Gaf logo download

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. 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. 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 pfam-help sanger. 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.

The GAF domain is a type of protein domain that is found in a wide range of proteins from all species. This page is based on a Wikipedia article. 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. The opposite hydrolysis reaction is catalysed by phosphodiesterase. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region.

This domain is also found in FhlA formate hydrogen lyase transcriptional activator and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation.

NifA interacts with sigma This domain can bind biliverdine and phycocyanobilin Matilla et al. Hughes J;, Biochem Soc Trans. This tab holds annotation information from the InterPro database. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally stable states that are reversibly inter-convertible by light, the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region [ PUBMED ].

The GAF domain is also found in FhlA formate hydrogen lyase transcriptional activator and NifA, a transcriptional activator required for activation of most Nif operons, which are directly involved in nitrogen fixation. 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.

The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:. 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.

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. 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. 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.

Key: available, not generated, — not available. 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. 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. 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 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.

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. Align selected sequences to HMM.

You cannot overwrite this file. The following other wikis use this file: Usage on en. Width Height Structured data Items portrayed in this file depicts. Wikimedia username : HapHaxion. Creative Commons Attribution-ShareAlike 4. Namespaces File Discussion. Views View Edit History. Browse our collection of free samples, loops, sample packs, royalty free sound libraries and synth presets.

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