Top Level Name

  ⌊ Superfamily (extended) Radical SAM Phosphonate Metabolism

Family known
Total 100% <100% Family unknown
Functional domains 1319 1207 52 60
UniProtKB 4320 4226 51 43
GI 7827 7639 102 86
Structures 1
Reactions 0
Functional domains of this superfamily were last updated on June 10, 2017
New functional domains were last added to this superfamily on Dec. 18, 2014

This superfamily performs the demethylation and cyclisation of a phosphine and contains a non-canonical Radical SAM Superfamily binding motif for a unique [4Fe-4S] cluster and has an absolute requirement for the pressence of this cluster and SAM. However, despite its conceptual similarity to the main RSS superfamily, it shares no sequence similarity with other members of that superfamily. It consists of several bacterial phosphonate metabolism (PhnJ) sequences and to date, the PhnJ family is the only family identified in the superfamily.

Kamat SS, Williams HJ, Raushel FM

Intermediates in the transformation of phosphonates to phosphate by bacteria

▸ Abstract

Nature 2011;480(7378):570-573 | PubMed ID: 22089136

Ghodge SV, Cummings JA, Williams HJ, Raushel FM

Discovery of a cyclic phosphodiesterase that catalyzes the sequential hydrolysis of both ester bonds to phosphorus

▸ Abstract

J Am Chem Soc 2013;135(44):16360-16363 | PubMed ID: 24147537

MSA based on EFD for family & SG


[4Fe-4S]+ Cluster (complex)

S-Adenosylmethionine (coenzyme)

Sequence Similarity Networks

Download a Sequence Similarity Network of this superfamily (XGMML format ).

Network downloads are XGMML files that are readable by program such as Cytoscape. In these networks, nodes represent proteins and edges represent pairwise similarities better than a given edge-score cutoff. The edge score is either a bit score for full networks or mean E values for a Repnet. Additionally, these networks contain several attributes with data from the SFLD.

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List of files included in the download. A detailed list of included node attributes, their definitions, and their uses [revised: 1/24/2014].

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Multiple Sequence Alignment

View the alignment of a representative set of sequences of this superfamily using

Multiple Sequence Alignment

Align one or multiple sequences to the alignment of a representative set of sequences of this superfamily.
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Data Type All (#) Known (#) Unknown (#)
Full length FASTA (1319) (1259) (60)
Complete annotation (.tsv) (1319) (1259) (60)
Annotation suitable for Excel ® (.tsv) (1319) (1259) (60)
Clear form

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Cutoff Value
The least significant edge-score at which pairwise similarities are included in the network. A bit score for the full network, or a mean E value for the Repnet.
XGMML format
Open in Cytoscape via:
 →Network (multiple file types)
Download the annotation of all sequences as shown in the table below as a ͟Tab ͟Separated ͟Value (TSV) file. This file can be imported into a spreadsheet application.
Full length FASTA
Full length sequences in FASTA format.
Functional Domain FASTA
Sequences of the Functional Domain in FASTA format.
Complete annotation
Download complete annotation of sequences sets of this superfamily as a ͟Tab ͟Separated ͟Value (TSV) file. This file has all data but cell size can exceed the maximum supported by spreadsheet programs (such as Microsoft Excel ®).
Spreadsheet ready annotation
Annotation of sequences sets of this superfamily in a ͟Tab ͟Separated ͟Value (TSV) file. This file can be imported into a spreadsheet application. Cells which exceed the allowed spreadsheet maximum (32.5K) are preceded by the word "Truncated" and clipped short.
Total number of functional domains in this group.
Number of Functional Domains that have been manually or automatically been assigned to a family.
Number of Functional Domains that have not been assigned to a family.
Number of structures available from the PDB for members of this group.
Number of Functional Domains with 100% of Conserved Residues
Number of Functional Domains with less than 100% Conserved Residues
Subgroup ▸ Legend T K C U S
Phosphonate metabolism (PhnJ) 1259 1259 1207 0 1
┗ Phosphonate metabolism (PhnJ) 1259 1259 1207 0
Depth of the multi-level Subgroup hierarchy.