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 (2,248) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 11,538 24,467 26
Proteins 11,507 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)
Biological Process (BP)response to stimulus0.19981Least InformativeInherited
Biological Process (BP)single-organism cellular process0.33961Least InformativeInherited
Biological Process (BP)cellular catabolic process0.0083990.007566Moderately InformativeInherited
Biological Process (BP)cellular response to chemical stimulus0.0031450.05686Moderately InformativeInherited
Biological Process (BP)xenobiotic metabolic process1.665e-073.483e-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 3.221e-05 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.1593 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.007957 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular catabolic process 0.007566 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.05686 Moderately Informative Inherited
Biological Process (BP) cell death 0.003212 Informative Inherited
Biological Process (BP) energy derivation by oxidation of organic compounds 0.1073 Informative Inherited
Biological Process (BP) xenobiotic metabolic process 3.483e-08 Highly Informative Direct
Biological Process (BP) electron transport chain 0.0004292 Highly Informative Direct
Biological Process (BP) benzene-containing compound metabolic process 2.066e-07 Highly Informative Direct
Biological Process (BP) execution phase of apoptosis 2.768e-08 Highly Informative Direct
Molecular Function (MF) binding 0.9942 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 1.049e-13 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.01942 Moderately Informative Inherited
Molecular Function (MF) inorganic cation transmembrane transporter activity 5.299e-05 Informative Direct
Molecular Function (MF) hydrogen ion transmembrane transporter activity 4.716e-09 Highly Informative Direct
Molecular Function (MF) metal cluster binding 0 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.00729 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.8379 Least Informative Inherited
Cellular Component (CC) protein complex 0.424 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.2068 Least Informative Inherited
Cellular Component (CC) membrane 0.0452 Least Informative Inherited
Cellular Component (CC) organelle membrane 1.932e-08 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 3.878e-11 Moderately Informative Direct
Cellular Component (CC) plastid 0.0009411 Informative Direct
Cellular Component (CC) mitochondrial membrane part 2.906e-07 Informative Direct
Cellular Component (CC) respiratory chain 4.021e-08 Informative Direct
Cellular Component (CC) mitochondrial respiratory chain 0.0005523 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 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 donors0.2529InformativeInherited
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 oxygen2.357e-07Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor7.431e-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 assimilation5.658e-09Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentMitochondrion5.714e-12Moderately InformativeDirect
Cellular componentPlastid1.065e-11Moderately InformativeDirect
Cellular componentThylakoid0InformativeDirect
Cellular componentMitochondrion inner membrane2.757e-08InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionNAD8.193e-12Moderately InformativeDirect
Molecular function2Fe-2S0InformativeDirect
Molecular functionIron-sulfur0InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationDioxygenase4.633e-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 metabolism3.355e-10Least InformativeDirect
UniPathway (UP)carbohydrate metabolism0.0325Least InformativeInherited
UniPathway (UP)amine and polyamine metabolism0Moderately InformativeDirect
UniPathway (UP)aromatic compound degradation2.656e-13InformativeDirect
UniPathway (UP)xenobiotic metabolism6.162e-12InformativeDirect
UniPathway (UP)betaine biosynthesis1.539e-07InformativeDirect
UniPathway (UP)choline metabolism0.4443InformativeInherited
UniPathway (UP)anthranilate degradation1.099e-07Highly InformativeDirect
UniPathway (UP)betaine biosynthesis via choline pathway1.376e-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 ]