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3  structures 2907  species 1  interaction 5598  sequences 51  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


External 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 and the cell proliferation protein KNR4 [PUBMED:7937796, PUBMED:8289782].

Saccharomyces cerevisiae protein Smi1 has a regulatory role in chitin deposition and in cell wall assembly [PUBMED:10206705].

KNR4 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].

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 US22

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...

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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
(177)
Full
(5598)
Representative proteomes NCBI
(6223)
Meta
(33)
RP15
(183)
RP35
(456)
RP55
(734)
RP75
(999)
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  Seed
(177)
Full
(5598)
Representative proteomes NCBI
(6223)
Meta
(33)
RP15
(183)
RP35
(456)
RP55
(734)
RP75
(999)
Alignment:
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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
(177)
Full
(5598)
Representative proteomes NCBI
(6223)
Meta
(33)
RP15
(183)
RP35
(456)
RP55
(734)
RP75
(999)
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: PSI2 target BIG_91
Previous IDs: DUF1988;
Type: Domain
Author: Bateman A
Number in seed: 177
Number in full: 5598
Average length of the domain: 130.90 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 58.34 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.0 24.0
Trusted cut-off 24.0 24.0
Noise cut-off 23.9 23.9
Model length: 133
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

There is 1 interaction for this family. More...

SMI1_KNR4

Structures

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 3 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 seqence.

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