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1146  structures 182  species 0  interactions 1889  sequences 8  architectures

Family: Phycobilisome (PF00502)

Summary: Phycobilisome protein

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Phycobilisome protein Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR012128

Cyanobacteria and red algae harvest light through water-soluble complexes, called phycobilisomes, which are attached to the outer face of the thylakoid membrane [ PUBMED:15238265 ]. These complexes are capable of transferring the absorbed energy to the photosynthetic reaction centre with greater than 95% efficiency. Phycobilisomes contain various photosynthetic light harvesting proteins known as biliproteins, and linker proteins which help assemble the structure. The two main structural elements of the complex are a core located near the photosynthetic reaction centre, and rods attached to this core. Allophycocyanin is the major component of the core, while the rods contain phycocyanins, phycoerythrins and linker proteins. The rod biliproteins harvest photons, with the excitation energy being passed through the rods into the allophycocyanin in the core. Other core biliproteins subsequently pass this energy to chlorophyll within the thylakoid membrane.

This entry represents the alpha and beta subunits found in biliproteins from cyanobacteria and red algae. Structural studies indicate that the basic structural unit of most biliproteins is a heterodimer composed of these alpha and beta subunits [ PUBMED:10388620 , PUBMED:11134927 , PUBMED:11463658 , PUBMED:7783202 ]. The full protein is a ring-like trimer assembly of these heterodimers. Each subunit of the heterodimer has eight helices and binds chromophores through thioester bonds formed at particular cysteine residues. These chromophores, also known as bilins, are open-chain tetrapyrroles whose number and type vary with the particular biliprotein eg R-phyocerythrin binds five phycoerythrobilins per heterodimer, while allophycocyanin binds two phycocyanobilins per heterodimer.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Globin (CL0090), which has the following description:

The globin fold is an evolutionary conserved six helical fold that is found in bacteria and eukaryotes.

The clan contains the following 8 members:

Bac_globin Globin HisK-N-like HisK_N Phycobilisome Protoglobin Rsbr_N RsbRD_N


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 and the UniProtKB sequence database. More...

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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.

Representative proteomes UniProt
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Representative proteomes UniProt

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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.

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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...


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 View help on the curation process

Seed source: Pfam-B_10 (release 1.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 132
Number in full: 1889
Average length of the domain: 142.30 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 64.12 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.2 22.2
Trusted cut-off 22.3 22.3
Noise cut-off 22.1 22.1
Model length: 155
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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...

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The tree shows the occurrence of this domain across different species. More...


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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 Phycobilisome domain has been found. There are 1146 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.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
B1XQM2 View 3D Structure Click here
O68966 View 3D Structure Click here
O68967 View 3D Structure Click here
O68970 View 3D Structure Click here
O68973 View 3D Structure Click here
P03943 View 3D Structure Click here
P03944 View 3D Structure Click here
P06539 View 3D Structure Click here
P07120 View 3D Structure Click here
P07121 View 3D Structure Click here
P13530 View 3D Structure Click here
P27288 View 3D Structure Click here
P27289 View 3D Structure Click here
P35796 View 3D Structure Click here
P35797 View 3D Structure Click here
P50030 View 3D Structure Click here
P50031 View 3D Structure Click here
P50032 View 3D Structure Click here
P50033 View 3D Structure Click here
P72870 View 3D Structure Click here
P74551 View 3D Structure Click here
P80555 View 3D Structure Click here
P80556 View 3D Structure Click here
P80557 View 3D Structure Click here
P80559 View 3D Structure Click here
Q01951 View 3D Structure Click here
Q01952 View 3D Structure Click here
Q08086 View 3D Structure Click here
Q08087 View 3D Structure Click here
Q54714 View 3D Structure Click here
Q54715 View 3D Structure Click here
Q55544 View 3D Structure Click here
Q7A2D6 View 3D Structure Click here
Q7VDN2 View 3D Structure Click here
Q8YZK7 View 3D Structure Click here