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34  structures 3229  species 1  interaction 3690  sequences 10  architectures

Family: CYTH (PF01928)

Summary: CYTH domain

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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.

CYTH domain Provide feedback

These sequences are functionally identified as members of the adenylate cyclase family, which catalyses the conversion of ATP to 3',5'-cyclic AMP and pyrophosphate. Six distinct non-homologous classes of AC have been identified. The structure of three classes of adenylyl cyclases have been solved [3].

Literature references

  1. Sismeiro O, Trotot P, Biville F, Vivares C, Danchin A; , J Bacteriol 1998;180:3339-3344.: Aeromonas hydrophila adenylyl cyclase 2: a new class of adenylyl cyclases with thermophilic properties and sequence similarities to proteins from hyperthermophilic archaebacteria. PUBMED:9642185 EPMC:9642185

  2. Iyer LM, Aravind L; , BMC Genomics 2002;3:33-33.: The catalytic domains of thiamine triphosphatase and CyaB-like adenylyl cyclase define a novel superfamily of domains that bind organic phosphates. PUBMED:12456267 EPMC:12456267

  3. Gallagher DT, Smith NN, Kim SK, Heroux A, Robinson H, Reddy PT; , J Mol Biol. 2006;362:114-122.: Structure of the class IV adenylyl cyclase reveals a novel fold. PUBMED:16905149 EPMC:16905149

  4. Smith N, Kim SK, Reddy PT, Gallagher DT; , Acta Crystallograph Sect F Struct Biol Cryst Commun. 2006;62:200-204.: Crystallization of the class IV adenylyl cyclase from Yersinia pestis. PUBMED:16511301 EPMC:16511301


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008172

The CYTH domain is an ancient enzymatic domain that was present in the Last Universal Common Ancestor and was involved in nucleotide or organic phosphate metabolism [PUBMED:12456267]. It is found in a variety of enzymes, including thiamine-triphosphatase and the CyaB-like adenlyl cyclases [PUBMED:12456267]. Structurally, this domain consists mainly of antiparallel beta sheets that form a wide barrel with a channel running through it.

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 CYTH (CL0273), which contains the following 2 members:

CYTH mRNA_triPase

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...

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
(51)
Full
(3690)
Representative proteomes NCBI
(2667)
Meta
(248)
RP15
(244)
RP35
(546)
RP55
(742)
RP75
(930)
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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
(51)
Full
(3690)
Representative proteomes NCBI
(2667)
Meta
(248)
RP15
(244)
RP35
(546)
RP55
(742)
RP75
(930)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(51)
Full
(3690)
Representative proteomes NCBI
(2667)
Meta
(248)
RP15
(244)
RP35
(546)
RP55
(742)
RP75
(930)
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.

Pfam alignments:

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: Aravind L
Previous IDs: Adenylate_cyc_2;
Type: Domain
Author: Aravind L
Number in seed: 51
Number in full: 3690
Average length of the domain: 182.60 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 64.24 %

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 23.1 23.1
Trusted cut-off 23.1 23.1
Noise cut-off 22.9 23.0
Model length: 185
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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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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Interactions

There is 1 interaction for this family. More...

CYTH

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 CYTH domain has been found. There are 34 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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