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0  structures 102  species 0  interactions 271  sequences 10  architectures

Family: LEA_5 (PF00477)

Summary: Small hydrophilic plant seed protein

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 "Plant seed proteins". More...

Plant seed proteins Edit Wikipedia article

Small hydrophilic plant seed protein
Identifiers
Symbol Seed_protein_pln
Pfam PF00477
InterPro IPR000389
PROSITE PDOC00355

Plant seed proteins are small hydrophilic proteins some of which are structurally related. These proteins contain from 83 to 153 amino acid residues and may play a role in equipping the seed for survival, maintaining a minimal level of hydration in the dry organism and preventing the denaturation of cytoplasmic components.[1][2] They may also play a role during imbibition by controlling water uptake.

References[edit]

  1. ^ Bray EA (1993). "Molecular Responses to Water Deficit". Plant Physiol. 103 (4): 1035–1040. PMC 159086. PMID 12231998. 
  2. ^ Gaubier P, Raynal M, Hull G, Huestis GM, Grellet F, Arenas C, Pages M, Delseny M (1993). "Two different Em-like genes are expressed in Arabidopsis thaliana seeds during maturation". Mol. Gen. Genet. 238 (3): 409–418. PMID 8492809. 

This article incorporates text from the public domain Pfam and InterPro IPR000389

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.

Small hydrophilic plant seed protein Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000389

This entry contains a number of bacterial proteins annotated as stress-induced and members of the plant LEA (late embryogenesis abundant) proteins, which are small hydrophilic plant seed proteins that are structurally related. These proteins contains from 83 to 153 amino acid residues and may play a role [PUBMED:12231998, PUBMED:8492809] in equipping the seed for survival, maintaining a minimal level of hydration in the dry organism and preventing the denaturation of cytoplasmic components. They may also play a role during imbibition by controlling water uptake.

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 Hydrophilin (CL0385), which has the following description:

This superfamily includes plant and bacterial hydrophilin families.

The clan contains the following 2 members:

KGG LEA_5

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
(5)
Full
(271)
Representative proteomes NCBI
(294)
Meta
(3)
RP15
(20)
RP35
(59)
RP55
(77)
RP75
(87)
Jalview View  View  View  View  View  View  View  View 
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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
(5)
Full
(271)
Representative proteomes NCBI
(294)
Meta
(3)
RP15
(20)
RP35
(59)
RP55
(77)
RP75
(87)
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
(5)
Full
(271)
Representative proteomes NCBI
(294)
Meta
(3)
RP15
(20)
RP35
(59)
RP55
(77)
RP75
(87)
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.

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: Prosite
Previous IDs: seed_protein;
Type: Family
Author: Finn RD
Number in seed: 5
Number in full: 271
Average length of the domain: 71.90 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 87.44 %

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 20.6 20.6
Trusted cut-off 21.1 20.8
Noise cut-off 20.5 20.3
Model length: 109
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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