Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
0  structures 11  species 0  interactions 106  sequences 4  architectures

Family: ACDC (PF14733)

Summary: AP2-coincident C-terminal

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 "ACDC domain". More...

ACDC domain Edit Wikipedia article

AP2-Coincident Domain mainly at the Carboxy-terminus domain
Identifiers
Symbol ACDC
Pfam PF14733

The AP2-Coincident Domain mainly at the Carboxy-terminus, or ACDC domain, is a protein domain that occurs in proteins from apicomplexan parasites.[1]

It is found exclusively in apicomplexan proteins that also contain AP2 (Apetala 2-integrase) DNA binding domains (ApiAP2 proteins). In 8 of 9 known examples in the malarial parasite Plasmodium falciparum it is near the carboxy terminus, with the remaining one being at the amino terminus. As yet, beyond its identification and the observation that it occurs only in ApiAP2 proteins, the function of the ACDC domain is unknown. Two proteins with the ACDC domain were found in the nucleus of P. falciparum, as detected by a proteomic method, suggesting a role in nuclear biology.[1]

[edit] References

  1. ^ a b Oehring, S. C.; Woodcroft, B. J.; Moes, S.; Wetzel, J.; Dietz, O.; Pulfer, A.; Dekiwadia, C.; Maeser, P. et al. (2012). "Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum". Genome Biology 13 (11): R108. doi:10.1186/gb-2012-13-11-r108. PMID 23181666. edit

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

AP2-coincident C-terminal Provide feedback

This family is found at the C-terminus of apicomplexan proteins containing the AP2 domain (PF00847).

External database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

Domain organisation

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

Loading domain graphics...

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
(28)
Full
(106)
Representative proteomes NCBI
(116)
Meta
(0)
RP15
(37)
RP35
(47)
RP55
(88)
RP75
(100)
Jalview View  View  View  View  View  View  View   
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

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

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

Format an alignment

  Seed
(28)
Full
(106)
Representative proteomes NCBI
(116)
Meta
(0)
RP15
(37)
RP35
(47)
RP55
(88)
RP75
(100)
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
(28)
Full
(106)
Representative proteomes NCBI
(116)
Meta
(0)
RP15
(37)
RP35
(47)
RP55
(88)
RP75
(100)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download    
Gzipped 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

This family is new in this Pfam release.

Seed source: Woodcroft B
Previous IDs: none
Type: Family
Author: Woodcroft B, Eberhardt R
Number in seed: 28
Number in full: 106
Average length of the domain: 94.70 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 6.97 %

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 25.0 25.0
Trusted cut-off 25.1 25.3
Noise cut-off 24.0 22.8
Model length: 92
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

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...

Loading sunburst data...

Tree controls

Hide

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

Loading...

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.