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 (2,324) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 28,692 103,628 61
Proteins 28,085 102,086 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 process3.621e-060Least InformativeDirect
Biological Process (BP)oxidation-reduction process1.518e-120Moderately InformativeDirect
Molecular Function (MF)binding0.91781Least InformativeInherited
Molecular Function (MF)oxidoreductase activity3.834e-080Moderately InformativeDirect
Molecular Function (MF)electron carrier activity00InformativeDirect
Molecular Function (MF)metal cluster binding3.771e-060Highly InformativeDirect
Cellular Component (CC)protein complex0.074440.002126Least InformativeInherited
Cellular Component (CC)ferredoxin hydrogenase complex2.574e-080Highly 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 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.09135 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.9911 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) oxidation-reduction process 0 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 5.966e-15 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 1.819e-12 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 2.545e-08 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0002477 Moderately Informative Direct
Biological Process (BP) homeostatic process 0.1854 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.02335 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.2562 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.4704 Moderately Informative Inherited
Biological Process (BP) energy derivation by oxidation of organic compounds 1.558e-05 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) nucleoside triphosphate metabolic process 6.014e-06 Informative Direct
Biological Process (BP) response to oxidative stress 0.000112 Informative Direct
Biological Process (BP) apoptotic process 0.0007589 Informative Direct
Biological Process (BP) ribose phosphate metabolic process 0.0009316 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.02083 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.2345 Informative Inherited
Biological Process (BP) ribonucleoside metabolic process 1 Informative Inherited
Biological Process (BP) purine nucleoside metabolic process 1 Informative Inherited
Biological Process (BP) purine nucleotide metabolic process 0.008374 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.0438 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 2.592e-06 Highly Informative Direct
Biological Process (BP) purine ribonucleoside triphosphate metabolic process 3.452e-06 Highly Informative Direct
Biological Process (BP) pyrimidine nucleoside metabolic process 7.315e-05 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 0.3194 Moderately Informative Inherited
Molecular Function (MF) heterocyclic compound binding 0.9374 Moderately Informative Inherited
Molecular Function (MF) organic cyclic compound binding 0.958 Moderately Informative Inherited
Molecular Function (MF) electron carrier activity 0 Informative Direct
Molecular Function (MF) cofactor binding 1.223e-06 Informative Direct
Molecular Function (MF) nucleotide binding 0.0001566 Informative Direct
Molecular Function (MF) metal cluster binding 0 Highly Informative Direct
Molecular Function (MF) NADH dehydrogenase activity 3.098e-10 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor 0.0001992 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.002126 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.02258 Least Informative Inherited
Cellular Component (CC) membrane 0.5681 Least Informative Inherited
Cellular Component (CC) mitochondrial part 6.771e-11 Moderately Informative Direct
Cellular Component (CC) organelle envelope 8.921e-09 Moderately Informative Direct
Cellular Component (CC) organelle membrane 1.533e-05 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 3.944e-13 Informative Direct
Cellular Component (CC) ferredoxin hydrogenase complex 0 Highly 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) mitochondrial respiratory chain complex I 7.932e-11 Highly Informative Direct
Cellular Component (CC) cell envelope 4.697e-09 Highly Informative Direct
Cellular Component (CC) mitochondrial intermembrane space 1.192e-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 the central nervous system0Least InformativeDirect
Phenotypic Abnormality (PA)Morphological abnormality of the central nervous system0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of muscle physiology0Moderately 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)male genitalia0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least 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)sensory 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)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)microgametophyte0Least 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 acceptor0.0001581InformativeDirect
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)NADH:ubiquinone reductase (H(+)-translocating)0Highly InformativeDirect
Enzyme Commission (EC)Formate dehydrogenase2.359e-15Highly InformativeDirect
Enzyme Commission (EC)With an iron-sulfur protein as acceptor1.967e-13Highly InformativeDirect
Enzyme Commission (EC)With other, known, acceptors1.246e-11Highly InformativeDirect
Enzyme Commission (EC)With other acceptors3.527e-06Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor3.403e-05Highly 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 processPhotosystem I0Highly InformativeDirect
Biological processMethanogenesis5.886e-10Highly InformativeDirect
Biological processNitrate assimilation0.0001407Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentCell membrane0.008795Moderately InformativeInherited
Cellular componentThylakoid0InformativeDirect
Cellular componentCell inner membrane0InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular function2Fe-2S0InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionIron-sulfur0InformativeDirect
Molecular functionNADP0InformativeDirect
Molecular functionMolybdenum9.898e-05InformativeDirect
Molecular functionFAD0.0003892InformativeDirect
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 metabolism9.419e-05Least InformativeDirect
UniPathway (UP)cofactor metabolism0.1363Least InformativeInherited
UniPathway (UP)amino-acid metabolism0.5246Least InformativeInherited
UniPathway (UP)one-carbon metabolism0Moderately InformativeDirect
UniPathway (UP)tRNA modification2.074e-12InformativeDirect
UniPathway (UP)nonprotein amino-acid biosynthesis1.72e-11InformativeDirect
UniPathway (UP)methanogenesis3.457e-05InformativeDirect
UniPathway (UP)beta-alanine biosynthesis0Highly InformativeDirect
UniPathway (UP)tRNA-queuosine biosynthesis0Highly InformativeDirect
UniPathway (UP)coenzyme M-coenzyme B heterodisulfide reduction0Highly InformativeDirect
UniPathway (UP)methylamine degradation8.202e-10Highly 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 ]