SUPERFAMILY 1.75 HMM library and genome assignments server


2Fe-2S ferredoxin-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   beta-Grasp (ubiquitin-like) [ 54235] (14)
Superfamily:   2Fe-2S ferredoxin-like [ 54292] (2)
Families:   2Fe-2S ferredoxin-related [ 54293] (3)
  2Fe-2S ferredoxin domains from multidomain proteins [ 54312] (13)


Superfamily statistics
Genomes (2,877) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 20,784 0 57
Proteins 20,761 0 57


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)protein metabolic process7.566e-061Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process3.136e-051Least InformativeInherited
Molecular Function (MF)binding7.829e-070.0001093Least InformativeDirect
Molecular Function (MF)cation binding1.451e-110.6159Moderately InformativeInherited
Molecular Function (MF)electron carrier activity00InformativeDirect
Molecular Function (MF)transition metal ion binding2.269e-144.284e-13InformativeDirect
Molecular Function (MF)iron ion binding06.079e-07Highly InformativeDirect
Molecular Function (MF)metal cluster binding1.354e-070Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.0032430.00264Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.10371.194e-09Least InformativeInherited
Cellular Component (CC)plastid06.885e-11InformativeDirect

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 0.9838 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.001871 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.6227 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) oxidation-reduction process 0 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 5.287e-09 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 8.015e-06 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 6.695e-05 Moderately Informative Direct
Biological Process (BP) lipid biosynthetic process 0.0002962 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0003668 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.153 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.01265 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.06325 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.5685 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.04561 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.8239 Moderately Informative Inherited
Biological Process (BP) cofactor metabolic process 0.1435 Moderately Informative Inherited
Biological Process (BP) isoprenoid metabolic process 8.71e-07 Informative Direct
Biological Process (BP) mitochondrion organization 6.57e-06 Informative Direct
Biological Process (BP) oxidoreduction coenzyme metabolic process 1.489e-05 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 0.0001714 Informative Direct
Biological Process (BP) programmed cell death 0.0002729 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 0.0003002 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0.0003864 Informative Direct
Biological Process (BP) regulation of hormone levels 0.0005606 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.0005656 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 0.5075 Informative Inherited
Biological Process (BP) phosphorylation 0.5306 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 0.0155 Informative Inherited
Biological Process (BP) alcohol metabolic process 0.03989 Informative Inherited
Biological Process (BP) nucleoside triphosphate metabolic process 0.3655 Informative Inherited
Biological Process (BP) nucleoside monophosphate metabolic process 0.08345 Informative Inherited
Biological Process (BP) nucleobase metabolic process 2.099e-14 Highly Informative Direct
Biological Process (BP) hormone biosynthetic process 7.124e-09 Highly Informative Direct
Biological Process (BP) isoprenoid biosynthetic process 7.503e-09 Highly Informative Direct
Biological Process (BP) oxidative phosphorylation 9.838e-09 Highly Informative Direct
Biological Process (BP) ATP metabolic process 1.034e-05 Highly Informative Direct
Biological Process (BP) regulation of epithelial cell differentiation 2.096e-05 Highly Informative Direct
Biological Process (BP) nicotinamide nucleotide metabolic process 4.182e-05 Highly Informative Direct
Biological Process (BP) regulation of membrane potential 5.907e-05 Highly Informative Direct
Biological Process (BP) electron transport chain 0.000302 Highly Informative Direct
Biological Process (BP) alcohol biosynthetic process 0.0006132 Highly Informative Direct
Biological Process (BP) sterol metabolic process 0.08199 Highly Informative Inherited
Biological Process (BP) aerobic respiration 1 Highly Informative Inherited
Molecular Function (MF) binding 0.0001093 Least Informative Direct
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 1 Moderately Informative Inherited
Molecular Function (MF) cation binding 0.6159 Moderately Informative Inherited
Molecular Function (MF) electron carrier activity 0 Informative Direct
Molecular Function (MF) transition metal ion binding 4.284e-13 Informative Direct
Molecular Function (MF) cofactor binding 0 Informative Direct
Molecular Function (MF) nucleotide binding 4.908e-11 Informative Direct
Molecular Function (MF) iron ion binding 6.079e-07 Highly Informative Direct
Molecular Function (MF) metal cluster binding 0 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the aldehyde or oxo group of donors 5.555e-06 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on NAD(P)H 0.000157 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0.007332 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 1.194e-09 Least Informative Direct
Cellular Component (CC) protein complex 5.819e-07 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.3911 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.00264 Least Informative Inherited
Cellular Component (CC) membrane 0.00387 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0 Moderately Informative Direct
Cellular Component (CC) organelle membrane 3.907e-13 Moderately Informative Direct
Cellular Component (CC) plastid 6.885e-11 Informative Direct
Cellular Component (CC) respiratory chain 0 Informative Direct
Cellular Component (CC) mitochondrial membrane part 0 Informative Direct
Cellular Component (CC) mitochondrial intermembrane space 0.0003725 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 the CH-CH group of donors0Moderately InformativeDirect
Enzyme Commission (EC)Acting on NADH or NADPH0Moderately InformativeDirect
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors0.03282Moderately InformativeInherited
Enzyme Commission (EC)NADH:ubiquinone reductase (H(+)-translocating)0InformativeDirect
Enzyme Commission (EC)With other acceptors0InformativeDirect
Enzyme Commission (EC)With other acceptors5.336e-12InformativeDirect
Enzyme Commission (EC)Acting on CH or CH(2) groups3.125e-06InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor1InformativeInherited
Enzyme Commission (EC)Acting on iron-sulfur proteins as donors0.008311InformativeInherited
Enzyme Commission (EC)With oxygen as acceptor0Highly InformativeDirect
Enzyme Commission (EC)Succinate dehydrogenase (ubiquinone)0Highly InformativeDirect
Enzyme Commission (EC)Formate dehydrogenase0Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor1.187e-10Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor2.174e-10Highly InformativeDirect
Enzyme Commission (EC)Succinate dehydrogenase2.77e-08Highly InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect

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
Fly Anatomy (FA)cell0Least 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)cell0Least 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)gamete0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)visual system0Moderately InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)seedling development stage5.833e-05InformativeDirect
Plant structure DEvelopment stage (PDE)0 seed germination stage0.0001448InformativeDirect

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 NADPH9.332e-13InformativeDirect
Enzyme Commission (EC)Acting on CH or CH(2) groups5.278e-05InformativeDirect
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors0.0001065InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen0.9959InformativeInherited
Enzyme Commission (EC)Formate dehydrogenase0Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor0Highly InformativeDirect
Enzyme Commission (EC)With a quinone or related compound as acceptor0Highly InformativeDirect
Enzyme Commission (EC)NADH:ubiquinone reductase (H(+)-translocating)0Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor2.107e-11Highly InformativeDirect
Enzyme Commission (EC)NADH dehydrogenase6.503e-09Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor5.181e-05Highly InformativeDirect
Enzyme Commission (EC)With other acceptors0.0006555Highly InformativeDirect
Enzyme Commission (EC)With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into one donor0.000713Highly InformativeDirect
Enzyme Commission (EC)Acting on hydrogen as donor0.0007206Highly InformativeDirect
Enzyme Commission (EC)Acting on iron-sulfur proteins as donors0.001449Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processIon transport1Moderately InformativeInherited
Biological processLipid metabolism1Moderately InformativeInherited
Biological processAromatic hydrocarbons catabolism0InformativeDirect
Biological processElectron transport0InformativeDirect
Biological processTricarboxylic acid cycle0InformativeDirect
Biological processSteroid metabolism2.93e-07InformativeDirect
Biological processNitrogen fixation1.303e-05InformativeDirect
Biological processAuxin biosynthesis0Highly InformativeDirect
Biological processSodium transport0Highly InformativeDirect
Biological processAbscisic acid biosynthesis0Highly InformativeDirect
Biological processCholesterol metabolism3.264e-09Highly InformativeDirect
Biological processPurine metabolism7.061e-07Highly InformativeDirect
Cellular componentMembrane5.489e-07Least InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentCell membrane0.2243Moderately InformativeInherited
Cellular componentCell inner membrane0InformativeDirect
Cellular componentPeroxisome2.056e-11InformativeDirect
Cellular componentMitochondrion inner membrane8.464e-08InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular function2Fe-2S0InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionIron-sulfur0InformativeDirect
Molecular functionMolybdenum0InformativeDirect
Molecular functionSodium0InformativeDirect
Molecular functionFAD3.141e-07InformativeDirect
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)carbohydrate metabolism0Least InformativeDirect
UniPathway (UP)aromatic compound metabolism0.1298Least InformativeInherited
UniPathway (UP)aromatic compound degradation5.888e-14Moderately InformativeDirect
UniPathway (UP)purine metabolism0.8581Moderately InformativeInherited
UniPathway (UP)tricarboxylic acid cycle0InformativeDirect
UniPathway (UP)purine degradation4.237e-07InformativeDirect
UniPathway (UP)purine base metabolism0.000901InformativeDirect
UniPathway (UP)purine biosynthesis via salvage pathway0.02208InformativeInherited
UniPathway (UP)xenobiotic degradation1InformativeInherited
UniPathway (UP)hypoxanthine degradation1.615e-10Highly InformativeDirect
UniPathway (UP)vanillyl-alcohol degradation1.294e-05Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR001041 SSF54292 Protein matches
Abstract

The ferredoxin protein family are electron carrier proteins with an iron-sulphur cofactor that act in a wide variety of metabolic reactions. Ferredoxins can be divided into several subgroups depending upon the physiological nature of the iron-sulphur cluster(s) and according to sequence similarities.

This entry represents members of the 2Fe-2S ferredoxin family that have a general core structure consisting of beta(2)-alpha-beta(2), which includes putidaredoxin and terpredoxin, and adrenodoxin [PubMed11173487, PubMed15755454, PubMed10220356, PubMed12069587]. They are proteins of around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This conserved region is also found as a domain in various metabolic enzymes and in multidomain proteins, such as aldehyde oxidoreductase (N-terminal), xanthine oxidase (N-terminal), phthalate dioxygenase reductase (C-terminal), succinate dehydrogenase iron-sulphur protein (N-terminal), and methane monooxygenase reductase (N-terminal).


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · 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 37 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 2Fe-2S ferredoxin-like 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 37 hidden Markov models representing the 2Fe-2S ferredoxin-like 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · 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 ]