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7653  structures 9472  species 0  interactions 677371  sequences 4114  architectures

Clan: TIM_barrel (CL0036)


Common phosphate binding-site TIM barrel superfamily Add an annotation

This large superfamily of TIM barrel enzymes all contain a common phosphate binding site. The phosphate is found in a variety of cofactors and ligands such as FMN [1,2].

This clan contains 61 families and the total number of domains in the clan is 677371. The clan was built by A Bateman.

Literature references

  1. Copley RR, Bork P; , J Mol Biol 2000;303:627-641.: Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways. PUBMED:11054297 EPMC:11054297
  2. Bork P, Gellerich J, Groth H, Hooft R, Martin F; , Protein Sci 1995;4:268-274.: Divergent evolution of a beta/alpha-barrel subclass: detection of numerous phosphate-binding sites by motif search. PUBMED:7757015 EPMC:7757015


This clan contains the following 61 member families:

4HFCP_synth Ala_racemase_N ALAD Aldolase AP_endonuc_2 BtpA CdhD ComA CutC DAHP_synth_1 DAHP_synth_2 DeoC DHDPS DHO_dh DHquinase_I DUF2090 DUF4862 DUF561 DUF692 DUF993 Dus F_bP_aldolase FMN_dh G3P_antiterm GatZ_KbaZ-like Glu_syn_central Glu_synthase His_biosynth HMGL-like IGPS IMPDH KDGP_aldolase Lys-AminoMut_A MtrH NanE NAPRTase NeuB NMO OAM_alpha OMPdecase Orn_Arg_deC_N Oxidored_FMN PcrB PdxJ PRAI PRMT5_TIM Pterin_bind QRPTase_C Radical_SAM Radical_SAM_2 RhaA Ribul_P_3_epim SOR_SNZ TAL_FSA ThiC_Rad_SAM ThiG TIM TMP-TENI Trp_syntA UvdE UxuA

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
Radical_SAM (PF04055) 134611 (19.9%) View
AP_endonuc_2 (PF01261) 45618 (6.7%) View
HMGL-like (PF00682) 33428 (4.9%) View
Oxidored_FMN (PF00724) 29326 (4.3%) View
DHDPS (PF00701) 25699 (3.8%) View
Ala_racemase_N (PF01168) 25691 (3.8%) View
Dus (PF01207) 20619 (3.0%) View
Orn_Arg_deC_N (PF02784) 19587 (2.9%) View
NMO (PF03060) 19058 (2.8%) View
His_biosynth (PF00977) 18102 (2.7%) View
FMN_dh (PF01070) 18001 (2.7%) View
Pterin_bind (PF00809) 17866 (2.6%) View
IMPDH (PF00478) 16983 (2.5%) View
DAHP_synth_1 (PF00793) 14572 (2.2%) View
DHO_dh (PF01180) 14239 (2.1%) View
Glu_synthase (PF01645) 13387 (2.0%) View
TIM (PF00121) 12345 (1.8%) View
F_bP_aldolase (PF01116) 12245 (1.8%) View
TAL_FSA (PF00923) 11953 (1.8%) View
Ribul_P_3_epim (PF00834) 11627 (1.7%) View
OMPdecase (PF00215) 11385 (1.7%) View
TMP-TENI (PF02581) 11283 (1.7%) View
DeoC (PF01791) 11095 (1.6%) View
Trp_syntA (PF00290) 9166 (1.4%) View
ALAD (PF00490) 9123 (1.3%) View
IGPS (PF00218) 8837 (1.3%) View
QRPTase_C (PF01729) 8777 (1.3%) View
Glu_syn_central (PF04898) 8501 (1.3%) View
Aldolase (PF01081) 8430 (1.2%) View
NAPRTase (PF04095) 7684 (1.1%) View
PRAI (PF00697) 7543 (1.1%) View
Pfam family Num. domains Alignment
DAHP_synth_2 (PF01474) 5743 (0.8%) View
ThiC_Rad_SAM (PF01964) 5545 (0.8%) View
ThiG (PF05690) 5129 (0.8%) View
SOR_SNZ (PF01680) 4493 (0.7%) View
DHquinase_I (PF01487) 4257 (0.6%) View
PdxJ (PF03740) 4181 (0.6%) View
NeuB (PF03102) 4001 (0.6%) View
CutC (PF03932) 3971 (0.6%) View
UxuA (PF03786) 3251 (0.5%) View
DUF692 (PF05114) 2720 (0.4%) View
PRMT5_TIM (PF17285) 2010 (0.3%) View
UvdE (PF03851) 1691 (0.2%) View
NanE (PF04131) 1505 (0.2%) View
ComA (PF02679) 1301 (0.2%) View
BtpA (PF03437) 1293 (0.2%) View
PcrB (PF01884) 1254 (0.2%) View
G3P_antiterm (PF04309) 1204 (0.2%) View
DUF993 (PF06187) 1072 (0.2%) View
Radical_SAM_2 (PF19238) 918 (0.1%) View
RhaA (PF06134) 776 (0.1%) View
DUF2090 (PF09863) 739 (0.1%) View
CdhD (PF03599) 694 (0.1%) View
GatZ_KbaZ-like (PF08013) 652 (0.1%) View
Lys-AminoMut_A (PF09043) 585 (0.1%) View
4HFCP_synth (PF04476) 464 (0.1%) View
DUF561 (PF04481) 383 (0.1%) View
KDGP_aldolase (PF07071) 331 (0.0%) View
OAM_alpha (PF16552) 145 (0.0%) View
MtrH (PF02007) 142 (0.0%) View
DUF4862 (PF16154) 140 (0.0%) View
Total: 61 Total: 677371
No alignment ℹ

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.

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