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 (2,922) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 35,938 103,628 61
Proteins 35,191 102,086 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 process0.00029270Least InformativeDirect
Molecular Function (MF)binding0.52531Least InformativeInherited
Molecular Function (MF)oxidoreductase activity3.382e-070Moderately InformativeDirect
Molecular Function (MF)electron carrier activity00InformativeDirect
Molecular Function (MF)metal cluster binding2.524e-060Highly 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) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.9833 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.08417 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.7996 Least Informative Inherited
Biological Process (BP) response to stimulus 0.6007 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 4.102e-14 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 6.127e-09 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0006491 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.2608 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.7094 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.003486 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.3281 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.3669 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.3901 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.1087 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound catabolic process 0.01422 Moderately Informative Inherited
Biological Process (BP) pyrimidine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) mitochondrion organization 1.037e-09 Informative Direct
Biological Process (BP) response to oxidative stress 1e-06 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 4.308e-06 Informative Direct
Biological Process (BP) nucleoside triphosphate metabolic process 4.43e-05 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.0001106 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 0.0001938 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.07974 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.5844 Informative Inherited
Biological Process (BP) glycosyl compound catabolic process 0.5956 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.00989 Informative Inherited
Biological Process (BP) protein complex assembly 0.04269 Informative Inherited
Biological Process (BP) energy derivation by oxidation of organic compounds 0.001737 Informative Inherited
Biological Process (BP) cell death 0.001633 Informative Inherited
Biological Process (BP) pyrimidine-containing compound catabolic process 0 Highly Informative Direct
Biological Process (BP) xenobiotic metabolic process 0 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0 Highly Informative Direct
Biological Process (BP) regulation of membrane potential 7.656e-07 Highly Informative Direct
Biological Process (BP) ATP metabolic process 1.083e-06 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 0.3085 Moderately Informative Inherited
Molecular Function (MF) electron carrier activity 0 Informative Direct
Molecular Function (MF) cofactor binding 1.046e-08 Informative Direct
Molecular Function (MF) nucleotide binding 1.076e-05 Informative Direct
Molecular Function (MF) metal cluster binding 0 Highly Informative Direct
Molecular Function (MF) NADH dehydrogenase activity 2.25e-12 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0.001922 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 0.9981 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.7852 Least Informative Inherited
Cellular Component (CC) protein complex 0.004807 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.003079 Least Informative Inherited
Cellular Component (CC) membrane 0.1628 Least Informative Inherited
Cellular Component (CC) mitochondrial part 6.328e-12 Moderately Informative Direct
Cellular Component (CC) organelle envelope 4.343e-10 Moderately Informative Direct
Cellular Component (CC) organelle membrane 1.121e-06 Moderately Informative Direct
Cellular Component (CC) respiratory chain 0 Informative Direct
Cellular Component (CC) mitochondrial membrane part 0 Informative Direct
Cellular Component (CC) external encapsulating structure 4.223e-14 Informative Direct
Cellular Component (CC) periplasmic space 0 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
Cellular Component (CC) mitochondrial respiratory chain 1.597e-11 Highly Informative Direct
Cellular Component (CC) cell envelope 9.687e-09 Highly Informative Direct
Cellular Component (CC) mitochondrial intermembrane space 2.054e-06 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 dehydrogenase1.404e-15Highly InformativeDirect
Enzyme Commission (EC)With an iron-sulfur protein as acceptor5.43e-14Highly InformativeDirect
Enzyme Commission (EC)With other acceptors7.567e-12Highly InformativeDirect
Enzyme Commission (EC)With other, known, acceptors9.104e-12Highly InformativeDirect
Enzyme Commission (EC)Nitrate reductase2.992e-06Highly 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)Muscular hypotonia0InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP 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 acceptor1.365e-05InformativeDirect
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 dehydrogenase9.573e-16Highly InformativeDirect
Enzyme Commission (EC)With an iron-sulfur protein as acceptor1.138e-13Highly InformativeDirect
Enzyme Commission (EC)With other, known, acceptors1.187e-11Highly InformativeDirect
Enzyme Commission (EC)With other acceptors3.424e-06Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor3.308e-05Highly InformativeDirect
Enzyme Commission (EC)Acting on hydrogen as donor0.0001864Highly 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 processMethanogenesis1.842e-12Highly InformativeDirect
Biological processNitrate assimilation0.0001418Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentCell membrane0.002024Moderately InformativeInherited
Cellular componentMitochondrion0.009107Moderately InformativeInherited
Cellular componentThylakoid0InformativeDirect
Cellular componentCell inner membrane0InformativeDirect
Cellular componentMitochondrion inner membrane0.0002741InformativeDirect
Cellular componentPhotosystem I0Highly InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular functionFlavoprotein0.00277Moderately InformativeInherited
Molecular function2Fe-2S0InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionIron-sulfur0InformativeDirect
Molecular functionNADP0InformativeDirect
Molecular functionMolybdenum0.0001051InformativeDirect
Molecular functionFAD0.0009272InformativeDirect
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)amino-acid metabolism0.001341Least InformativeInherited
UniPathway (UP)cofactor metabolism0.006532Least InformativeInherited
UniPathway (UP)one-carbon metabolism1.289e-10Moderately InformativeDirect
UniPathway (UP)methanogenesis0InformativeDirect
UniPathway (UP)nonprotein amino-acid biosynthesis2.146e-16InformativeDirect
UniPathway (UP)beta-alanine biosynthesis0Highly InformativeDirect
UniPathway (UP)coenzyme M-coenzyme B heterodisulfide reduction0Highly 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 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 Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]