Summary: SMI1 / KNR4 family (SUKH-1)
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SMI1 / KNR4 family (SUKH-1) Provide feedback
Proteins in this family are involved in the regulation of 1,3-beta-glucan synthase activity and cell-wall formation [1]. Genome contextual information showed that SMI1 are primary immunity proteins in bacterial toxin systems [3].
Literature references
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Enderlin CS, Selitrennikoff CP; , Proc Natl Acad Sci U S A. 1994;91:9500-9504.: Cloning and characterization of a Neurospora crassa gene required for (1,3) beta-glucan synthase activity and cell wall formation. PUBMED:7937796 EPMC:7937796
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Hong Z, Mann P, Brown NH, Tran LE, Shaw KJ, Hare RS, DiDomenico B; , Mol Cell Biol. 1994;14:1017-1025.: Cloning and characterization of KNR4, a yeast gene involved in (1,3)-beta-glucan synthesis. PUBMED:8289782 EPMC:8289782
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Zhang D, Iyer LM, Aravind L;, Nucleic Acids Res. 2011;39:4532-4552.: A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. PUBMED:21306995 EPMC:21306995
Internal database links
SCOOP: | SUKH_5 SUKH_6 |
Similarity to PfamA using HHSearch: | Syd SUKH_5 SUKH_6 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR018958
This domain is found in the yeast cell wall assembly regulator Smi1 (also known as Knr4) [PUBMED:7937796, PUBMED:8289782].
Saccharomyces cerevisiae Knr4 has a regulatory role in chitin deposition and in cell wall assembly [PUBMED:10206705]. It is believed to connect the PKC1-SLT2 MAPK pathway with cell proliferation. It has been shown to interact with Bck2, a gene involved in cell cycle progression in S. cerevisiae (forming a complex) to allow PKC1 to coordinate the cell cycle (cell proliferation) with cell wall integrity [PUBMED:12185498, PUBMED:12823808]. Knr4 also interacts with the tyrosine-tRNA synthetase protein encoded by Tys1 and is involved in sporulation process [PUBMED:11410349].
Proteins containing this domain also include the animal F-box only protein 3 (FBXO3). In humans, FBXO3 is a substrate recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex [PUBMED:18809579].
Interestingly, Smi1/Knr4 homologues from bacteria are potential immunity proteins in a subset of these contact-dependent inhibitory toxin systems [PUBMED:21306995].
Note: previously reported evidence that Knr4 may interact with nuclear matrix-association region [PUBMED:8516310] may be due to an artefact [PUBMED:10206705].
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 SUKH (CL0526), which has the following description:
SUKH superfamily unites a diverse group of proteins including Smi1/Knr4, PGs2, Fbxo3, Skip16, Syd, herpesviral US22, IRS1 and TRS1, and their bacterial homologs [1].
The clan contains the following 7 members:
SMI1_KNR4 SUKH-3 SUKH-4 SUKH_5 SUKH_6 Syd US22Alignments
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 (156) |
Full (3373) |
Representative proteomes | UniProt (13045) |
NCBI (34308) |
Meta (30) |
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RP15 (324) |
RP35 (1262) |
RP55 (3047) |
RP75 (5592) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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Seed (156) |
Full (3373) |
Representative proteomes | UniProt (13045) |
NCBI (34308) |
Meta (30) |
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RP15 (324) |
RP35 (1262) |
RP55 (3047) |
RP75 (5592) |
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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: | PSI2 target BIG_91 |
Previous IDs: | DUF1988; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 156 |
Number in full: | 3373 |
Average length of the domain: | 140.20 aa |
Average identity of full alignment: | 15 % |
Average coverage of the sequence by the domain: | 42.73 % |
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: | 133 | ||||||||||||
Family (HMM) version: | 11 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There is 1 interaction for this family. More...
SMI1_KNR4Structures
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 SMI1_KNR4 domain has been found. There are 5 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 sequence.
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