Summary: Prokaryotic cytochrome b561
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Prokaryotic cytochrome b561 Provide feedback
This family includes cytochrome b561 and related proteins, in addition to the nickel-dependent hydrogenases b-type cytochrome subunit. Cytochrome b561 is a secretory vesicle-specific electron transport protein. It is an integral membrane protein, that binds two heme groups non-covalently. This is a prokaryotic family. Members of the 'eukaryotic cytochrome b561' family can be found in Pfam: PF03188.
Internal database links
SCOOP: | COX15-CtaA Cytochrom_B561 Cytochrome_B DUF2231 DUF4405 DUF998 Ferric_reduct PepSY_TM |
Similarity to PfamA using HHSearch: | DUF4405 |
External database links
PROSITE: | PDOC00688 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR011577
Cytochrome b561 is an integral membrane and electron transport protein, that binds two haem groups non-covalently. This domain is also found in a number of nickel-dependent hydrogenase subunits which are also B-type cytochromes that interact with quinones and anchor the hydrogenase to the membrane. This domain is found in prokaryotes. Members of the 'eukaryotic cytochrome b561' family can be found in INTERPRO.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | integral component of membrane (GO:0016021) |
Molecular function | electron transfer activity (GO:0009055) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
Loading domain graphics...
Pfam Clan
This family is a member of clan 2heme_cytochrom (CL0328), which has the following description:
This superfamily includes a variety of different heme binding cytochromes.
The clan contains the following 9 members:
COX15-CtaA Cytochrom_B561 Cytochrom_B_N_2 Cytochrom_C_asm Cytochrome_B DUF2427 DUF4405 Ferric_reduct Ni_hydr_CYTBAlignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
View options
We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
Seed (81) |
Full (9456) |
Representative proteomes | UniProt (52410) |
NCBI (72226) |
Meta (1385) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (1009) |
RP35 (3925) |
RP55 (9540) |
RP75 (18836) |
||||||
Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
Download options
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
Seed (81) |
Full (9456) |
Representative proteomes | UniProt (52410) |
NCBI (72226) |
Meta (1385) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (1009) |
RP35 (3925) |
RP55 (9540) |
RP75 (18836) |
||||||
Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | Prosite |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Finn RD |
Number in seed: | 81 |
Number in full: | 9456 |
Average length of the domain: | 180.20 aa |
Average identity of full alignment: | 18 % |
Average coverage of the sequence by the domain: | 76.71 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
|
||||||||||||
Model details: |
|
||||||||||||
Model length: | 182 | ||||||||||||
Family (HMM) version: | 21 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
Sunburst controls
HideWeight segments by...
Change the size of the sunburst
Colour assignments
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
Selections
Align selected sequences to HMM
Generate a FASTA-format file
Clear selection
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...
Tree controls
HideThe tree shows the occurrence of this domain across different species. More...
Loading...
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
Structures
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Ni_hydr_CYTB domain has been found. There are 7 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
Loading structure mapping...