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HydA/Nqo6-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Multi-domain proteins (alpha and beta) [ 56572] (66)
Fold:   HydA/Nqo6-like [ 56769]
Superfamily:   HydA/Nqo6-like [ 56770] (2)
Families:   Nickel-iron hydrogenase, small subunit [ 56771]
  Nq06-like [ 144031]

 Superfamily statistics
Genomes (1,746) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 3,719 12,616 8
Proteins 3,715 12,610 8

 Functional annotation
General category Metabolism
Detailed category Other enzymes

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 component organization or biogenesis0.00025530.008784Least InformativeInherited
Biological Process (BP)single-organism cellular process0.047850.4485Least InformativeInherited
Biological Process (BP)organelle organization8.113e-050.0005007Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization1.549e-082.258e-07Moderately InformativeDirect
Biological Process (BP)cellular component biogenesis2.139e-073.636e-06Moderately InformativeDirect
Biological Process (BP)mitochondrion organization7.909e-111.351e-10InformativeDirect
Biological Process (BP)cellular macromolecular complex assembly3.765e-125.381e-11InformativeDirect
Molecular Function (MF)oxidoreductase activity3.857e-132.605e-14Moderately InformativeDirect
Molecular Function (MF)NADH dehydrogenase activity00Highly InformativeDirect
Cellular Component (CC)membrane0.00012910.0001944Least InformativeDirect
Cellular Component (CC)protein complex1.351e-091.974e-07Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.088530.1887Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.0026690.03762Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.55720.1569Least InformativeInherited
Cellular Component (CC)organelle membrane0.00014614.579e-05Moderately InformativeDirect
Cellular Component (CC)organelle envelope8.652e-064.074e-07Moderately InformativeDirect
Cellular Component (CC)mitochondrial part3.066e-061.725e-07Moderately InformativeDirect
Cellular Component (CC)mitochondrial membrane part3.375e-082.117e-10InformativeDirect
Cellular Component (CC)respiratory chain00InformativeDirect
Cellular Component (CC)mitochondrial respiratory chain complex I6.96e-063.225e-06Highly 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) cellular component organization or biogenesis 0.008784 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.4485 Least Informative Inherited
Biological Process (BP) organelle organization 0.0005007 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 2.258e-07 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 3.636e-06 Moderately Informative Direct
Biological Process (BP) mitochondrion organization 1.351e-10 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 5.381e-11 Informative Direct
Molecular Function (MF) oxidoreductase activity 2.605e-14 Moderately Informative Direct
Molecular Function (MF) NADH dehydrogenase activity 0 Highly Informative Direct
Cellular Component (CC) membrane 0.0001944 Least Informative Direct
Cellular Component (CC) protein complex 1.974e-07 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.1887 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.03762 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1569 Least Informative Inherited
Cellular Component (CC) organelle membrane 4.579e-05 Moderately Informative Direct
Cellular Component (CC) organelle envelope 4.074e-07 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 1.725e-07 Moderately Informative Direct
Cellular Component (CC) mitochondrial membrane part 2.117e-10 Informative Direct
Cellular Component (CC) respiratory chain 0 Informative Direct
Cellular Component (CC) mitochondrial respiratory chain complex I 3.225e-06 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 NADH or NADPH0Moderately InformativeDirect
Enzyme Commission (EC)NADH:ubiquinone reductase (H(+)-translocating)0InformativeDirect
Enzyme Commission (EC)With other acceptors0InformativeDirect
Enzyme Commission (EC)Acting on hydrogen as donor0Highly InformativeDirect
Enzyme Commission (EC)NADH dehydrogenase (quinone)2.565e-08Highly InformativeDirect

Document: EC 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 NADH or NADPH0InformativeDirect
Enzyme Commission (EC)Acting on hydrogen as donor0Highly InformativeDirect
Enzyme Commission (EC)NADH:ubiquinone reductase (H(+)-translocating)0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processElectron transport1InformativeInherited
Biological processRespiratory chain0.0001889Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentThylakoid0InformativeDirect
Cellular componentCell inner membrane0InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular functionIron-sulfur0InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionNADP0InformativeDirect
Molecular function3Fe-4S0Highly InformativeDirect
Molecular functionUbiquinone0Highly InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationQuinone0Highly InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

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 6 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 HydA/Nqo6-like 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 6 hidden Markov models representing the HydA/Nqo6-like 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 · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.