Summary: Senescence-associated protein
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Senescence-associated protein Provide feedback
This family contains a number of plant senescence-associated proteins of approximately 450 residues in length. In Hemerocallis, petals have a genetically based program that leads to senescence and cell death approximately 24 hours after the flower opens, and it is believed that senescence proteins produced around that time have a role in this program [1]. This family extends to the higher vertebrates where the full-length protein is often a Spartin, associated with mitochondrial membranes and transportation along microtubules [2].
Literature references
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Panavas T, Pikula A, Reid PD, Rubinstein B, Walker EL; , Plant Mol Biol 1999;40:237-248.: Identification of senescence-associated genes from daylily petals. PUBMED:10412903 EPMC:10412903
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Lu J, Rashid F, Byrne PC;, J Neurochem. 2006;98:1908-1919.: The hereditary spastic paraplegia protein spartin localises to mitochondria. PUBMED:16945107 EPMC:16945107
This tab holds annotation information from the InterPro database.
InterPro entry IPR009686
This domain is found in a number of plant senescence-associated proteins of approximately 450 residues in length. In Hemerocallis, petals have a genetically based program that leads to senescence and cell death approximately 24 hours after the, flower opens, and it is believed that senescence proteins produced around that time have a role in this program [PUBMED:10412903]. This domain is also found in a number of Spartin proteins which may be implicated in endosomal trafficking, or microtubule dynamics, or both [PUBMED:12676568].
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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, 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 (129) |
Full (1711) |
Representative proteomes | UniProt (2642) |
NCBI (3412) |
Meta (2) |
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RP15 (242) |
RP35 (788) |
RP55 (1256) |
RP75 (1736) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
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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 (129) |
Full (1711) |
Representative proteomes | UniProt (2642) |
NCBI (3412) |
Meta (2) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (242) |
RP35 (788) |
RP55 (1256) |
RP75 (1736) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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
Seed source: | Pfam-B_7525 (release 10.0) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Vella Briffa B |
Number in seed: | 129 |
Number in full: | 1711 |
Average length of the domain: | 168.70 aa |
Average identity of full alignment: | 25 % |
Average coverage of the sequence by the domain: | 34.81 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 183 | ||||||||||||
Family (HMM) version: | 13 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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