Summary: Photosynthetic reaction centre protein
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
This is the Wikipedia entry entitled "Photosynthetic reaction centre protein family". More...
The Wikipedia text that you see displayed here is a download from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button next to the article title ("Edit Wikipedia article") takes you to the edit page for the article directly within Wikipedia. You should be aware you are not editing our local copy of this information. Any changes that you make to the Wikipedia article will not be displayed here until we next download the article from Wikipedia. We currently download new content on a nightly basis.
Does Pfam agree with the content of the Wikipedia entry ?
Pfam has chosen to link families to Wikipedia articles. In some case we have created or edited these articles but in many other cases we have not made any direct contribution to the content of the article. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Pfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.
Editing Wikipedia articles
Before you edit for the first time
Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.
You should take a few minutes to view the following pages:
How your contribution will be recorded
Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia article" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer's IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.
If you have problems editing a particular page, contact us at firstname.lastname@example.org and we will try to help.
The community annotation is a new facility of the Pfam web site. If you have problems editing or experience problems with these pages please contact us.
Photosynthetic reaction centre protein family Edit Wikipedia article
|Photosynthetic reaction centre protein|
Structure of the photosynthetic reaction centre from Rhodopseudomonas viridis.
|Photosynthetic reaction centre cytochrome C subunit|
1.96 a x-ray structure of photosynthetic reaction centre from rhodopseudomonas viridis:crystals grown by microfluidic technique
Photosynthetic reaction centre proteins are main protein components of photosynthetic reaction centres of bacteria and plants.
The photosynthetic apparatus in non-oxygenic bacteria consists of light-harvesting protein-pigment complexes LH1 and LH2, which use carotenoid and bacteriochlorophyll as primary donors. LH1 acts as the energy collection hub, temporarily storing it before its transfer to the photosynthetic reaction centre (RC). Electrons are transferred from the primary donor via an intermediate acceptor (bacteriophaeophytin) to the primary acceptor (quinine Qa), and finally to the secondary acceptor (quinone Qb), resulting in the formation of ubiquinol QbH2. RC uses the excitation energy to shuffle electrons across the membrane, transferring them via ubiquinol to the cytochrome bc1 complex in order to establish a proton gradient across the membrane, which is used by ATP synthetase to form ATP.
The core complex is anchored in the cell membrane, consisting of one unit of RC surrounded by LH1; in some species there may be additional subunits. RC consists of three subunits: L (light), M (medium), and H (heavy). Subunits L and M provide the scaffolding for the chromophore, while subunit H contains a cytoplasmic domain. In Rhodopseudomonas viridis, there is also a non-membranous tetrahaem cytochrome (4Hcyt) subunit on the periplasmic surface.
Photosynthetic reaction centre genes from PSII (PsbA, PsbD) have been discovered within marine bacteriophage. Though it is widely accepted dogma that arbitrary pieces of DNA can be borne by phage between hosts (transduction), one would hardly expect to find transduced DNA within a large number of viruses. Transduction is presumed to be common in general, but for any single piece of DNA to be routinely transduced would be highly unexpected. Instead, conceptually, a gene routinely found in surveys of viral DNA would have to be a functional element of the virus itself (this does not imply that the gene would not be transferred among hosts - which the photosystem within viruses is - but instead that there is a viral function for the gene, that it is not merely hitchhiking with the virus). However, free viruses lack the machinery needed to support metabolism, let alone photosynthesis. As a result, photosystem genes are not likely to be a functional component of the virus like a capsid protein or tail fibre. Instead, it is expressed within an infected host cell. Most virus genes that are expressed in the host context are useful for hijacking the host machinery to produce viruses or for replication of the viral genome. These can include reverse transcriptases, integrases, nucleases or other enzymes. Photosystem components do not fit this mould either. The production of an active photosystem during viral infection provides active photosynthesis to dying cells. This is not viral altruism towards the host, however. The problem with viral infections tends to be that they disable the host relatively rapidly. As protein expression is shunted from the host genome to the viral genome, the photosystem degrades relatively rapidly (due in part to the interaction with light, which is highly corrosive), cutting off the supply of nutrients to the replicating virus. A solution to this problem is to add rapidly degraded photosystem genes to the virus, such that the nutrient flow is uninhibited and more viruses are produced. One would expect that this discovery will lead to other discoveries of a similar nature; that elements of the host metabolism key to viral production and easily damaged during infection are actively replaced or supported by the virus during infection.
Indeed, recently, PSI gene cassettes containing whole gene suites [(psaJF, C, A, B, K, E and D) and (psaD, C, A and B)] were also reported to exist in marine cyanophages from the Pacific and Indian Oceans 
In plant photosystems
This entry describes the photosynthetic reaction centre L and M subunits, and the homologous D1 (PsbA) and D2 (PsbD) photosystem II (PSII) reaction centre proteins from cyanobacteria, algae and plants. The D1 and D2 proteins only show approximately 15% sequence homology with the L and M subunits, however the conserved amino acids correspond to the binding sites of the photochemically active cofactors. As a result, the reaction centres (RCs) of purple photosynthetic bacteria and PSII display considerable structural similarity in terms of cofactor organisation.
The D1 and D2 proteins occur as a heterodimer that form the reaction core of PSII, a multisubunit protein-pigment complex containing over forty different cofactors, which are anchored in the cell membrane in cyanobacteria, and in the thylakoid membrane in algae and plants. Upon absorption of light energy, the D1/D2 heterodimer undergoes charge separation, and the electrons are transferred from the primary donor (chlorophyll a) via phaeophytin to the primary acceptor quinone Qa, then to the secondary acceptor Qb, which like the bacterial system, culminates in the production of ATP. However, PSII has an additional function over the bacterial system. At the oxidising side of PSII, a redox-active residue in the D1 protein reduces P680, the oxidised tyrosine then withdrawing electrons from a manganese cluster, which in turn withdraw electrons from water, leading to the splitting of water and the formation of molecular oxygen. PSII thus provides a source of electrons that can be used by photosystem I to produce the reducing power (NADPH) required to convert CO2 to glucose.
- Photosynthetic reaction centre, M subunit InterPro: IPR005781
- Photosystem II reaction centre protein PsbA/D1 InterPro: IPR005867
- Photosystem II reaction centre protein PsbD/D2 InterPro: IPR005868
- Photosynthetic reaction centre, L subunit InterPro: IPR005871
- Deisenhofer J, Epp O, Sinning I, Michel H (February 1995). "Crystallographic refinement at 2.3 A resolution and refined model of the photosynthetic reaction centre from Rhodopseudomonas viridis". J. Mol. Biol. 246 (3): 429–57. PMID 7877166. doi:10.1006/jmbi.1994.0097.
- Michel H, Oesterhelt D, Lancaster CR, Bibikova MV, Sabatino P (2000). "Structural basis of the drastically increased initial electron transfer rate in the reaction center from a Rh odopseudomonas viridis mutant described at 2.00-A resolution". J. Biol. Chem. 275 (50): 39364–39368. PMID 11005826. doi:10.1074/jbc.M008225200.
- Hunter CN, Bullough PA, Otto C, Bahatyrova S, Frese RN, Siebert CA, Olsen JD, Van Der Werf KO, Van Grondelle R, Niederman RA (2004). "The native architecture of a photosynthetic membrane". Nature. 430 (7003): 1058–62. PMID 15329728. doi:10.1038/nature02823.
- Scheuring S (2006). "AFM studies of the supramolecular assembly of bacterial photosynthetic core-complexes". Curr Opin Chem Biol. 10 (5): 387–93. PMID 16931113. doi:10.1016/j.cbpa.2006.08.007.
- Remy A, GerwertK; Gerwert, K (2003). "Coupling of light-induced electron transfer to proton uptake in photosynthesis". Nat. Struct. Biol. 10 (8): 637–644. PMID 12872158. doi:10.1038/nsb954.
- Michel H, Deisenhofer J (1989). "Nobel lecture. The photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis". EMBO J. 8 (8): 2149–2170. PMC . PMID 2676514.
- Miki K, Kobayashi M, Nogi T, Fathir I, Nozawa T (2000). "Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: thermostability and electron transfer". Proc. Natl. Acad. Sci. U.S.A. 97 (25): 13561–13566. PMC . PMID 11095707. doi:10.1073/pnas.240224997.
- Michel H, Ermler U, Schiffer M (1994). "Structure and function of the photosynthetic reaction center from Rhodobacter sphaeroides". J. Bioenerg. Biomembr. 26 (1): 5–15. PMID 8027023. doi:10.1007/BF00763216.
- Sharon I, Tzahor S, Williamson S, Shmoish M, Man-Aharonovich D, Rusch DB, Yooseph S, Zeidner G, Golden SS, Mackey SR, Adir N, Weingart U, Horn D, Venter JC, Mandel-Gutfreund Y, Béjà O (2007). "Viral photosynthetic reaction center genes and transcripts in the marine environment". ISME J. 1 (6): 492–501. PMID 18043651. doi:10.1038/ismej.2007.67.
- Millard A, Clokie MR, Shub DA, Mann NH (2004). "Genetic organization of the psbAD region in phages infecting marine Synechococcus strains". Proc. Natl. Acad. Sci. U.S.A. 101 (30): 11007–12. PMC . PMID 15263091. doi:10.1073/pnas.0401478101.
- Sullivan MB, Lindell D, Lee JA, Thompson LR, Bielawski JP, Chisholm SW (2006). "Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts". PLoS Biol. 4 (8): e234. PMC . PMID 16802857. doi:10.1371/journal.pbio.0040234.
- Lindell D, Sullivan MB, Johnson ZI, Tolonen AC, Rohwer F, Chisholm SW (2004). "Transfer of photosynthesis genes to and from Prochlorococcus viruses". Proc. Natl. Acad. Sci. U.S.A. 101 (30): 11013–8. PMC . PMID 15256601. doi:10.1073/pnas.0401526101.
- Lindell D, Jaffe JD, Johnson ZI, Church GM, Chisholm SW (2005). "Photosynthesis genes in marine viruses yield proteins during host infection". Nature. 438 (7064): 86–9. PMID 16222247. doi:10.1038/nature04111.
- Clokie MR, Shan J, Bailey S, Jia Y, Krisch HM, West S, Mann NH (2006). "Transcription of a 'photosynthetic' T4-type phage during infection of a marine cyanobacterium". Environ. Microbiol. 8 (5): 827–35. PMID 16623740. doi:10.1111/j.1462-2920.2005.00969.x.
- Bailey S, Clokie MR, Millard A, Mann NH (2004). "Cyanophage infection and photoinhibition in marine cyanobacteria". Res. Microbiol. 155 (9): 720–5. PMID 15501648. doi:10.1016/j.resmic.2004.06.002.
- Sharon I, Alperovitch A, Rohwer F, Haynes M, Glaser F, Atamna-Ismaeel N, Pinter RY, Partensky F, Koonin EV, Wolf YI, Nelson N, Béjà O (2009). "Photosystem-I gene cassettes are present in marine virus genomes". Nature. 461 (7261): 258–262. PMID 19710652. doi:10.1038/nature08284.
- Alperovitch-Lavy A, Sharon I, Rohwer F, Aro EM, Glaser F, Milo R, Nelson N, Béjà O (2011). "Reconstructing a puzzle: existence of cyanophages containing both photosystem-I and photosystem-II gene suites inferred from oceanic metagenomic datasets". Environ. Microbiol. 13 (1): 24–32. PMID 20649642. doi:10.1111/j.1462-2920.2010.02304.x.
- Béjà O, Fridman S, Glaser F (2012). "Viral clones from the GOS expedition with an unusual photosystem-I gene cassette organization". ISME J. 6 (8): 1617–20. PMID 22456446. doi:10.1038/ismej.2012.23.
- Kamiya N, Shen JR (2003). "Crystal structure of oxygen-evolving photosystem II from Thermosynechococcus vulcanus at 3.7-A resolution". Proc. Natl. Acad. Sci. U.S.A. 100 (1): 98–103. PMC . PMID 12518057. doi:10.1073/pnas.0135651100.
- Schroder WP, Shi LX (2004). "The low molecular mass subunits of the photosynthetic supracomplex, photosystem II". Biochim. Biophys. Acta. 1608 (2–3): 75–96. PMID 14871485. doi:10.1016/j.bbabio.2003.12.004.
- Deisenhofer, J.; Epp, O.; Miki, K.; Huber, R.; Michel, H. (1984). "X-ray structure analysis of a membrane protein complex. Electron density map at 3 a resolution and a model of the chromophores of the photosynthetic reaction center from Rhodopseudomonas viridis". Journal of Molecular Biology. 180 (2): 385–398. PMID 6392571. doi:10.1016/s0022-2836(84)80011-x.
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.
Photosynthetic reaction centre protein Provide feedback
No Pfam abstract.
Deisenhofer J, Epp O, Miki K, Huber R, Michel H; , J Mol Biol 1984;180:385-398.: X-ray structure analysis of a membrane protein complex. Electron density map at 3 A resolution and a model of the chromophores of the photosynthetic reaction center from Rhodopseudomonas viridis. PUBMED:6392571 EPMC:6392571
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000484
The photosynthetic apparatus in non-oxygenic bacteria consists of light-harvesting (LH) protein-pigment complexes LH1 and LH2, which use carotenoid and bacteriochlorophyll as primary donors [PUBMED:11005826]. LH1 acts as the energy collection hub, temporarily storing it before its transfer to the photosynthetic reaction centre (RC) [PUBMED:15329728]. Electrons are transferred from the primary donor via an intermediate acceptor (bacteriopheophytin) to the primary acceptor (quinine Qa), and finally to the secondary acceptor (quinone Qb), resulting in the formation of ubiquinol QbH2. RC uses the excitation energy to shuffle electrons across the membrane, transferring them via ubiquinol to the cytochrome bc1 complex in order to establish a proton gradient across the membrane, which is used by ATP synthetase to form ATP [PUBMED:16931113, PUBMED:12872158, PUBMED:2676514].
The core complex is anchored in the cell membrane, consisting of one unit of RC surrounded by LH1; in some species there may be additional subunits [PUBMED:11095707]. RC consists of three subunits: L (light), M (medium), and H (heavy). Subunits L and M provide the scaffolding for the chromophore, while subunit H contains a cytoplasmic domain [PUBMED:8027023]. In Rhodopseudomonas viridis, there is also a non-membranous tetrahaem cytochrome (4Hcyt) subunit on the periplasmic surface.
This entry describes the photosynthetic reaction centre L and M subunits, and the homologous D1 (PsbA) and D2 (PsbD) photosystem II (PSII) reaction centre proteins from cyanobacteria, algae and plants. The D1 and D2 proteins only show approximately 15% sequence homology with the L and M subunits, however the conserved amino acids correspond to the binding sites of the phytochemically active cofactors. As a result, the reaction centres (RCs) of purple photosynthetic bacteria and PSII display considerable structural similarity in terms of cofactor organisation.
The D1 and D2 proteins occur as a heterodimer that form the reaction core of PSII, a multisubunit protein-pigment complex containing over forty different cofactors, which are anchored in the cell membrane in cyanobacteria, and in the thylakoid membrane in algae and plants. Upon absorption of light energy, the D1/D2 heterodimer undergoes charge separation, and the electrons are transferred from the primary donor (chlorophyll a) via pheophytin to the primary acceptor quinone Qa, then to the secondary acceptor Qb, which like the bacterial system, culminates in the production of ATP. However, PSII has an additional function over the bacterial system. At the oxidising side of PSII, a redox-active residue in the D1 protein reduces P680, the oxidised tyrosine then withdrawing electrons from a manganese cluster, which in turn withdraw electrons from water, leading to the splitting of water and the formation of molecular oxygen. PSII thus provides a source of electrons that can be used by photosystem I to produce the reducing power (NADPH) required to convert CO2 to glucose [PUBMED:12518057, PUBMED:14871485].
Also in this entry is the light-dependent chlorophyll f synthase (ChlF) from cyanobacteria such as Chlorogloeopsis fritschii. ChlF synthesizes chlorophyll f or chlorophyllide f, which is able to absorb far red light, probably by oxidation of chlorophyll a or chlorophyllide a and reduction of plastoquinone [PUBMED:27386923].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
Loading domain graphics...
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...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
- an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
- an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.
You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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...
If you find these logos useful in your own work, please consider citing the following article:
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.
|Number in seed:||42|
|Number in full:||988|
|Average length of the domain:||242.20 aa|
|Average identity of full alignment:||39 %|
|Average coverage of the sequence by the domain:||82.63 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
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.
There are 23 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 Photo_RC domain has been found. There are 376 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 seqence.
Loading structure mapping...