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0  structures 288  species 0  interactions 447  sequences 13  architectures

Family: Not1 (PF04054)

Summary: CCR4-Not complex component, Not1

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CCR4-Not complex component, Not1 Provide feedback

The Ccr4-Not complex is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID [1].

Literature references

  1. Maillet L, Collart MA; , J Biol Chem 2002;277:2835-2842.: Interaction between Not1p, a component of the Ccr4-not complex, a global regulator of transcription, and Dhh1p, a putative RNA helicase. PUBMED:11696541 EPMC:11696541


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007196

The Ccr4-Not complex is a global regulator of gene expression that is conserved from yeast to human. It affects genes positively and negatively and is thought to regulate transcription factor IID function. In Saccharomyces cerevisiae, it exists in two prominent forms and consists of at least nine core subunits: the five Not proteins (Not1p to Not5p), Caf1p, Caf40p, Caf130p and Ccr4p [PUBMED:10637334]. The Ccr4-Not complex regulates many different cellular functions, including RNA degradation and transcription initiation. It may be a regulatory platform that senses nutrient levels and stress [PUBMED:12957374]. Caf1p and Ccr4p, are directly involved in mRNA deadenylation, and Caf1p is associated with Dhh1p, a putative RNA helicase thought to be a component of the decapping complex [PUBMED:11696541]. Pop2, a component of the Ccr4-Not complex, functions as a deadenylase [PUBMED:18430587].

The Ccr4-Not complex is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID [PUBMED:11696541].

Domain organisation

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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
(30)
Full
(447)
Representative proteomes NCBI
(459)
Meta
(11)
RP15
(116)
RP35
(177)
RP55
(255)
RP75
(299)
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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
(30)
Full
(447)
Representative proteomes NCBI
(459)
Meta
(11)
RP15
(116)
RP35
(177)
RP55
(255)
RP75
(299)
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
(30)
Full
(447)
Representative proteomes NCBI
(459)
Meta
(11)
RP15
(116)
RP35
(177)
RP55
(255)
RP75
(299)
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: Pfam-B_13503 (release 7.3);
Previous IDs: none
Type: Family
Author: Wood V, Finn RD
Number in seed: 30
Number in full: 447
Average length of the domain: 319.90 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 17.68 %

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 22.5 22.5
Trusted cut-off 32.1 23.9
Noise cut-off 22.4 22.4
Model length: 379
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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