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497  structures 9051  species 0  interactions 66723  sequences 333  architectures

Clan: SPOUT (CL0098)


SPOUT Methyltransferase Superfamily Add an annotation

A distinct class of methylases that includes the SpoU and TrmD superfamilies and two superfamilies of predicted methylases defined by the YbeA and MJ0421 proteins in bacteria and archaea, respectively [1] (PFAM:PF00588 PFAM:PF01746). SPOUT is structurally distinct compared to more classical methyltransferases [1]. More specifically, the members of this clan form alpha/beta knots. Knots are extremely rare in protein structures as they pose a folding problem. The mechanism that allow a domain to be folded as a knot are unclear, but are discussed in [2] and reference therein. All members with known structure form homodimers.

This clan contains 14 families and the total number of domains in the clan is 66723. The clan was built by RD Finn.

Literature references

  1. Anantharaman V, Koonin EV, Aravind L;, J Mol Microbiol Biotechnol. 2002;4:71-75.: SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases. PUBMED:11763972 EPMC:11763972
  2. Lim K, Zhang H, Tempczyk A, Krajewski W, Bonander N, Toedt J, Howard A, Eisenstein E, Herzberg O; , Proteins 2003;51:56-67.: Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): a cofactor bound at a site formed by a knot. PUBMED:12596263 EPMC:12596263
  3. Tkaczuk KL, Dunin-Horkawicz S, Purta E, Bujnicki JM; , BMC Bioinformatics. 2007;8:73.: Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. PUBMED:17338813 EPMC:17338813


This clan contains the following 14 member families:

DUF2122 DUF531 EMG1 Methyltrans_RNA Methyltrn_RNA_2 Methyltrn_RNA_3 Methyltrn_RNA_4 RNA_Me_trans SpoU_methylas_C SpoU_methylase SPOUT_MTase SPOUT_MTase_2 Trm56 tRNA_m1G_MT

External database links

Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

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The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
SpoU_methylase (PF00588) 35228 (52.8%) View
tRNA_m1G_MT (PF01746) 10849 (16.3%) View
Methyltrans_RNA (PF04452) 8472 (12.7%) View
SPOUT_MTase (PF02590) 6122 (9.2%) View
EMG1 (PF03587) 2117 (3.2%) View
Methyltrn_RNA_3 (PF02598) 1751 (2.6%) View
RNA_Me_trans (PF04252) 814 (1.2%) View
SpoU_methylas_C (PF12105) 433 (0.6%) View
Methyltrn_RNA_4 (PF09936) 299 (0.4%) View
Trm56 (PF01994) 271 (0.4%) View
Methyltrn_RNA_2 (PF04013) 261 (0.4%) View
DUF2122 (PF09895) 46 (0.1%) View
DUF531 (PF04407) 35 (0.1%) View
SPOUT_MTase_2 (PF14419) 25 (0.0%) View
Total: 14 Total: 66723 Clan alignment

Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.

Family relationships

This diagram shows the relationships between members of this clan. More...

Species distribution

Tree controls


This tree shows the occurrence of the domains in this clan across different species. More...



For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

Loading structure mapping...