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 (2,884) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 20,857 95,607 57
Proteins 20,834 95,593 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 process0.0000063221Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.000023751Least InformativeInherited
Molecular Function (MF)binding0.0000016710.0005262Least InformativeDirect
Molecular Function (MF)cation binding0.000000000028820.7869Moderately InformativeInherited
Molecular Function (MF)electron carrier activity00InformativeDirect
Molecular Function (MF)iron ion binding00.000001083Highly InformativeDirect
Molecular Function (MF)metal cluster binding0.00000015210Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.0030880.001174Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.1110.000000001932Least InformativeInherited
Cellular Component (CC)plastid00.0000000001251InformativeDirect

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) organic cyclic compound metabolic process 0.00002426 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.9444 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.2315 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.05077 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 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) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
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) organophosphate metabolic process 0.00001208 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 0.00003295 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0002909 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0.0003667 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.002597 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) small molecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.1682 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.2407 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.0186 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.2667 Moderately Informative Inherited
Biological Process (BP) cofactor metabolic process 0.1932 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.002379 Moderately Informative Inherited
Biological Process (BP) energy derivation by oxidation of organic compounds 0 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.00000000009849 Informative Direct
Biological Process (BP) isoprenoid metabolic process 0.000006835 Informative Direct
Biological Process (BP) mitochondrion organization 0.00001054 Informative Direct
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.00002129 Informative Direct
Biological Process (BP) apoptotic process 0.0001225 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 0.0003642 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 0.0006216 Informative Direct
Biological Process (BP) cellular aldehyde metabolic process 0.0007164 Informative Direct
Biological Process (BP) regulation of hormone levels 0.0007473 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 0.2236 Informative Inherited
Biological Process (BP) phosphorylation 0.6657 Informative Inherited
Biological Process (BP) alcohol metabolic process 0.07571 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 0.0105 Informative Inherited
Biological Process (BP) nucleoside triphosphate metabolic process 0.02498 Informative Inherited
Biological Process (BP) pyridine-containing compound metabolic process 0.001569 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.06236 Informative Inherited
Biological Process (BP) electron transport chain 0 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0.000000000001631 Highly Informative Direct
Biological Process (BP) oxidative phosphorylation 0.000000001174 Highly Informative Direct
Biological Process (BP) hormone biosynthetic process 0.000000009956 Highly Informative Direct
Biological Process (BP) isoprenoid biosynthetic process 0.00000001435 Highly Informative Direct
Biological Process (BP) regulation of membrane potential 0.000007442 Highly Informative Direct
Biological Process (BP) regulation of epithelial cell differentiation 0.00003289 Highly Informative Direct
Biological Process (BP) nicotinamide nucleotide metabolic process 0.00005722 Highly Informative Direct
Biological Process (BP) sterol metabolic process 0.03494 Highly Informative Inherited
Biological Process (BP) aerobic respiration 1 Highly Informative Inherited
Molecular Function (MF) binding 0.0005262 Least Informative Direct
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.0000001294 Moderately Informative Direct
Molecular Function (MF) anion binding 0.9192 Moderately Informative Inherited
Molecular Function (MF) cation binding 0.7869 Moderately Informative Inherited
Molecular Function (MF) electron carrier activity 0 Informative Direct
Molecular Function (MF) cofactor binding 0 Informative Direct
Molecular Function (MF) nucleotide binding 0.000000000002375 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on NAD(P)H 0.0003029 Informative Direct
Molecular Function (MF) iron ion binding 0.000001083 Highly Informative Direct
Molecular Function (MF) metal cluster binding 0 Highly Informative Direct
Molecular Function (MF) NADH dehydrogenase activity 0.00000002164 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the aldehyde or oxo group of donors 0.0000004754 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor 0.000009705 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0.004826 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.000000001932 Least Informative Direct
Cellular Component (CC) protein complex 0.000001889 Least Informative Direct
Cellular Component (CC) membrane 0.00902 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.001174 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.3701 Least Informative Inherited
Cellular Component (CC) organelle envelope 0 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0 Moderately Informative Direct
Cellular Component (CC) plastid 0.0000000001251 Informative Direct
Cellular Component (CC) respiratory chain 0 Informative Direct
Cellular Component (CC) oxidoreductase complex 0 Informative Direct
Cellular Component (CC) mitochondrial membrane part 0 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 acceptors0.000000000005336InformativeDirect
Enzyme Commission (EC)Acting on CH or CH(2) groups0.000003125InformativeDirect
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 acceptor0.0000000001187Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.0000000002174Highly InformativeDirect
Enzyme Commission (EC)Succinate dehydrogenase0.0000000277Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)syndrome0Moderately InformativeDirect

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

Document: HP 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 stage0.00005833InformativeDirect
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 NADPH0.0000000000003051InformativeDirect
Enzyme Commission (EC)Acting on CH or CH(2) groups0.00006039InformativeDirect
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors0.0001324InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen1InformativeInherited
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 acceptor0.0000000000207Highly InformativeDirect
Enzyme Commission (EC)NADH dehydrogenase0.00000001013Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.00004948Highly InformativeDirect
Enzyme Commission (EC)With other acceptors0.0006478Highly InformativeDirect
Enzyme Commission (EC)With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into one donor0.0007076Highly InformativeDirect
Enzyme Commission (EC)Acting on hydrogen as donor0.0007432Highly InformativeDirect
Enzyme Commission (EC)Acting on iron-sulfur proteins as donors0.001549Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processLipid metabolism0.9991Moderately InformativeInherited
Biological processIon transport1Moderately InformativeInherited
Biological processAromatic hydrocarbons catabolism0InformativeDirect
Biological processElectron transport0InformativeDirect
Biological processTricarboxylic acid cycle0InformativeDirect
Biological processSteroid metabolism0.00000002262InformativeDirect
Biological processNitrogen fixation0.00001374InformativeDirect
Biological processAuxin biosynthesis0Highly InformativeDirect
Biological processSodium transport0Highly InformativeDirect
Biological processAbscisic acid biosynthesis0Highly InformativeDirect
Biological processCholesterol metabolism0.000000003556Highly InformativeDirect
Biological processPurine metabolism0.0000008023Highly InformativeDirect
Cellular componentMembrane0.0000009938Least InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentCell membrane0.239Moderately InformativeInherited
Cellular componentCell inner membrane0InformativeDirect
Cellular componentPeroxisome0.00000000002333InformativeDirect
Cellular componentMitochondrion inner membrane0.00000008085InformativeDirect
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 functionFAD0.0000001908InformativeDirect
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 metabolism0.1472Least InformativeInherited
UniPathway (UP)aromatic compound degradation0.00000000000005798Moderately InformativeDirect
UniPathway (UP)purine metabolism0.8584Moderately InformativeInherited
UniPathway (UP)tricarboxylic acid cycle0InformativeDirect
UniPathway (UP)purine degradation0.0000004757InformativeDirect
UniPathway (UP)purine base metabolism0.001005InformativeInherited
UniPathway (UP)purine biosynthesis via salvage pathway0.02448InformativeInherited
UniPathway (UP)xenobiotic degradation1InformativeInherited
UniPathway (UP)hypoxanthine degradation0.0000000001818Highly InformativeDirect
UniPathway (UP)vanillyl-alcohol degradation0.00001296Highly 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) · 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 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) · 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 ]