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17  structures 2276  species 0  interactions 4195  sequences 68  architectures

Family: SMI1_KNR4 (PF09346)

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

  1. 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

  2. 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

  3. 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

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:



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 and the UniProtKB 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.

Representative proteomes UniProt
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Representative proteomes UniProt

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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...


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: PSI2 target BIG_91
Previous IDs: DUF1988;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 154
Number in full: 4195
Average length of the domain: 139.2 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 42.36 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.4 25.4
Trusted cut-off 25.4 25.4
Noise cut-off 25.3 25.3
Model length: 133
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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The tree shows the occurrence of this domain across different species. More...


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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 17 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0D2ENR0 View 3D Structure Click here
A0A175VQE2 View 3D Structure Click here
A0A1C1CQ98 View 3D Structure Click here
A0A1D8PE53 View 3D Structure Click here
A0A1D8PK79 View 3D Structure Click here
A0A3Q0KQG2 View 3D Structure Click here
A0A5K4ES52 View 3D Structure Click here
A0A5K4ESE5 View 3D Structure Click here
A0A5K4EU38 View 3D Structure Click here
A6H7H7 View 3D Structure Click here
C0NE61 View 3D Structure Click here
C1H9D2 View 3D Structure Click here
D4ABP9 View 3D Structure Click here
E0SIS1 View 3D Structure Click here
F1R287 View 3D Structure Click here
K0EX85 View 3D Structure Click here
O14362 View 3D Structure Click here
O31997 View 3D Structure Click here
O31999 View 3D Structure Click here
O34377 View 3D Structure Click here
P32566 View 3D Structure Click here
P38678 View 3D Structure Click here
Q6BJY4 View 3D Structure Click here
Q6BW41 View 3D Structure Click here
Q6CDX0 View 3D Structure Click here
Q6CN28 View 3D Structure Click here
Q6FL35 View 3D Structure Click here
Q75AQ9 View 3D Structure Click here
Q9DC63 View 3D Structure Click here
Q9I5W6 View 3D Structure Click here
Q9LND7 View 3D Structure Click here
Q9UK99 View 3D Structure Click here
U7PJA9 View 3D Structure Click here
X8F794 View 3D Structure Click here