SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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 (1,956) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 6,664 46,383 10
Proteins 4,277 32,962 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) single-organism metabolic process 0.0000991 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.3307 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.1163 Least Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.0000000000002723 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.09732 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.01109 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.0353 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.06292 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.1072 Moderately Informative Inherited
Biological Process (BP) oxidation-reduction process 0.001013 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.06202 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.07741 Moderately Informative Inherited
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.0007978 Informative Direct
Biological Process (BP) chromosome organization 0.00022 Informative Direct
Biological Process (BP) negative regulation of cellular biosynthetic process 0.001003 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.002089 Informative Inherited
Biological Process (BP) regulation of DNA metabolic process 0.0000009058 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 0.0003569 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity 0.00000000000001826 Moderately Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on a sulfur group of donors 0.0000000002545 Highly Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.02066 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.9033 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.2992 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1283 Least Informative Inherited
Cellular Component (CC) plastid 0.000001002 Informative Direct
Cellular Component (CC) chloroplast stroma 0.0000000003178 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

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 functionIron-sulfur0Moderately InformativeDirect
Molecular functionNADP0Moderately InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionHeme0InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationThioether bond0Highly InformativeDirect

Document: KW 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) · 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 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) · UniProtKB KeyWords (KW) · Internal database links ]