Summary: Nucleotidyl transferase AbiEii toxin, Type IV TA system
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.
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.
Nucleotidyl transferase AbiEii toxin, Type IV TA system Provide feedback
This family was recently identified as belonging to the nucleotidyltransferase superfamily [1]. AbiEii is the cognate toxin of the type IV toxin-antitoxin 'innate immunity' bacterial abortive infection (Abi) system that protects bacteria from the spread of a phage infection. The Abi system is activated upon infection with phage to abort the cell thus preventing the spread of phage through viral replication. There are some 20 or more Abis, and they are predominantly plasmid-encoded lactococcal systems. TA, toxin-antitoxin, systems on plasmids function by killing cells that lose the plasmid upon division. AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea. The cognate antitoxin is PF13338 [2].
Literature references
-
Kuchta K, Knizewski L, Wyrwicz LS, Rychlewski L, Ginalski K;, Nucleic Acids Res. 2009; [Epub ahead of print]: Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human. PUBMED:19833706 EPMC:19833706
-
Dy RL, Przybilski R, Semeijn K, Salmond GP, Fineran PC;, Nucleic Acids Res. 2014;42:4590-4605.: A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. PUBMED:24465005 EPMC:24465005
Internal database links
SCOOP: | DUF2204 NTP_transf_5 |
Similarity to PfamA using HHSearch: | DUF2204 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR014942
This family was recently identified as belonging to the nucleotidyltransferase superfamily [PUBMED:19833706]. AbiEii is the cognate toxin of the type IV toxin-antitoxin 'innate immunity' bacterial abortive infection (Abi) system that protects bacteria from the spread of a phage infection. The Abi system is activated upon infection with phage to abort the cell thus preventing the spread of phage through viral replication. There are some 20 or more Abis, and they are predominantly plasmid-encoded lactococcal systems. TA, toxin-antitoxin, systems on plasmids function by killing cells that lose the plasmid upon division. AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea. The cognate antitoxin is INTERPRO [PUBMED:24465005].
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
Loading domain graphics...
Pfam Clan
This family is a member of clan NTP_transf (CL0260), which has the following description:
This clan contains a diverse set of nucleotidyltransferase enzymes.
The clan contains the following 26 members:
AbiEii Adenyl_cycl_N Adenyl_transf Aminoglyc_resit DNA_pol3_alpha DNA_pol_B_palm DUF2204 DUF294 DZF GlnE GrpB LicD MdcG Mmp37 Nrap Nrap_D4 NTP_transf_2 NTP_transf_5 NTP_transf_6 NTP_transf_7 NTP_transf_8 Nuc-transf PolyA_pol Pox_polyA_pol RelA_SpoT RsfSAlignments
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, the UniProtKB sequence database, 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 (170) |
Full (3028) |
Representative proteomes | UniProt (7787) |
NCBI (14588) |
Meta (232) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (782) |
RP35 (1885) |
RP55 (3100) |
RP75 (4552) |
||||||
Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
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 (170) |
Full (3028) |
Representative proteomes | UniProt (7787) |
NCBI (14588) |
Meta (232) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (782) |
RP35 (1885) |
RP55 (3100) |
RP75 (4552) |
||||||
Raw Stockholm | |||||||||
Gzipped |
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...
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
Seed source: | PSI2 target CAD86002.1 |
Previous IDs: | DUF1814; |
Type: | Domain |
Author: | Bateman A |
Number in seed: | 170 |
Number in full: | 3028 |
Average length of the domain: | 209.90 aa |
Average identity of full alignment: | 14 % |
Average coverage of the sequence by the domain: | 82.25 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|
||||||||||||
Model details: |
|
||||||||||||
Model length: | 239 | ||||||||||||
Family (HMM) version: | 10 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
Sunburst controls
HideWeight segments by...
Change the size of the sunburst
Colour assignments
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
Selections
Align selected sequences to HMM
Generate a FASTA-format file
Clear selection
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...
Tree controls
HideThe tree shows the occurrence of this domain across different species. More...
Loading...
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
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 AbiEii 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 sequence.
Loading structure mapping...