Summary: Putative type VI secretion system Rhs element Vgr
Putative type VI secretion system Rhs element Vgr Provide feedback
This is a family of putative type VI secretion system Rhs element Vgr proteins from Proteobacteria.
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR028244
Rsh (rearrangement hot-spot) elements are repetitious sequences identified in certain Escherichia coli strains. These elements are genetic composites, each containing a Rhs core sequence that is conserved from one element to another. As reservoirs of sequence repetition, Rhs elements mediate major chromosomal rearrangements. Eight distinct Rhs elements have identified in E. coli strains [PUBMED:9696756, PUBMED:10673005].
This domain is found in putative type VI secretion system Rhs element-associated Vgr proteins from Proteobacteria.
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Loading domain graphics...
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Seed source:||Pfam-B_2052 (release 24.0)|
|Number in seed:||103|
|Number in full:||284|
|Average length of the domain:||106.40 aa|
|Average identity of full alignment:||38 %|
|Average coverage of the sequence by the domain:||12.22 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||3|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree