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7  structures 652  species 2  interactions 684  sequences 7  architectures

Family: PSI_PsaJ (PF01701)

Summary: Photosystem I reaction centre subunit IX / PsaJ

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Photosystem I reaction centre subunit IX / PsaJ Provide feedback

This family consists of the photosystem I reaction centre subunit IX or PsaJ from various organisms including Synechocystis sp. (strain pcc 6803), Pinus thunbergii (green pine) and Zea mays (maize). PsaJ P19443 is a small 4.4kDa, chloroplastal encoded, hydrophobic subunit of the photosystem I reaction complex its function is not yet fully understood [1]. PsaJ can be cross-linked to PsaF P12356 and has a single predicted transmembrane domain it has a proposed role in maintaining PsaF in the correct orientation to allow for fast electron transfer from soluble donor proteins to P700+ [1].

Literature references

  1. Fischer N, Boudreau E, Hippler M, Drepper F, Haehnel W, Rochaix JD; , Biochemistry 1999;38:5546-5552.: A large fraction of PsaF is nonfunctional in photosystem I complexes lacking the PsaJ subunit. PUBMED:10220342 EPMC:10220342

  2. Muhlenhoff U, Haehnel W, Witt H, Herrmann RG; , Gene 1993;127:71-78.: Genes encoding eleven subunits of photosystem I from the thermophilic cyanobacterium Synechococcus sp. PUBMED:8486290 EPMC:8486290


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002615

Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product.

This family consists of the photosystem I reaction centre subunit IX or PsaJ from various organisms including Synechocystis sp. (strain PCC 6803), Pinus thunbergii (Green pine) and Zea mays (Maize). PsaJ (SWISSPROT) is a small 4.4kDa, chloroplast encoded, hydrophobic subunit of the photosystem I reaction complex whose function is not yet fully understood [PUBMED:10220342]. PsaJ can be cross-linked to PsaF (SWISSPROT) and has a single predicted transmembrane domain. It has a proposed role in maintaing PsaF in the correct orientation to allow for fast electron transfer from soluble donor proteins to P700+ [PUBMED:10220342].

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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Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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.

  Seed
(31)
Full
(684)
Representative proteomes NCBI
(324)
Meta
(19)
RP15
(13)
RP35
(38)
RP55
(47)
RP75
(51)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(31)
Full
(684)
Representative proteomes NCBI
(324)
Meta
(19)
RP15
(13)
RP35
(38)
RP55
(47)
RP75
(51)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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.

  Seed
(31)
Full
(684)
Representative proteomes NCBI
(324)
Meta
(19)
RP15
(13)
RP35
(38)
RP55
(47)
RP75
(51)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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 View help on the curation process

Seed source: Pfam-B_1599 (release 4.1)
Previous IDs: none
Type: Family
Author: Bashton M, Bateman A
Number in seed: 31
Number in full: 684
Average length of the domain: 36.80 aa
Average identity of full alignment: 72 %
Average coverage of the sequence by the domain: 80.63 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.5 20.5
Trusted cut-off 21.2 21.3
Noise cut-off 19.8 20.4
Model length: 37
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

PSI_PsaF PsaA_PsaB

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 PSI_PsaJ 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 seqence.

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