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15  structures 114  species 1  interaction 2410  sequences 26  architectures

Family: NAM (PF02365)

Summary: No apical meristem (NAM) protein

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No apical meristem (NAM) protein Provide feedback

This is a family of no apical meristem (NAM) proteins these are plant development proteins. Mutations in NAM result in the failure to develop a shoot apical meristem in petunia embryos [2]. NAM is indicated as having a role in determining positions of meristems and primordial [2]. One member of this family NAP (NAC-like, activated by AP3/PI) is encoded by the target genes of the AP3/PI transcriptional activators and functions in the transition between growth by cell division and cell expansion in stamens and petals [1].

Literature references

  1. Sablowski RW, Meyerowitz EM; , Cell 1998;92:93-103.: A homolog of NO APICAL MERISTEM is an immediate target of the floral homeotic genes APETALA3/PISTILLATA PUBMED:9489703 EPMC:9489703

  2. Souer E, van Houwelingen A, Kloos D, Mol J, Koes R; , Cell 1996;85:159-170.: The no apical meristem gene of Petunia is required for pattern formation in embryos and flowers and is expressed at meristem and primordia boundaries. PUBMED:8612269 EPMC:8612269


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003441

The NAC domain (for Petunia hybrida (Petunia) NAM and for Arabidopsis ATAF1, ATAF2, and CUC2) is an N-terminal module of ~160 amino acids, which is found in proteins of the NAC family of plant-specific transcriptional regulators (no apical meristem (NAM) proteins) [PUBMED:9212461]. NAC proteins are involved in developmental processes, including formation of the shoot apical meristem, floral organs and lateral shoots, as well as in plant hormonal control and defence. The NAC domain is accompanied by diverse C-terminal transcriptional activation domains. The NAC domain has been shown to be a DNA-binding domain (DBD) and a dimerization domain [PUBMED:11114891,PUBMED:12175016].

The NAC domain can be subdivided into five subdomains (A-E). Each subdomain is distinguishable by blocks of heterogeneous amino acids or gaps. While the NAC domains were rich in basic amino acids (R, K and H) as a whole, the distribution of positive and negative amino acids in each subdomain were unequal. Subdomains C and D are rich in basic amino acids but poor in acidic amino acids, while subdomain B contains a high proportion of acidic amino acids. Putative nuclear localization signals (NLS) have been detected in subdomains C and D [PUBMED:10660065]. The DBD is contained within a 60 amino acid region located within subdomains D and E [PUBMED:12175016]. The overall structure of the NAC domain monomer consists of a very twisted antiparallel beta-sheet, which packs against an N-terminal alpha-helix on one side and one shorter helix on the other side surrounded by a few helical elements. The structure suggests that the NAC domain mediates dimerization through conserved interactions including a salt bridge, and DNA binding through the NAC dimer face rich in positive charges [PUBMED:15083810].

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...

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
(133)
Full
(2410)
Representative proteomes NCBI
(2332)
Meta
(1)
RP15
(160)
RP35
(722)
RP55
(1039)
RP75
(1319)
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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
(133)
Full
(2410)
Representative proteomes NCBI
(2332)
Meta
(1)
RP15
(160)
RP35
(722)
RP55
(1039)
RP75
(1319)
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
(133)
Full
(2410)
Representative proteomes NCBI
(2332)
Meta
(1)
RP15
(160)
RP35
(722)
RP55
(1039)
RP75
(1319)
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_530 (release 5.2)
Previous IDs: none
Type: Family
Author: Bashton M, Bateman A
Number in seed: 133
Number in full: 2410
Average length of the domain: 125.10 aa
Average identity of full alignment: 42 %
Average coverage of the sequence by the domain: 37.77 %

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 21.2 21.2
Trusted cut-off 21.2 21.5
Noise cut-off 20.8 21.0
Model length: 129
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Interactions

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

NAM

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 NAM domain has been found. There are 15 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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