SUPERFAMILY 1.75 HMM library and genome assignments server


C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   8-bladed beta-propeller [ 50997] (3)
Superfamily:   C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase [ 51004]
Families:   C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase [ 51005]


Superfamily statistics
Genomes (1,608) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,962 0 8
Proteins 2,923 0 8


Functional annotation
General category Metabolism
Detailed category E- transfer

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0.0004324Least InformativeDirect
Enzyme Commission (EC)Acting on other nitrogenous compounds as donors2.109e-11InformativeDirect
Enzyme Commission (EC)With a cytochrome as acceptor9.582e-16Highly InformativeDirect
Enzyme Commission (EC)With other acceptors2.851e-15Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1.785e-07Least InformativeDirect
Biological processProtein transport6.724e-05Moderately InformativeDirect
Biological processER-Golgi transport5.24e-12Highly InformativeDirect
Cellular componentCytoplasmic vesicle4.813e-13Moderately InformativeDirect
Cellular componentGolgi apparatus3.476e-11Moderately InformativeDirect
DomainWD repeat2.414e-13InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011048 SSF51004 Protein matches
Abstract

Cytochrome cd1 (cyt cd1) nitrite reductase is a dimeric enzyme of the bacterial periplasm that plays a key role in denitrification, the respiratory reduction of nitrite to nitric oxide in the nitrogen cycle. Each subunit of the cyt cd1 dimer contains one cytochrome c and one d1 haem group [PubMed12556530]. The active site contains a specialised d1 haem, where the nitrite substrate is bound and reduced. This d1 haem is bound in an 8-bladed beta-propeller, which is also found in some members of the WD40 repeat-containing proteins .


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 · 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 2 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 C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase 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 2 hidden Markov models representing the C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase 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 · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]