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0  structures 142  species 0  interactions 7120  sequences 111  architectures

Family: Methyltransf_29 (PF03141)

Summary: Putative S-adenosyl-L-methionine-dependent methyltransferase

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.

Putative S-adenosyl-L-methionine-dependent methyltransferase Provide feedback

This family is a putative S-adenosyl-L-methionine (SAM)-dependent methyltransferase [1,2].

Literature references

  1. Krupkova E, Immerzeel P, Pauly M, Schmulling T;, Plant J. 2007;50:735-750.: The TUMOROUS SHOOT DEVELOPMENT2 gene of Arabidopsis encoding a putative methyltransferase is required for cell adhesion and co-ordinated plant development. PUBMED:17461780 EPMC:17461780

  2. Gao P, Xin Z, Zheng ZL;, PLoS One. 2008;3:e1387.: The OSU1/QUA2/TSD2-encoded putative methyltransferase is a critical modulator of carbon and nitrogen nutrient balance response in Arabidopsis. PUBMED:18167546 EPMC:18167546


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004159

This is a family of putative S-adenosyl-L-methionine (SAM)-dependent methyltransferase [ PUBMED:17461780 , PUBMED:18167546 , PUBMED:17425712 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 NADP_Rossmann (CL0063), which has the following description:

A class of redox enzymes are two domain proteins. One domain, termed the catalytic domain, confers substrate specificity and the precise reaction of the enzyme. The other domain, which is common to this class of redox enzymes, is a Rossmann-fold domain. The Rossmann domain binds nicotinamide adenine dinucleotide (NAD+) and it is this cofactor that reversibly accepts a hydride ion, which is lost or gained by the substrate in the redox reaction. Rossmann domains have an alpha/beta fold, which has a central beta sheet, with approximately five alpha helices found surrounding the beta sheet.The strands forming the beta sheet are found in the following characteristic order 654123. The inter sheet crossover of the stands in the sheet form the NAD+ binding site [1]. In some more distantly relate Rossmann domains the NAD+ cofactor is replaced by the functionally similar cofactor FAD.

The clan contains the following 206 members:

2-Hacid_dh_C 3Beta_HSD 3HCDH_N 3HCDH_RFF adh_short adh_short_C2 ADH_zinc_N ADH_zinc_N_2 AdoHcyase_NAD AdoMet_MTase AlaDh_PNT_C Amino_oxidase ApbA AviRa B12-binding Bac_GDH Bin3 Bmt2 CbiJ CheR CMAS CmcI CoA_binding CoA_binding_2 CoA_binding_3 Cons_hypoth95 CoV_ExoN CoV_Methyltr_2 DAO DapB_N DFP DNA_methylase DOT1 DRE2_N DREV DUF1442 DUF1611_N DUF166 DUF1776 DUF2431 DUF268 DUF2855 DUF3410 DUF364 DUF43 DUF5129 DUF5130 DUF6094 DUF938 DXP_reductoisom DXPR_C Eco57I ELFV_dehydrog Eno-Rase_FAD_bd Eno-Rase_NADH_b Enoyl_reductase Epimerase F420_oxidored FAD_binding_2 FAD_binding_3 FAD_oxidored Fibrillarin FMO-like FmrO FtsJ fvmX7 G6PD_N GCD14 GDI GDP_Man_Dehyd GFO_IDH_MocA GIDA GidB GLF Glu_dehyd_C Glyco_hydro_4 Glyco_tran_WecG GMC_oxred_N Gp_dh_N GRAS GRDA HcgC HI0933_like HIM1 IlvN ISPD_C K_oxygenase KR LCM Ldh_1_N LpxI_N Lycopene_cycl Malic_M Mannitol_dh MCRA Met_10 Methyltr_RsmB-F Methyltr_RsmF_N Methyltrans_Mon Methyltrans_SAM Methyltransf_10 Methyltransf_11 Methyltransf_12 Methyltransf_14 Methyltransf_15 Methyltransf_16 Methyltransf_17 Methyltransf_18 Methyltransf_19 Methyltransf_2 Methyltransf_20 Methyltransf_21 Methyltransf_22 Methyltransf_23 Methyltransf_24 Methyltransf_25 Methyltransf_28 Methyltransf_29 Methyltransf_3 Methyltransf_30 Methyltransf_31 Methyltransf_32 Methyltransf_33 Methyltransf_34 Methyltransf_4 Methyltransf_5 Methyltransf_7 Methyltransf_8 Methyltransf_9 Methyltransf_PK MethyltransfD12 MetW Mg-por_mtran_C MOLO1 Mqo MT-A70 MTS Mur_ligase N2227 N6-adenineMlase N6_Mtase N6_N4_Mtase NAD_binding_10 NAD_binding_2 NAD_binding_3 NAD_binding_4 NAD_binding_5 NAD_binding_7 NAD_binding_8 NAD_binding_9 NAD_Gly3P_dh_N NAS NmrA NNMT_PNMT_TEMT NodS OCD_Mu_crystall Orbi_VP4 PALP PARP_regulatory PCMT PDH PglD_N Polysacc_syn_2C Polysacc_synt_2 Pox_MCEL Pox_mRNA-cap Prenylcys_lyase PrmA PRMT5 Pyr_redox Pyr_redox_2 Pyr_redox_3 Reovirus_L2 RmlD_sub_bind Rossmann-like rRNA_methylase RrnaAD Rsm22 RsmJ Sacchrp_dh_NADP SAM_MT SE Semialdhyde_dh Shikimate_DH Spermine_synth TehB THF_DHG_CYH_C Thi4 ThiF TPM_phosphatase TPMT TrkA_N TRM TRM13 TrmK tRNA_U5-meth_tr Trp_halogenase TylF Ubie_methyltran UDPG_MGDP_dh_N UPF0020 UPF0146 Urocanase V_cholerae_RfbT XdhC_C YjeF_N

Alignments

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 and the UniProtKB 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
(20)
Full
(7120)
Representative proteomes UniProt
(10408)
RP15
(719)
RP35
(3857)
RP55
(5938)
RP75
(7758)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(20)
Full
(7120)
Representative proteomes UniProt
(10408)
RP15
(719)
RP35
(3857)
RP55
(5938)
RP75
(7758)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(20)
Full
(7120)
Representative proteomes UniProt
(10408)
RP15
(719)
RP35
(3857)
RP55
(5938)
RP75
(7758)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

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 View help on the curation process

Seed source: Pfam-B_1462 (release 6.5)
Previous IDs: DUF248;
Type: Family
Sequence Ontology: SO:0100021
Author: Mifsud W , Moxon SJ , Eberhardt R
Number in seed: 20
Number in full: 7120
Average length of the domain: 375.20 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 72.77 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 19.4 19.4
Trusted cut-off 19.4 19.4
Noise cut-off 19.3 19.3
Model length: 506
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Selections

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0B4J368 View 3D Structure Click here
A0A0P0W7Y1 View 3D Structure Click here
A0A0P0WM31 View 3D Structure Click here
A0A0P0XWT2 View 3D Structure Click here
A0A0P0Y7H7 View 3D Structure Click here
A0A0P0Y7X0 View 3D Structure Click here
A0A0P0Y859 View 3D Structure Click here
A0A0R0E5W6 View 3D Structure Click here
A0A0R0EII6 View 3D Structure Click here
A0A0R0EQE5 View 3D Structure Click here
A0A0R0EXK4 View 3D Structure Click here
A0A0R0F382 View 3D Structure Click here
A0A0R0FSB1 View 3D Structure Click here
A0A0R0GAF9 View 3D Structure Click here
A0A0R0JUI2 View 3D Structure Click here
A0A0R0KK28 View 3D Structure Click here
A0A0R0L2G4 View 3D Structure Click here
A0A0R0L7B7 View 3D Structure Click here
A0A0R4J2J8 View 3D Structure Click here
A0A1D6E2F8 View 3D Structure Click here
A0A1D6E2G9 View 3D Structure Click here
A0A1D6EH77 View 3D Structure Click here
A0A1D6EZM8 View 3D Structure Click here
A0A1D6EZM8 View 3D Structure Click here
A0A1D6F6Z5 View 3D Structure Click here
A0A1D6F7C2 View 3D Structure Click here
A0A1D6F7C2 View 3D Structure Click here
A0A1D6FII9 View 3D Structure Click here
A0A1D6FLQ3 View 3D Structure Click here
A0A1D6FS92 View 3D Structure Click here
A0A1D6FS92 View 3D Structure Click here
A0A1D6G8I6 View 3D Structure Click here
A0A1D6G8I6 View 3D Structure Click here
A0A1D6G8I6 View 3D Structure Click here
A0A1D6G8J7 View 3D Structure Click here
A0A1D6GPI2 View 3D Structure Click here
A0A1D6GPI2 View 3D Structure Click here
A0A1D6HFU7 View 3D Structure Click here
A0A1D6HFU7 View 3D Structure Click here
A0A1D6HHK6 View 3D Structure Click here
A0A1D6I1S1 View 3D Structure Click here
A0A1D6I498 View 3D Structure Click here
A0A1D6IM64 View 3D Structure Click here
A0A1D6IXZ5 View 3D Structure Click here
A0A1D6K4G6 View 3D Structure Click here
A0A1D6K4H3 View 3D Structure Click here
A0A1D6K4M1 View 3D Structure Click here
A0A1D6K7I6 View 3D Structure Click here
A0A1D6K808 View 3D Structure Click here
A0A1D6K8X8 View 3D Structure Click here
A0A1D6KKH8 View 3D Structure Click here
A0A1D6KP52 View 3D Structure Click here
A0A1D6KR35 View 3D Structure Click here
A0A1D6KR35 View 3D Structure Click here
A0A1D6KZG1 View 3D Structure Click here
A0A1D6L6E0 View 3D Structure Click here
A0A1D6LN32 View 3D Structure Click here
A0A1D6LN32 View 3D Structure Click here
A0A1D6LPA5 View 3D Structure Click here
A0A1D6LPA5 View 3D Structure Click here
A0A1D6M6V7 View 3D Structure Click here
A0A1D6MEH0 View 3D Structure Click here
A0A1D6MEH1 View 3D Structure Click here
A0A1D6MYP6 View 3D Structure Click here
A0A1D6N4I3 View 3D Structure Click here
A0A1D6N5E4 View 3D Structure Click here
A0A1D6N787 View 3D Structure Click here
A0A1D6N811 View 3D Structure Click here
A0A1D6P7L0 View 3D Structure Click here
A0A1D6P7L0 View 3D Structure Click here
A0A1D6PRY9 View 3D Structure Click here
A0A1D6QEB9 View 3D Structure Click here
B4FW69 View 3D Structure Click here
B6U1Y2 View 3D Structure Click here
B9DFI7 View 3D Structure Click here
B9FDS3 View 3D Structure Click here
C0P6F6 View 3D Structure Click here
C0PBW1 View 3D Structure Click here
I1J3Y4 View 3D Structure Click here
I1J5Q3 View 3D Structure Click here
I1J8Q9 View 3D Structure Click here
I1JB59 View 3D Structure Click here
I1JCL0 View 3D Structure Click here
I1JE40 View 3D Structure Click here
I1JGD2 View 3D Structure Click here
I1JI17 View 3D Structure Click here
I1JIE7 View 3D Structure Click here
I1JKE2 View 3D Structure Click here
I1JT45 View 3D Structure Click here
I1JVD1 View 3D Structure Click here
I1JWV5 View 3D Structure Click here
I1JY06 View 3D Structure Click here
I1JZ02 View 3D Structure Click here
I1K108 View 3D Structure Click here
I1K510 View 3D Structure Click here
I1K9X5 View 3D Structure Click here
I1KAG4 View 3D Structure Click here
I1KBK8 View 3D Structure Click here
I1KCS6 View 3D Structure Click here
I1KIH2 View 3D Structure Click here
I1KIH5 View 3D Structure Click here
I1KMD4 View 3D Structure Click here
I1KNV8 View 3D Structure Click here
I1KPN9 View 3D Structure Click here
I1KRD3 View 3D Structure Click here
I1KXT4 View 3D Structure Click here
I1KZI1 View 3D Structure Click here
I1L555 View 3D Structure Click here
I1L6R1 View 3D Structure Click here
I1L7H1 View 3D Structure Click here
I1L8E8 View 3D Structure Click here
I1LHW9 View 3D Structure Click here
I1LMU2 View 3D Structure Click here
I1LVY0 View 3D Structure Click here
I1LXD0 View 3D Structure Click here
I1LYL9 View 3D Structure Click here
I1M7R2 View 3D Structure Click here
I1M832 View 3D Structure Click here
I1MA92 View 3D Structure Click here
I1MAU6 View 3D Structure Click here
I1MC57 View 3D Structure Click here
I1MFX9 View 3D Structure Click here
I1MMJ4 View 3D Structure Click here
I1MVC1 View 3D Structure Click here
I1MY18 View 3D Structure Click here
I1MZ96 View 3D Structure Click here
I1N5F1 View 3D Structure Click here
I1NGQ6 View 3D Structure Click here
K7K806 View 3D Structure Click here
K7KRU5 View 3D Structure Click here
K7LBC3 View 3D Structure Click here
K7LDX5 View 3D Structure Click here
K7LG88 View 3D Structure Click here
K7LK48 View 3D Structure Click here
K7LRL8 View 3D Structure Click here
K7MEY9 View 3D Structure Click here
K7MFQ7 View 3D Structure Click here
K7MFR0 View 3D Structure Click here
K7MIL2 View 3D Structure Click here
K7MPH7 View 3D Structure Click here
K7MRH9 View 3D Structure Click here
K7MU41 View 3D Structure Click here
K7TVN3 View 3D Structure Click here
K7TZA6 View 3D Structure Click here
K7UYE3 View 3D Structure Click here
K7VF17 View 3D Structure Click here
K7VSG7 View 3D Structure Click here
O22285 View 3D Structure Click here
O80844 View 3D Structure Click here
Q0IU48 View 3D Structure Click here
Q0JGW4 View 3D Structure Click here
Q0JH49 View 3D Structure Click here
Q0WT31 View 3D Structure Click here
Q10KL9 View 3D Structure Click here
Q2R1K9 View 3D Structure Click here
Q336Q2 View 3D Structure Click here
Q3EC77 View 3D Structure Click here
Q3EC77 View 3D Structure Click here
Q5QLT2 View 3D Structure Click here
Q5VRG9 View 3D Structure Click here
Q5Z5X8 View 3D Structure Click here
Q653G1 View 3D Structure Click here
Q65XH2 View 3D Structure Click here
Q6ATW5 View 3D Structure Click here
Q6EP94 View 3D Structure Click here
Q6EQ17 View 3D Structure Click here
Q6NPR7 View 3D Structure Click here
Q6Z692 View 3D Structure Click here
Q7XRW8 View 3D Structure Click here
Q7XU42 View 3D Structure Click here
Q84TJ0 View 3D Structure Click here
Q8GYW9 View 3D Structure Click here
Q8H118 View 3D Structure Click here
Q8H636 View 3D Structure Click here
Q8H8N4 View 3D Structure Click here
Q8L7V3 View 3D Structure Click here
Q8RWB7 View 3D Structure Click here
Q8VZV7 View 3D Structure Click here
Q93W95 View 3D Structure Click here
Q93YV7 View 3D Structure Click here
Q940J9 View 3D Structure Click here
Q941U5 View 3D Structure Click here
Q94EJ6 View 3D Structure Click here
Q94GX1 View 3D Structure Click here
Q94II3 View 3D Structure Click here
Q94KE1 View 3D Structure Click here
Q9AV02 View 3D Structure Click here
Q9C6S7 View 3D Structure Click here
Q9C884 View 3D Structure Click here
Q9C9Q8 View 3D Structure Click here
Q9FG39 View 3D Structure Click here
Q9FKS3 View 3D Structure Click here
Q9LK30 View 3D Structure Click here
Q9LN50 View 3D Structure Click here
Q9LYN3 View 3D Structure Click here
Q9LZA4 View 3D Structure Click here
Q9M144 View 3D Structure Click here
Q9MA52 View 3D Structure Click here
Q9SD39 View 3D Structure Click here
Q9SIZ3 View 3D Structure Click here
Q9SZX8 View 3D Structure Click here
Q9ZPH9 View 3D Structure Click here
Q9ZW75 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;