) mitochondrial respiratory chain 0.0000000000001653 Informative Direct
Cellular Component (CC) ferredoxin hydrogenase complex 0 Highly Informative Direct
Cellular Component (CC) mitochondrial respiratory chain complex I 0.0000000000007183 Highly Informative Direct
Cellular Component (CC) outer membrane-bounded periplasmic space 0.00001159 Highly Informative Direct
Cellular Component (CC) mitochondrial intermembrane space 0.00001359 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 digestive system0.1617Least InformativeInherited
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 acid-base homeostasis0.005016Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of carbohydrate metabolism/homeostasis0.02688Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.02766Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of digestive system physiology0.05592Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skull size0InformativeDirect
Phenotypic Abnormality (PA)Muscular hypotonia0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of mitochondrial metabolism0.00000912InformativeDirect
Phenotypic Abnormality (PA)Hypoglycemia0.00007146InformativeDirect
Phenotypic Abnormality (PA)Abdominal symptom0.02834InformativeInherited
Phenotypic Abnormality (PA)Hepatic necrosis0.0000003685Highly InformativeDirect
Phenotypic Abnormality (PA)Vomiting0.00006715Highly InformativeDirect

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)visual 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 acceptor0.000008578InformativeDirect
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 a quinone or similar compound as acceptor0Highly InformativeDirect
Enzyme Commission (EC)NADH dehydrogenase0Highly InformativeDirect
Enzyme Commission (EC)Formate dehydrogenase0.000000000000001469Highly InformativeDirect
Enzyme Commission (EC)With an iron-sulfur protein as acceptor0.00000000000003658Highly InformativeDirect
Enzyme Commission (EC)NADH dehydrogenase (quinone)0.000000003408Highly InformativeDirect
Enzyme Commission (EC)With other acceptors0.00001548Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.00004873Highly InformativeDirect
Enzyme Commission (EC)Acting on hydrogen as donors0.0002038Highly 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 processMethanogenesis0.000000000001931Highly InformativeDirect
Biological processNitrate assimilation0.00001998Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentCell membrane0.008743Moderately InformativeInherited
Cellular componentMitochondrion0.01239Moderately InformativeInherited
Cellular componentThylakoid0InformativeDirect
Cellular componentCell inner membrane0InformativeDirect
Cellular componentMitochondrion inner membrane0.0002248InformativeDirect
Cellular componentPhotosystem I0Highly InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionIron-sulfur0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular functionNADP0Moderately InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular function2Fe-2S0.000000000000004899InformativeDirect
Molecular functionMolybdenum0.0004545InformativeDirect
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 metabolism0.0002066Least InformativeDirect
UniPathway (UP)cofactor metabolism0.08506Least InformativeInherited
UniPathway (UP)amino-acid metabolism0.594Least InformativeInherited
UniPathway (UP)one-carbon metabolism0Moderately InformativeDirect
UniPathway (UP)tRNA modification0.000000000003354InformativeDirect
UniPathway (UP)nonprotein amino-acid biosynthesis0.00000000003859InformativeDirect
UniPathway (UP)methanogenesis0.00003644InformativeDirect
UniPathway (UP)beta-alanine biosynthesis0Highly InformativeDirect
UniPathway (UP)tRNA-queuosine biosynthesis0Highly InformativeDirect
UniPathway (UP)coenzyme M-coenzyme B heterodisulfide reduction0Highly InformativeDirect
UniPathway (UP)methylamine degradation0.0000000007707Highly 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 ]