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10  structures 745  species 0  interactions 769  sequences 2  architectures

Family: KicB (PF03882)

Summary: KicB killing factor

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

KicB killing factor Provide feedback

The kicA and kicB genes are found upstream of mukB. It has been suggested that the kicB gene encodes a killing factor and the kicA gene codes for a protein that suppresses the killing function of the kicB gene product [1]. It was also demonstrated that KicA and KicB can function as a post-segregational killing system, when the genes are transferred from the E. coli chromosome onto a plasmid [1].

Literature references

  1. Feng J, Yamanaka K, Niki H, Ogura T, Hiraga S; , Mol Gen Genet 1994;243:136-147.: New killing system controlled by two genes located immediately upstream of the mukB gene in Escherichia coli. PUBMED:7513784 EPMC:7513784


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005582

This family contains MukF, which are proteins involved in chromosome condensation, segregation and cell cycle progression. MukE (INTERPRO) along with MukF interact with MukB (INTERPRO) in vivo forming a complex, which is required for chromosome condensation and segregation in Escherichia coli [PUBMED:10545099]. The Muk complex appears to be similar to the SMC-ScpA-ScpB complex in other prokaryotes where MukB is the homologue of SMC [PUBMED:12065423]. ScpA (INTERPRO) and ScpB (INTERPRO) have little sequence similarity to MukE or MukF, though they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 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
(3)
Full
(769)
Representative proteomes NCBI
(342)
Meta
(4)
RP15
(8)
RP35
(23)
RP55
(49)
RP75
(73)
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Format an alignment

  Seed
(3)
Full
(769)
Representative proteomes NCBI
(342)
Meta
(4)
RP15
(8)
RP35
(23)
RP55
(49)
RP75
(73)
Alignment:
Format:
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Sequence:
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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
(3)
Full
(769)
Representative proteomes NCBI
(342)
Meta
(4)
RP15
(8)
RP35
(23)
RP55
(49)
RP75
(73)
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.

Pfam alignments:

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: COG3006
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 3
Number in full: 769
Average length of the domain: 428.70 aa
Average identity of full alignment: 78 %
Average coverage of the sequence by the domain: 99.75 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.0 20.0
Trusted cut-off 20.3 21.2
Noise cut-off 18.0 19.9
Model length: 440
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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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 KicB domain has been found. There are 10 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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