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 (1,843) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 9,365 24,467 26
Proteins 9,340 24,408 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)
Molecular Function (MF)oxidoreductase activity0.00050270Moderately 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 5.292e-07 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0009004 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.6865 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.04589 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) organic substance catabolic process 0.0002344 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0.0008817 Moderately Informative Direct
Biological Process (BP) regulation of molecular function 0.1108 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.081 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.01399 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.3146 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.1153 Moderately Informative Inherited
Biological Process (BP) apoptotic process 0.0008934 Informative Direct
Biological Process (BP) positive regulation of catalytic activity 0.007675 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 0.002445 Informative Inherited
Biological Process (BP) energy derivation by oxidation of organic compounds 0.07379 Informative Inherited
Biological Process (BP) regulation of apoptotic process 0.7366 Informative Inherited
Biological Process (BP) positive regulation of peptidase activity 4.014e-07 Highly Informative Direct
Biological Process (BP) xenobiotic metabolic process 7.468e-07 Highly Informative Direct
Biological Process (BP) regulation of cysteine-type endopeptidase activity involved in apoptotic process 1.153e-06 Highly Informative Direct
Biological Process (BP) regulation of membrane potential 2.267e-05 Highly Informative Direct
Biological Process (BP) benzene-containing compound metabolic process 4.817e-05 Highly Informative Direct
Biological Process (BP) positive regulation of apoptotic process 0.0001852 Highly Informative Direct
Molecular Function (MF) binding 0.3564 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) enzyme regulator activity 0.004423 Moderately Informative Inherited
Molecular Function (MF) transporter activity 0.003724 Moderately Informative Inherited
Molecular Function (MF) peptidase regulator activity 1.153e-06 Informative Direct
Molecular Function (MF) inorganic cation transmembrane transporter activity 3.592e-06 Informative Direct
Molecular Function (MF) enzyme activator activity 2.962e-05 Informative Direct
Molecular Function (MF) metal cluster binding 0 Highly Informative Direct
Molecular Function (MF) hydrogen ion transmembrane transporter activity 5.019e-12 Highly Informative Direct
Molecular Function (MF) cysteine-type endopeptidase regulator activity involved in apoptotic process 1.684e-10 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxyge 0.0006303 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.0001386 Least Informative Direct
Cellular Component (CC) membrane 0.0007337 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.001031 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.06678 Least Informative Inherited
Cellular Component (CC) protein complex 0.02528 Least Informative Inherited
Cellular Component (CC) organelle envelope 0 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 3.107e-12 Moderately Informative Direct
Cellular Component (CC) organelle membrane 1.262e-10 Moderately Informative Direct
Cellular Component (CC) respiratory chain 2.077e-13 Informative Direct
Cellular Component (CC) mitochondrial membrane part 6.168e-08 Informative Direct
Cellular Component (CC) plastid 0.0004148 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)plant cell0.1891Least InformativeInherited
Plant ANatomical entity (PAN)guard cell0.0005551Moderately 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 donors0.262InformativeInherited
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 oxygen1.975e-07Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor7.153e-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 assimilation5.124e-09Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentMitochondrion5.743e-12Moderately InformativeDirect
Cellular componentPlastid1.346e-11Moderately InformativeDirect
Cellular componentThylakoid0InformativeDirect
Cellular componentMitochondrion inner membrane4.032e-08InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionNAD2.757e-10Moderately InformativeDirect
Molecular function2Fe-2S0InformativeDirect
Molecular functionIron-sulfur0InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationDioxygenase1.82e-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 metabolism7.218e-12Least InformativeDirect
UniPathway (UP)carbohydrate metabolism0.1946Least InformativeInherited
UniPathway (UP)aromatic compound degradation0Moderately InformativeDirect
UniPathway (UP)amine and polyamine metabolism3.394e-14Moderately InformativeDirect
UniPathway (UP)nitrogen metabolism0.01Moderately InformativeInherited
UniPathway (UP)amino-sugar metabolism7.984e-13InformativeDirect
UniPathway (UP)nitrate reduction1.778e-05InformativeDirect
UniPathway (UP)phenylpropanoid degradation0.004956InformativeInherited
UniPathway (UP)xenobiotic degradation1InformativeInherited
UniPathway (UP)amine and polyamine biosynthesis1InformativeInherited
UniPathway (UP)betaine biosynthesis1.16e-08Highly InformativeDirect
UniPathway (UP)nitrate reduction (assimilation)2.02e-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 ]