SUPERFAMILY 1.75 HMM library and genome assignments server


Nitrite/Sulfite reductase N-terminal domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ferredoxin-like [ 54861] (59)
Superfamily:   Nitrite/Sulfite reductase N-terminal domain-like [ 55124] (2)
Families:   Duplicated SiR/NiR-like domains 1 and 3 [ 55125] (3)
  DsrA/DsrB N-terminal-domain-like [ 160336] (2)


Superfamily statistics
Genomes (1,950) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 6,631 39,623 10
Proteins 4,258 29,468 7


Functional annotation
General category Metabolism
Detailed category Redox

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) nitrogen compound metabolic process 0.0004988 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.1722 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.6443 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.4592 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.002229 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.1486 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.3476 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.5048 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.531 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.9708 Least Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.0000000000001505 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.0000882 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0.0001013 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0288 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.001415 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 0.02898 Moderately Informative Inherited
Biological Process (BP) oxidation-reduction process 0.001032 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.03408 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.01036 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.03352 Moderately Informative Inherited
Biological Process (BP) sulfur compound biosynthetic process 0.0000557 Informative Direct
Biological Process (BP) DNA metabolic process 0.0001001 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.0001651 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.0002405 Informative Direct
Biological Process (BP) sulfur amino acid metabolic process 0.00207 Informative Inherited
Biological Process (BP) regulation of DNA metabolic process 0.00000006739 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-dependent 0.00008868 Highly Informative Direct
Molecular Function (MF) binding 0.2888 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 7.982e-16 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.5582 Moderately Informative Inherited
Molecular Function (MF) DNA binding 0.0004559 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on a sulfur group of donors 0.000000004044 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.1564 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.6281 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.03082 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1226 Least Informative Inherited
Cellular Component (CC) plastid 0.00000008683 Informative Direct
Cellular Component (CC) chloroplast stroma 0.00000000002239 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 a sulfur group of donors0Moderately InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor1InformativeInherited
Enzyme Commission (EC)Sulfite reductase (NADPH)0Highly InformativeDirect
Enzyme Commission (EC)Nitrite reductase (NAD(P)H)0.000000000000002328Highly InformativeDirect
Enzyme Commission (EC)With other acceptors0.000383Highly InformativeDirect
Enzyme Commission (EC)With an iron-sulfur protein as acceptor0.0004265Highly 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 a sulfur group of donors0InformativeDirect
Enzyme Commission (EC)Acting on other nitrogenous compounds as donors0.002883InformativeInherited
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0Moderately InformativeDirect
Biological processCysteine biosynthesis0Highly InformativeDirect
Biological processNitrate assimilation0Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionHeme0InformativeDirect
Molecular functionIron-sulfur0InformativeDirect
Molecular functionNADP0InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationThioether bond0Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)energy metabolism0Moderately InformativeDirect
UniPathway (UP)nitrogen metabolism0.0000148Moderately InformativeDirect
UniPathway (UP)hydrogen sulfide biosynthesis0InformativeDirect
UniPathway (UP)nitrate reduction0.0000000000003876InformativeDirect
UniPathway (UP)nitrate reduction (assimilation)0Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR005117 SSF55124 Protein matches
Abstract

Sulphite reductases (SiRs) and related nitrite reductases (NiRs) catalyse the six-electron reduction reactions of sulphite to sulphide, and nitrite to ammonia, respectively. The Escherichia coli SiR enzyme is a complex composed of two proteins, a flavoprotein alpha-component (SiR-FP) and a hemoprotein beta-component (SiR-HP), and has an alpha(8)beta(4) quaternary structure [PubMed10984484]. SiR-FP contains both FAD and FMN, while SiR-HP contains a Fe(4)S(4) cluster coupled to a sirohaem through a cysteine bridge. Electrons are transferred from NADPH to FAD, and on to FMN in SiR-FP, from which they are transferred to the metal centre of SiR-HP, where they reduce the siroheme-bound sulphite.

SiR-HP has a two-fold symmetry, which generates a distinctive three-domain alpha/beta fold that controls assembly and reactivity [PubMed7569952]. This entry describes the ferrodoxin-like (alpha/beta sandwich) domain, which consists of a duplication containing two subdomains of this fold.


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-coverage) · Enzyme Commission (EC) · 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 10 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 Nitrite/Sulfite reductase N-terminal domain-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 10 hidden Markov models representing the Nitrite/Sulfite reductase N-terminal domain-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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]