SUPERFAMILY 1.75 HMM library and genome assignments server

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 (2,967) 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 process0.014410Least InformativeInherited
Biological Process (BP)single-organism cellular process0.98070.002176Least InformativeInherited
Biological Process (BP)oxidation-reduction process0.0000000035940Moderately InformativeDirect
Biological Process (BP)energy derivation by oxidation of organic compounds0.00025620InformativeDirect
Molecular Function (MF)binding0.28621Least InformativeInherited
Molecular Function (MF)oxidoreductase activity0.00000093920Moderately InformativeDirect
Molecular Function (MF)electron carrier activity00InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on NAD(P)H0.00021280.000000006426InformativeDirect
Molecular Function (MF)metal cluster binding0.000008290Highly InformativeDirect
Cellular Component (CC)protein complex0.029010.001652Least InformativeInherited
Cellular Component (CC)oxidoreductase complex0.0000000016620InformativeDirect

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) nitrogen compound metabolic process 0.9656 Least Informative Inherited
Biological Process (BP) response to stimulus 0.5573 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.04874 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.7294 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.002176 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.4882 Least Informative Inherited
Biological Process (BP) cellular catabolic process 0.000000001164 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.0000008376 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0001106 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.00000000001096 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.8914 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.005432 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.45 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.1043 Moderately Informative Inherited
Biological Process (BP) apoptotic process 0.0003976 Informative Direct
Biological Process (BP) response to oxidative stress 0.000000343 Informative Direct
Biological Process (BP) mitochondrion organization 0.000000001608 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 0.00000005277 Informative Direct
Biological Process (BP) nucleoside triphosphate metabolic process 0.000001028 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 0.00000611 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 0 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.000003235 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.1247 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.6857 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.1526 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) electron transport chain 0.0000000004068 Highly Informative Direct
Biological Process (BP) regulation of membrane potential 0.0000000983 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound catabolic process 0 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 0.0008023 Moderately Informative Direct
Molecular Function (MF) anion binding 0.38 Moderately Informative Inherited
Molecular Function (MF) nucleotide binding 0.00008497 Informative Direct
Molecular Function (MF) electron carrier activity 0 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on NAD(P)H 0.000000006426 Informative Direct
Molecular Function (MF) cofactor binding 0.00000002419 Informative Direct
Molecular Function (MF) NADH dehydrogenase activity 0.0000000000005095 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor 0.00002239 Highly Informative Direct
Molecular Function (MF) metal cluster binding 0 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0.00209 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.846 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.003186 Least Informative Inherited
Cellular Component (CC) protein complex 0.001652 Least Informative Inherited
Cellular Component (CC) membrane 0.2069 Least Informative Inherited
Cellular Component (CC) organelle envelope 0.0000000004563 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.000000000007509 Moderately Informative Direct
Cellular Component (CC) external encapsulating structure 0.00000000000005044 Informative Direct
Cellular Component (CC) mitochondrial membrane part 0 Informative Direct
Cellular Component (CC) respiratory chain 0 Informative Direct
Cellular Component (CC) oxidoreductase complex 0 Informative Direct
Cellular Component (CC) cell envelope 0.000000004934 Highly Informative Direct
Cellular Component (CC) external encapsulating structure part 0 Highly Informative Direct
Cellular Component (CC) respiratory chain complex I 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 metabolism/homeostasis0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of higher mental function0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of muscle physiology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the globe0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of brain morphology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.005063Moderately InformativeInherited
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)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system0Least InformativeDirect

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)alimentary system0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)intestine0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)visual system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)heart0InformativeDirect
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 acceptor0.00001386InformativeDirect
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:ubiquinone reductase (H(+)-translocating)0Highly InformativeDirect
Enzyme Commission (EC)Formate dehydrogenase0.000000000000001441Highly InformativeDirect
Enzyme Commission (EC)With an iron-sulfur protein as acceptor0.0000000000001282Highly InformativeDirect
Enzyme Commission (EC)With other, known, acceptors0.00000000001133Highly InformativeDirect
Enzyme Commission (EC)With other acceptors0.00001565Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.00003176Highly InformativeDirect
Enzyme Commission (EC)Acting on hydrogen as donor0.0001802Highly 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 processMethanogenesis0.000000000001789Highly InformativeDirect
Biological processNitrate assimilation0.00001783Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentCell membrane0.002254Moderately InformativeInherited
Cellular componentMitochondrion0.009581Moderately InformativeInherited
Cellular componentThylakoid0InformativeDirect
Cellular componentCell inner membrane0InformativeDirect
Cellular componentMitochondrion inner membrane0.0002573InformativeDirect
Cellular componentPhotosystem I0Highly InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular functionFlavoprotein0.002735Moderately InformativeInherited
Molecular function2Fe-2S0InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionIron-sulfur0InformativeDirect
Molecular functionNADP0InformativeDirect
Molecular functionMolybdenum0.00009876InformativeDirect
Molecular functionFAD0.0009306InformativeDirect
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 metabolism0.00009981Least InformativeDirect
UniPathway (UP)cofactor metabolism0.1383Least InformativeInherited
UniPathway (UP)amino-acid metabolism0.5187Least InformativeInherited
UniPathway (UP)one-carbon metabolism0Moderately InformativeDirect
UniPathway (UP)tRNA modification0.000000000001859InformativeDirect
UniPathway (UP)nonprotein amino-acid biosynthesis0.00000000002198InformativeDirect
UniPathway (UP)methanogenesis0.00003243InformativeDirect
UniPathway (UP)beta-alanine biosynthesis0Highly InformativeDirect
UniPathway (UP)tRNA-queuosine biosynthesis0Highly InformativeDirect
UniPathway (UP)coenzyme M-coenzyme B heterodisulfide reduction0Highly InformativeDirect
UniPathway (UP)methylamine degradation0.0000000007786Highly 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 ]