Summary: Putative stress-responsive nuclear envelope protein
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Putative stress-responsive nuclear envelope protein Provide feedback
This entry represents a repeat found in the fungal protein Ish1, a putative stress-responsive nuclear envelope protein [1].
Literature references
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Taricani L, Tejada ML, Young PG;, J Biol Chem. 2002;277:10562-10572.: The fission yeast ES2 homologue, Bis1, interacts with the Ish1 stress-responsive nuclear envelope protein. PUBMED:11751918 EPMC:11751918
Internal database links
SCOOP: | HeH |
Similarity to PfamA using HHSearch: | SAP HeH |
This tab holds annotation information from the InterPro database.
InterPro entry IPR018803
This entry includes the stress response protein Ish1 from fission yeasts and meiotic sister chromatid recombination protein 1 (Msc1) from budding yeasts. This entry also includes some uncharacterised proteins from Acinetobacter baumannii.
Ish1 has a role in maintaining cell viability during stationary phase induced by stress response. It can be activated by the spc1 MAPK pathway [PUBMED:11751918].
Msc1 was identified in a screen for mutants that show an increase in meiotic unequal sister-chromatid recombination (SCR) [PUBMED:10511544]. Its function is not clear.
Domain organisation
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Alignments
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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 (255) |
Full (3208) |
Representative proteomes | UniProt (5064) |
NCBI (5507) |
Meta (0) |
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RP15 (334) |
RP35 (1155) |
RP55 (1945) |
RP75 (3064) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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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 (255) |
Full (3208) |
Representative proteomes | UniProt (5064) |
NCBI (5507) |
Meta (0) |
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RP15 (334) |
RP35 (1155) |
RP55 (1945) |
RP75 (3064) |
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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_11056 (release 21.0) |
Previous IDs: | none |
Type: | Repeat |
Sequence Ontology: | SO:0001068 |
Author: |
Wood V |
Number in seed: | 255 |
Number in full: | 3208 |
Average length of the domain: | 36.10 aa |
Average identity of full alignment: | 34 % |
Average coverage of the sequence by the domain: | 34.69 % |
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: | 37 | ||||||||||||
Family (HMM) version: | 10 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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