SUPERFAMILY 1.75 HMM library and genome assignments server


alpha-helical ferredoxin superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Globin-like [ 46457] (2)
Superfamily:   alpha-helical ferredoxin [ 46548] (2)
Families:   Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain [ 46549] (2)
  Dihydropyrimidine dehydrogenase, N-terminal domain [ 46553]


Superfamily statistics
Genomes (2,990) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 14,863 79,810 6
Proteins 14,516 77,076 6


Functional annotation
General category Metabolism
Detailed category Redox

Document:
Function annotation of SCOP domain superfamilies

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 0.3138 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.2775 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.000142 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0.0004961 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.002048 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.1432 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.2965 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.8117 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.04286 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.01434 Moderately Informative Inherited
Biological Process (BP) pyrimidine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 3.847e-07 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.006079 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.002439 Informative Inherited
Biological Process (BP) phosphorylation 0.004687 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.0153 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.001833 Informative Inherited
Biological Process (BP) nucleobase metabolic process 0 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound catabolic process 0 Highly Informative Direct
Biological Process (BP) oxidative phosphorylation 4.369e-06 Highly Informative Direct
Biological Process (BP) electron transport chain 0.000218 Highly Informative Direct
Biological Process (BP) glutamate metabolic process 0.004831 Highly Informative Inherited
Biological Process (BP) aerobic respiration 0.6411 Highly Informative Inherited
Molecular Function (MF) binding 0.7764 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) cofactor binding 0 Informative Direct
Molecular Function (MF) electron carrier activity 3.22e-12 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 6.076e-14 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.0005647 Least Informative Direct
Cellular Component (CC) protein complex 8.534e-06 Least Informative Direct
Cellular Component (CC) membrane 1.319e-05 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.02787 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.2997 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 6.424e-12 Moderately Informative Direct
Cellular Component (CC) respiratory chain 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 a sulfur group of donors0.01252Moderately InformativeInherited
Enzyme Commission (EC)Acting on NADH or NADPH0.3724Moderately InformativeInherited
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors0.08933Moderately InformativeInherited
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect
Enzyme Commission (EC)With other acceptors3.239e-09InformativeDirect
Enzyme Commission (EC)With other acceptors4.674e-07InformativeDirect
Enzyme Commission (EC)Dihydropyrimidine dehydrogenase (NADP(+))0Highly InformativeDirect
Enzyme Commission (EC)With other, known, acceptors0Highly InformativeDirect
Enzyme Commission (EC)Succinate dehydrogenase0Highly InformativeDirect
Enzyme Commission (EC)Succinate dehydrogenase (ubiquinone)0Highly InformativeDirect
Enzyme Commission (EC)With other acceptors0Highly InformativeDirect
Enzyme Commission (EC)NADH dehydrogenase (quinone)1.776e-07Highly InformativeDirect
Enzyme Commission (EC)Glutamate synthase (NADH)1.803e-07Highly InformativeDirect
Enzyme Commission (EC)Glutamate synthase (NADPH)5.37e-06Highly InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect
Fly Phenotype (FP)fertile0Moderately InformativeDirect

Document: FP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)0 seed germination stage7e-08InformativeDirect

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 a sulfur group of donors0.004152InformativeInherited
Enzyme Commission (EC)Acting on the CH-NH(2) group of donors0.009584InformativeInherited
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors0.1237InformativeInherited
Enzyme Commission (EC)Acting on NADH or NADPH0.4538InformativeInherited
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor1InformativeInherited
Enzyme Commission (EC)With other acceptors0Highly InformativeDirect
Enzyme Commission (EC)With a quinone or related compound as acceptor0Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0Highly InformativeDirect
Enzyme Commission (EC)With other, known, acceptors0Highly InformativeDirect
Enzyme Commission (EC)Formate dehydrogenase7.801e-09Highly 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 processTricarboxylic acid cycle0InformativeDirect
Biological processMethanogenesis0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentMitochondrion2.945e-10Moderately InformativeDirect
Cellular componentCell membrane4.805e-06Moderately InformativeDirect
Cellular componentCell inner membrane0InformativeDirect
Cellular componentMitochondrion inner membrane0InformativeDirect
DomainRepeat0Least InformativeDirect
DomainTransit peptide4.383e-05Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionFlavoprotein0.0002426Moderately InformativeDirect
Molecular function2Fe-2S0InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionIron-sulfur0InformativeDirect
Molecular functionNickel2.453e-13InformativeDirect
Molecular functionFAD2.855e-09InformativeDirect
Molecular functionFMN9.683e-07InformativeDirect
Molecular function3Fe-4S0Highly InformativeDirect
Molecular functionUbiquinone6.299e-06Highly InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationQuinone4.773e-06Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)carbohydrate metabolism1.712e-11Least InformativeDirect
UniPathway (UP)biopolymer metabolism0.03653Least InformativeInherited
UniPathway (UP)amino-acid metabolism0.7891Least InformativeInherited
UniPathway (UP)cofactor metabolism1Least InformativeInherited
UniPathway (UP)one-carbon metabolism4.527e-16Moderately InformativeDirect
UniPathway (UP)organic acid metabolism1.626e-11Moderately InformativeDirect
UniPathway (UP)nitrogen metabolism7.706e-08Moderately InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis1Moderately InformativeInherited
UniPathway (UP)L-glutamate metabolism0InformativeDirect
UniPathway (UP)tricarboxylic acid cycle0InformativeDirect
UniPathway (UP)methanogenesis0InformativeDirect
UniPathway (UP)organic acid biosynthesis0InformativeDirect
UniPathway (UP)tRNA modification8.435e-10InformativeDirect
UniPathway (UP)nonprotein amino-acid biosynthesis1.286e-06InformativeDirect
UniPathway (UP)beta-alanine biosynthesis0Highly InformativeDirect
UniPathway (UP)L-glutamate biosynthesis0Highly InformativeDirect
UniPathway (UP)coenzyme M-coenzyme B heterodisulfide reduction0Highly InformativeDirect
UniPathway (UP)tRNA-queuosine biosynthesis8.993e-16Highly InformativeDirect
UniPathway (UP)methanogenesis from acetate0.0009113Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR009051 SSF46548 Protein matches
Abstract

The alpha-helical ferredoxin domain contains two Fe4-S4 clusters, typical of bacterial ferredoxin. Iron-sulphur proteins play an important role in electron transfer processes and in various enzymatic reactions. In eukaryotes, the mitochondria are the major site of Fe-S cluster biosynthesis in the cell, used for the assembly of mitochondrial and non-mitochondrial Fe-S proteins. The alpha-helical ferredoxin domain is present in several proteins involved in redox reactions, including the C-terminal of the respiratory proteins succinate dehydrogenase (SQR) in bacteria/mitochondria, and fumarate reductase (QFR) in bacteria. SQR is analogous to the mitochondrial respiratory complex II, and is involved in the electron transport pathway from succinate as a donor to the acceptor ubiquinone. SQR helps prevent the formation of reactive oxygen species and is used during aerobic respiration, whereas QFR does not and, consequently, is used to catalyse the final step of anaerobic respiration using the acceptor fumarate [PubMed11850430].

The alpha-helical ferredoxin domain is also present in the N-terminal of the cytosolic protein dihydropyrimidine dehydrogenase, (DPD) which catalyses the NADPH-dependent, rate-limiting step in pyrimidine degradation, converting pyrimidines to 5,6-dihydro compounds [PubMed11796730]. DPD catalysis involves electron transfer from NADPH to the substrate via the Fe4-S4 centre and FAD. In mammals, this pathway produces the neurotransmitter beta-alanine.


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-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Fly Phenotype (FP) · 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 4 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 alpha-helical ferredoxin 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 4 hidden Markov models representing the alpha-helical ferredoxin 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-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Fly Phenotype (FP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]