SUPERFAMILY 1.75 HMM library and genome assignments server


Cupredoxins superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Cupredoxin-like [ 49502] (2)
Superfamily:   Cupredoxins [ 49503] (7)
Families:   Plastocyanin/azurin-like [ 49504] (9)
  Nitrosocyanin [ 63392] (2)
  Periplasmic domain of cytochrome c oxidase subunit II [ 49541] (2)
  Multidomain cupredoxins [ 49550] (7)
  Ephrin ectodomain [ 74874] (2)
  Peptidylarginine deiminase Pad4, N-terminal domain [ 110107]
  SO1698-like [ 141095]


Superfamily statistics
Genomes (2,407) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 32,568 91,261 222
Proteins 17,936 68,337 151


Functional annotation
General category Processes_IC
Detailed category Ion metabolism and transport

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)cellular macromolecule metabolic process0.063761Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.0029421Least InformativeInherited
Biological Process (BP)biosynthetic process0.46991Least InformativeInherited
Biological Process (BP)single-organism cellular process0.0015961Least InformativeInherited
Biological Process (BP)response to stimulus0.075261Least InformativeInherited
Biological Process (BP)regulation of cellular process0.35971Least InformativeInherited
Biological Process (BP)signal transduction0.0010190.9872Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.062081Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.28451Moderately InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.023590.565Moderately InformativeInherited
Biological Process (BP)enzyme linked receptor protein signaling pathway8.816e-102.268e-10InformativeDirect
Biological Process (BP)polysaccharide metabolic process0.00029520.0001033InformativeDirect
Biological Process (BP)cellular carbohydrate metabolic process0.0003430.02805InformativeInherited
Biological Process (BP)carbohydrate biosynthetic process0.0022980.002865InformativeInherited
Biological Process (BP)transmembrane receptor protein tyrosine kinase signaling pathway6.997e-111.431e-14Highly InformativeDirect
Biological Process (BP)cellular component macromolecule biosynthetic process3.928e-061.094e-05Highly InformativeDirect
Biological Process (BP)cell wall biogenesis6.762e-061.412e-05Highly InformativeDirect
Biological Process (BP)cell wall macromolecule metabolic process1.027e-059.89e-06Highly InformativeDirect
Biological Process (BP)cellular polysaccharide biosynthetic process0.00090150.001597Highly InformativeInherited
Molecular Function (MF)binding0.1861Least InformativeInherited
Molecular Function (MF)oxidoreductase activity0.07050Moderately InformativeInherited
Molecular Function (MF)cation binding0.0033180.0001984Moderately InformativeInherited
Molecular Function (MF)receptor binding3.41e-053.333e-07InformativeDirect
Molecular Function (MF)transition metal ion binding0.00015630.001822InformativeInherited
Molecular Function (MF)copper ion binding1.165e-080Highly InformativeDirect
Cellular Component (CC)membrane2.18e-060Least InformativeDirect
Cellular Component (CC)intrinsic to membrane4.42e-071Moderately InformativeInherited
Cellular Component (CC)anchored to membrane00Highly 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) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.8844 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.0003319 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.3583 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.4778 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.9118 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.6805 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.9163 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.408 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.9872 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 1 Moderately Informative Inherited
Biological Process (BP) regulation of phosphate metabolic process 0.5067 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 1 Moderately Informative Inherited
Biological Process (BP) ion transport 0.05811 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.2208 Moderately Informative Inherited
Biological Process (BP) lipid biosynthetic process 0.5762 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.9861 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.565 Moderately Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 2.268e-10 Informative Direct
Biological Process (BP) polysaccharide metabolic process 0.0001033 Informative Direct
Biological Process (BP) metal ion transport 4.468e-05 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.0006662 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.5844 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.6392 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.2982 Informative Inherited
Biological Process (BP) generation of neurons 0.2348 Informative Inherited
Biological Process (BP) regulation of cell development 0.2789 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.1512 Informative Inherited
Biological Process (BP) cation homeostasis 0.0253 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.02609 Informative Inherited
Biological Process (BP) response to inorganic substance 0.004145 Informative Inherited
Biological Process (BP) cellular carbohydrate metabolic process 0.02805 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 0.002865 Informative Inherited
Biological Process (BP) energy derivation by oxidation of organic compounds 0.04645 Informative Inherited
Biological Process (BP) regulation of nucleotide catabolic process 0.3616 Informative Inherited
Biological Process (BP) regulation of nucleoside metabolic process 0.3851 Informative Inherited
Biological Process (BP) regulation of purine nucleotide metabolic process 0.5935 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.2811 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.2782 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0.005073 Informative Inherited
Biological Process (BP) organic hydroxy compound biosynthetic process 0.003814 Informative Inherited
Biological Process (BP) steroid metabolic process 0.03335 Informative Inherited
Biological Process (BP) alcohol metabolic process 0.3635 Informative Inherited
Biological Process (BP) secondary metabolic process 0.01766 Informative Inherited
Biological Process (BP) regulation of body fluid levels 0.003056 Informative Inherited
Biological Process (BP) response to wounding 0.1729 Informative Inherited
Biological Process (BP) phosphorylation 0.9541 Informative Inherited
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 1.431e-14 Highly Informative Direct
Biological Process (BP) cellular component macromolecule biosynthetic process 1.094e-05 Highly Informative Direct
Biological Process (BP) cell wall biogenesis 1.412e-05 Highly Informative Direct
Biological Process (BP) cell wall macromolecule metabolic process 9.89e-06 Highly Informative Direct
Biological Process (BP) electron transport chain 7.919e-09 Highly Informative Direct
Biological Process (BP) oxidative phosphorylation 8.05e-08 Highly Informative Direct
Biological Process (BP) transition metal ion transport 2.725e-07 Highly Informative Direct
Biological Process (BP) cellular modified amino acid biosynthetic process 1.533e-06 Highly Informative Direct
Biological Process (BP) transition metal ion homeostasis 1.948e-05 Highly Informative Direct
Biological Process (BP) phenylpropanoid metabolic process 5.177e-05 Highly Informative Direct
Biological Process (BP) coagulation 0.0003654 Highly Informative Direct
Biological Process (BP) external encapsulating structure organization 0.0005755 Highly Informative Direct
Biological Process (BP) protein activation cascade 0.0008272 Highly Informative Direct
Biological Process (BP) hemostasis 0.02511 Highly Informative Inherited
Biological Process (BP) cellular polysaccharide biosynthetic process 0.001597 Highly Informative Inherited
Biological Process (BP) regulation of cell morphogenesis involved in differentiation 0.002002 Highly Informative Inherited
Biological Process (BP) regulation of neuron projection development 0.01076 Highly Informative Inherited
Biological Process (BP) regulation of cell adhesion 0.03206 Highly Informative Inherited
Biological Process (BP) regulation of Rho protein signal transduction 0.02336 Highly Informative Inherited
Biological Process (BP) regulation of Ras GTPase activity 0.07328 Highly Informative Inherited
Biological Process (BP) steroid biosynthetic process 0.001224 Highly Informative Inherited
Biological Process (BP) sterol metabolic process 0.001687 Highly Informative Inherited
Biological Process (BP) alcohol biosynthetic process 0.04287 Highly Informative Inherited
Biological Process (BP) wound healing 0.01597 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) cation binding 0.0001984 Moderately Informative Direct
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) transporter activity 0 Moderately Informative Direct
Molecular Function (MF) receptor binding 3.333e-07 Informative Direct
Molecular Function (MF) inorganic cation transmembrane transporter activity 0 Informative Direct
Molecular Function (MF) transition metal ion binding 0.001822 Informative Inherited
Molecular Function (MF) peptidase activity 0.5886 Informative Inherited
Molecular Function (MF) copper ion binding 0 Highly Informative Direct
Molecular Function (MF) hydrogen ion transmembrane transporter activity 0 Highly Informative Direct
Molecular Function (MF) endopeptidase activity 0.05739 Highly Informative Inherited
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) protein complex 0 Least Informative Direct
Cellular Component (CC) plasma membrane part 0.7874 Moderately Informative Inherited
Cellular Component (CC) intrinsic to membrane 1 Moderately Informative Inherited
Cellular Component (CC) respiratory chain 0 Informative Direct
Cellular Component (CC) intrinsic to plasma membrane 0.07838 Informative Inherited
Cellular Component (CC) cell surface 0.5657 Informative Inherited
Cellular Component (CC) cell-cell junction 0.0263 Informative Inherited
Cellular Component (CC) external encapsulating structure 0.003979 Informative Inherited
Cellular Component (CC) anchored to membrane 0 Highly Informative Direct
Cellular Component (CC) respiratory chain complex IV 0 Highly Informative Direct
Cellular Component (CC) symplast 1.638e-05 Highly Informative Direct
Cellular Component (CC) external side of plasma membrane 0.174 Highly Informative Inherited
Cellular Component (CC) cell wall 0.226 Highly Informative Inherited

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 a heme group of donors0Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor0Highly InformativeDirect
Enzyme Commission (EC)With a cytochrome as acceptor0Highly InformativeDirect
Enzyme Commission (EC)In linear amidines3.021e-15Highly InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.01783Least InformativeInherited
Worm Phenotype (WP)cell death variant0.0001827Moderately InformativeDirect
Worm Phenotype (WP)cell corpse number variant3.888e-06InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus DEvelopment stage (XDE)embryonic stage0.06079Least InformativeInherited
Xenopus DEvelopment stage (XDE)late tailbud stage0.0007685InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)flower0.05214Least InformativeInherited
Plant ANatomical entity (PAN)collective phyllome structure0.2844Least InformativeInherited
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.3724Least InformativeInherited
Plant ANatomical entity (PAN)whole plant0.4523Least InformativeInherited
Plant ANatomical entity (PAN)leaf0.9868Least InformativeInherited
Plant ANatomical entity (PAN)microsporophyll1Least InformativeInherited
Plant ANatomical entity (PAN)cotyledon1Moderately InformativeInherited
Plant ANatomical entity (PAN)vascular system2.953e-08InformativeDirect
Plant ANatomical entity (PAN)fruit9.396e-05InformativeDirect
Plant ANatomical entity (PAN)rosette leaf0.0002848InformativeDirect
Plant ANatomical entity (PAN)filament0Highly InformativeDirect
Plant ANatomical entity (PAN)leaf epidermis1.474e-14Highly InformativeDirect
Plant ANatomical entity (PAN)leaf vascular system1.398e-10Highly InformativeDirect
Plant ANatomical entity (PAN)trichome1.899e-10Highly InformativeDirect
Plant ANatomical entity (PAN)embryo sac cell0.005482Highly InformativeInherited
Plant structure DEvelopment stage (PDE)seedling development stage9.49e-06InformativeDirect

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)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0.1149Moderately InformativeInherited
Enzyme Commission (EC)Acting on other nitrogenous compounds as donors5.667e-06InformativeDirect
Enzyme Commission (EC)Acting on diphenols and related substances as donors0Highly InformativeDirect
Enzyme Commission (EC)With a cytochrome as acceptor0Highly InformativeDirect
Enzyme Commission (EC)Acting on a heme group of donors0Highly InformativeDirect
Enzyme Commission (EC)In linear amidines4.808e-16Highly InformativeDirect
Enzyme Commission (EC)Oxidizing metal ions0.02797Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processDifferentiation0.000352Moderately InformativeDirect
Biological processIon transport1Moderately InformativeInherited
Biological processElectron transport0InformativeDirect
Biological processNeurogenesis1.075e-09InformativeDirect
Biological processHemostasis1.679e-09InformativeDirect
Biological processAngiogenesis2.547e-06InformativeDirect
Biological processRespiratory chain0Highly InformativeDirect
Biological processBlood coagulation8.496e-11Highly InformativeDirect
Biological processNitrate assimilation6.744e-08Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentSecreted2.361e-13Moderately InformativeDirect
Cellular componentPlastid0.1128Moderately InformativeInherited
Cellular componentPeriplasm0InformativeDirect
Cellular componentMitochondrion inner membrane0InformativeDirect
Cellular componentGPI-anchor1.268e-15InformativeDirect
Cellular componentThylakoid4.216e-07InformativeDirect
Cellular componentChloroplast6.741e-05InformativeDirect
Coding sequence diversityRNA editing4.765e-06Moderately InformativeDirect
DiseaseTumor suppressor0.0002211Moderately InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionCalcium2.854e-08Moderately InformativeDirect
Molecular functionIron1Moderately InformativeInherited
Molecular functionCopper0InformativeDirect
Molecular functionIron transport7.022e-11Highly InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationSulfation1.389e-07InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)one-carbon metabolism7.137e-07Moderately InformativeDirect
UniPathway (UP)energy metabolism4.174e-05Moderately InformativeDirect
UniPathway (UP)methylamine degradation0Highly InformativeDirect
UniPathway (UP)oxidative phosphorylation8.244e-08Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR008972 SSF49503 Protein matches
Abstract

Copper is one of the most prevalent transition metals in living organisms and its biological function is intimately related to its redox properties. Since free copper is toxic, even at very low concentrations, its homeostasis in living organisms is tightly controlled by subtle molecular mechanisms. In eukaryotes, before being transported inside the cell via the high-affinity copper transporters of the CTR family, the copper (II) ion is reduced to copper (I). In blue copper proteins such as Cupredoxin, the copper (I) ion form is stabilised by a constrained His2Cys coordination environment.

This entry represents cupredoxin proteins, as well as structural homologues to cupredoxin. Structurally, the cupredoxin-like fold consists of a beta-sandwich with 7 strands in 2 beta-sheets, which is arranged in a Greek-key beta-barrel [PubMed11867755]. Some of these proteins have lost the ability to bind copper. Proteins with a cupredoxin-type fold are found in the following family groups:

  • Mono-domain cupredoxins, such as amicyanin, plastocyanin, pseudoazurin, plantacyanin, azurin, auracyanin, rusticyanin, stellacyanin, and mavicyanin.
  • Multi-domain cupredoxins, such as nitrite reductase (2 domains of this fold), multicopper oxidase CueO, spore coat protein A, ascorbate oxidase (3 domains of this fold), laccase (3 domains of this fold), ceruloplamin (6 domains of this fold), and coagulation factor V.
  • Red copper protein nitrocyanin and the C-terminal of nitrous oxide reductase.
  • Quinol oxidase and the periplasmic domain of cytochrome c oxidase subunit II.
  • Ephrin-a5 and ephrin-b2 ectodomain, which are related to cupredoxins but lack the metal-binding site.
  • The N-terminal domain of protein arginine deiminase Pad4, which is related to cupredoxin but lacks the metal-biding site.


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) · Yeast Phenotype (YP) · 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 93 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 Cupredoxins 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 93 hidden Markov models representing the Cupredoxins 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) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]