SUPERFAMILY 1.75 HMM library and genome assignments server


ISP domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   ISP domain [ 50021]
Superfamily:   ISP domain [ 50022] (3)
Families:   Rieske iron-sulfur protein (ISP) [ 50023] (8)
  Ring hydroxylating alpha subunit ISP domain [ 50033] (6)
  NirD-like [ 158991]


Superfamily statistics
Genomes (2,286) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 11,677 0 26
Proteins 11,615 0 26


Functional annotation
General category Metabolism
Detailed category E- transfer

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)response to stimulus0.18721Least InformativeInherited
Biological Process (BP)single-organism cellular process0.32311Least InformativeInherited
Biological Process (BP)cellular catabolic process0.0074150.007226Moderately InformativeInherited
Biological Process (BP)cellular response to chemical stimulus0.0028430.05307Moderately InformativeInherited
Biological Process (BP)xenobiotic metabolic process1.411e-072.987e-08Highly 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 2.956e-06 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.1559 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.006923 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) oxidation-reduction process 0.0002928 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0008221 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.007226 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.05307 Moderately Informative Inherited
Biological Process (BP) programmed cell death 0.8958 Informative Inherited
Biological Process (BP) energy derivation by oxidation of organic compounds 0.2273 Informative Inherited
Biological Process (BP) xenobiotic metabolic process 2.987e-08 Highly Informative Direct
Biological Process (BP) benzene-containing compound metabolic process 1.899e-07 Highly Informative Direct
Biological Process (BP) execution phase of apoptosis 2.288e-08 Highly Informative Direct
Molecular Function (MF) binding 0.9895 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 7.982e-16 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.006464 Moderately Informative Inherited
Molecular Function (MF) inorganic cation transmembrane transporter activity 7.017e-06 Informative Direct
Molecular Function (MF) hydrogen ion transmembrane transporter activity 1.559e-10 Highly Informative Direct
Molecular Function (MF) metal cluster binding 0 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.01516 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.9297 Least Informative Inherited
Cellular Component (CC) protein complex 0.4217 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.2163 Least Informative Inherited
Cellular Component (CC) membrane 0.04082 Least Informative Inherited
Cellular Component (CC) organelle membrane 2.381e-08 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 2.862e-11 Moderately Informative Direct
Cellular Component (CC) plastid 0.0006686 Informative Direct
Cellular Component (CC) mitochondrial membrane part 2.733e-07 Informative Direct
Cellular Component (CC) respiratory chain 3.591e-08 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 paired donors, with incorporation or red0Moderately InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor5.571e-07InformativeDirect
Enzyme Commission (EC)Nitrite reductase (NAD(P)H)0Highly InformativeDirect
Enzyme Commission (EC)With a cytochrome as acceptor0Highly InformativeDirect
Enzyme Commission (EC)With a reduced iron-sulfur protein as one donor, a0.002936Highly InformativeInherited

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP 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 paired donors, with incorporation or reduction of molecular oxygen0InformativeDirect
Enzyme Commission (EC)Acting on other nitrogenous compounds as donors0.2536InformativeInherited
Enzyme Commission (EC)Acting on diphenols and related substances as donors0Highly InformativeDirect
Enzyme Commission (EC)With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into one donor0Highly InformativeDirect
Enzyme Commission (EC)With another compound as one donor, and incorporation of one atom of oxygen2.299e-07Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor6.885e-07Highly InformativeDirect
Enzyme Commission (EC)With NADH or NADPH as one donor, and incorporation of one atom of oxygen1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processAromatic hydrocarbons catabolism0InformativeDirect
Biological processElectron transport0InformativeDirect
Biological processNitrate assimilation1.683e-10Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentMitochondrion5.576e-12Moderately InformativeDirect
Cellular componentPlastid1.063e-11Moderately InformativeDirect
Cellular componentThylakoid0InformativeDirect
Cellular componentMitochondrion inner membrane2.643e-08InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionNAD6.097e-12Moderately InformativeDirect
Molecular function2Fe-2S0InformativeDirect
Molecular functionIron-sulfur0InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationDioxygenase4.414e-12Highly InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)aromatic compound metabolism2.4e-11Least InformativeDirect
UniPathway (UP)carbohydrate metabolism0.2166Least InformativeInherited
UniPathway (UP)lipid metabolism1Least InformativeInherited
UniPathway (UP)aromatic compound degradation0Moderately InformativeDirect
UniPathway (UP)amine and polyamine metabolism4.461e-14Moderately InformativeDirect
UniPathway (UP)nitrogen metabolism0.01155Moderately InformativeInherited
UniPathway (UP)lipid biosynthesis0.9285Moderately InformativeInherited
UniPathway (UP)amino-sugar metabolism7.469e-13InformativeDirect
UniPathway (UP)nitrate reduction2.013e-05InformativeDirect
UniPathway (UP)terpene metabolism0.0001413InformativeDirect
UniPathway (UP)phenylpropanoid degradation0.003142InformativeInherited
UniPathway (UP)choline metabolism0.01134InformativeInherited
UniPathway (UP)xenobiotic degradation1InformativeInherited
UniPathway (UP)amine and polyamine biosynthesis1InformativeInherited
UniPathway (UP)betaine biosynthesis1.365e-08Highly InformativeDirect
UniPathway (UP)nitrate reduction (assimilation)2.252e-07Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR005806 SSF50022 Protein matches
Abstract

Ubiquinol-cytochrome c reductase (bc1 complex or complex III) is an enzyme complex of bacterial and mitochondrial oxidative phosphorylation systems It catalyses the oxidoreduction of the mobile redox components ubiquinol and cytochrome c, generating an electrochemical potential, which is linked to ATP synthesis [PubMed2986972, PubMed3004982]. The complex consists of three subunits in most bacteria, and nine in mitochondria: both bacterial and mitochondrial complexes contain cytochrome b and cytochrome c1 subunits, and an iron-sulphur `Rieske' subunit, which contains a high potential 2Fe-2S cluster [PubMed2820981].The mitochondrial form also includes six other subunits that do not possess redox centres. Plastoquinone-plastocyanin reductase (b6f complex), present in cyanobacteria and the chloroplasts of plants, catalyses the oxidoreduction of plastoquinol and cytochrome f. This complex, which is functionally similar to ubiquinol-cytochrome c reductase, comprises cytochrome b6, cytochrome f and Rieske subunits [PubMed1391772].

The Rieske subunit acts by binding either a ubiquinol or plastoquinol anion, transferring an electron to the 2Fe-2S cluster, then releasing the electron to the cytochrome c or cytochrome f haem iron [PubMed2986972, PubMed1391772]. The rieske domain has a [2Fe-2S] centre. Two conserved cysteines that one Fe ion while the other Fe ion is coordinated by two conserved histidines. The 2Fe-2S cluster is bound in the highly conserved C-terminal region of the Rieske subunit.


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) · 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 20 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 ISP domain 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 20 hidden Markov models representing the ISP domain 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) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]