Summary: Second Messenger Oligonucleotide or Dinucleotide Synthetase domain
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Second Messenger Oligonucleotide or Dinucleotide Synthetase domain Provide feedback
Nucleotide synthetase enzyme of the DNA polymerase beta superfamily. Experimental studies have demonstrated cGAMP synthetase activity in the Vibrio cholerae DncV protein, a member of the SMODS family. The diversity inherent to the SMODS family suggests members of the family could generate a range of nucleotides, cyclic and/or linear. The nucleotide second messengers generated by the SMODS domains are predicted to activate effectors in a class of conflict systems reliant on the production and sensing of the nucleotide second messengers [1] [2].
Literature references
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Burroughs AM, Zhang D, Schaffer DE, Iyer LM, Aravind L;, Nucleic Acids Res. 2015;43:10633-10654.: Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. PUBMED:26590262 EPMC:26590262
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Davies BW, Bogard RW, Young TS, Mekalanos JJ;, Cell. 2012;149:358-370.: Coordinated regulation of accessory genetic elements produces cyclic di-nucleotides for V. cholerae virulence. PUBMED:22500802 EPMC:22500802
Internal database links
SCOOP: | NTP_transf_2 Polbeta |
Similarity to PfamA using HHSearch: | NTP_transf_2 |
This tab holds annotation information from the InterPro database.
No InterPro data for this Pfam family.
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 NTP_transf (CL0260), which has the following description:
This clan contains a diverse set of nucleotidyltransferase enzymes.
The clan contains the following 31 members:
AbiEii Adenyl_cycl_N Adenyl_transf Aminoglyc_resit DNA_pol3_alpha DNA_pol_B_palm DUF2204 DUF294 DUF4269 DZF GlnE GrpB LicD MdcG Nrap Nrap_D4 NTF-like NTP_transf_2 NTP_transf_5 NTP_transf_6 NTP_transf_7 NTP_transf_8 Polbeta PolyA_pol Pox_polyA_pol RelA_SpoT RlaP RsfS SMODS Tam41_Mmp37 TUTaseAlignments
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 (34) |
Full (766) |
Representative proteomes | UniProt (3754) |
NCBI (5890) |
Meta (29) |
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RP15 (86) |
RP35 (339) |
RP55 (763) |
RP75 (1438) |
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Jalview | |||||||||
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
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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 (34) |
Full (766) |
Representative proteomes | UniProt (3754) |
NCBI (5890) |
Meta (29) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (86) |
RP35 (339) |
RP55 (763) |
RP75 (1438) |
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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: | Laks |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Iyer LM |
Number in seed: | 34 |
Number in full: | 766 |
Average length of the domain: | 157.50 aa |
Average identity of full alignment: | 17 % |
Average coverage of the sequence by the domain: | 44.19 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 164 | ||||||||||||
Family (HMM) version: | 2 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Selections
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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...
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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 SMODS 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.
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