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0  structures 94  species 0  interactions 294  sequences 1  architecture

Family: RebB (PF11747)

Summary: Killing trait

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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.

Killing trait Provide feedback

RebB is one of three proteins necessary for the production of R- bodies, refractile inclusion bodies produced by a small number of bacterial species, essential for the expression of the killing trait of the endosymbiont bacteria that produce them for attack upon the host Paramecium. R-bodies are highly insoluble protein ribbons which coil into cylindrical structures in the cell and the genes for their synthesis and assembly are encoded on a plasmid. One of these three proteins is RebB.

Literature references

  1. Heruth DP, Pond FR, Dilts JA, Quackenbush RL; , J Bacteriol. 1994;176:3559-3567.: Characterization of genetic determinants for R body synthesis and assembly in Caedibacter taeniospiralis 47 and 116. PUBMED:8206833 EPMC:8206833

  2. Jeblick J, Kusch J; , J Mol Evol. 2005;60:164-173.: Sequence, transcription activity, and evolutionary origin of the R-body coding plasmid pKAP298 from the intracellular parasitic bacterium Caedibacter taeniospiralis. PUBMED:15785846 EPMC:15785846


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR021070

R-bodies are highly insoluble protein ribbons which coil into cylindrical structures in the cell and the genes for their synthesis and assembly are encoded on a plasmid. One of these three proteins is RebB, which this entry represents.

RebB is one of three proteins necessary for the production of R- bodies, refractile inclusion bodies produced by a small number of bacterial species, essential for the expression of the killing trait of the endosymbiont bacteria that produce them for attack upon the host Paramecium. Note that many members are uncharacterised proteins [PUBMED:8206833, PUBMED:15785846].

Domain organisation

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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...

View options

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
(32)
Full
(294)
Representative proteomes NCBI
(256)
Meta
(12)
RP15
(31)
RP35
(51)
RP55
(92)
RP75
(104)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(32)
Full
(294)
Representative proteomes NCBI
(256)
Meta
(12)
RP15
(31)
RP35
(51)
RP55
(92)
RP75
(104)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

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
(32)
Full
(294)
Representative proteomes NCBI
(256)
Meta
(12)
RP15
(31)
RP35
(51)
RP55
(92)
RP75
(104)
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: Pfam-B_983 (release 23.0)
Previous IDs: none
Type: Family
Author: Mistry J, Coggill P
Number in seed: 32
Number in full: 294
Average length of the domain: 66.90 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 67.18 %

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 18.8 18.8
Trusted cut-off 19.5 20.7
Noise cut-off 16.4 17.8
Model length: 69
Family (HMM) version: 3
Download: download the raw HMM for this family

Species distribution

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