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5047  structures 26738  species 128  interactions 1335500  sequences 1890  architectures

Clan: TIM_barrel (CL0036)

Summary

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 57 families and the total number of domains in the clan is 1335500. 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

Members

This clan contains the following 57 member families:

Ala_racemase_N ALAD Aldolase AP_endonuc_2 BtpA CdhD CutC DAHP_synth_1 DAHP_synth_2 DeoC DHDPS DHO_dh DHquinase_I DUF1341 DUF2090 DUF556 DUF561 DUF692 DUF993 Dus F_bP_aldolase FMN_dh G3P_antiterm Glu_syn_central Glu_synthase His_biosynth HMGL-like IGPS IMPDH Lys-AminoMut_A MtrH NanE NAPRTase NeuB NMO OAM_alpha OMPdecase Orn_Arg_deC_N Oxidored_FMN PcrB PdxJ PRAI Pterin_bind QRPTase_C Radical_SAM RhaA Ribul_P_3_epim SOR_SNZ Tagatose_6_P_K ThiC_Rad_SAM ThiG TIM TMP-TENI Transaldolase 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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Alignments

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

Pfam family Num. domains Alignment
Radical_SAM (PF04055) 270437 (20.2%) View
AP_endonuc_2 (PF01261) 65264 (4.9%) View
Ala_racemase_N (PF01168) 62545 (4.7%) View
HMGL-like (PF00682) 53468 (4.0%) View
Oxidored_FMN (PF00724) 47000 (3.5%) View
DHDPS (PF00701) 43629 (3.3%) View
DeoC (PF01791) 39951 (3.0%) View
Orn_Arg_deC_N (PF02784) 37159 (2.8%) View
Dus (PF01207) 36634 (2.7%) View
DAHP_synth_1 (PF00793) 35716 (2.7%) View
IMPDH (PF00478) 35674 (2.7%) View
Pterin_bind (PF00809) 34202 (2.6%) View
F_bP_aldolase (PF01116) 34056 (2.6%) View
His_biosynth (PF00977) 34008 (2.5%) View
OMPdecase (PF00215) 32415 (2.4%) View
NMO (PF03060) 31428 (2.4%) View
Transaldolase (PF00923) 29985 (2.2%) View
FMN_dh (PF01070) 27791 (2.1%) View
DHO_dh (PF01180) 26772 (2.0%) View
Ribul_P_3_epim (PF00834) 25537 (1.9%) View
TIM (PF00121) 24559 (1.8%) View
Glu_synthase (PF01645) 24519 (1.8%) View
TMP-TENI (PF02581) 22546 (1.7%) View
NAPRTase (PF04095) 18868 (1.4%) View
IGPS (PF00218) 18446 (1.4%) View
Trp_syntA (PF00290) 17382 (1.3%) View
ALAD (PF00490) 16815 (1.3%) View
Aldolase (PF01081) 16186 (1.2%) View
Glu_syn_central (PF04898) 16085 (1.2%) View
continued
Pfam family Num. domains Alignment
QRPTase_C (PF01729) 15492 (1.2%) View
PRAI (PF00697) 15144 (1.1%) View
NanE (PF04131) 12240 (0.9%) View
DHquinase_I (PF01487) 12240 (0.9%) View
ThiG (PF05690) 10853 (0.8%) View
ThiC_Rad_SAM (PF01964) 10826 (0.8%) View
SOR_SNZ (PF01680) 9149 (0.7%) View
CutC (PF03932) 7926 (0.6%) View
PdxJ (PF03740) 7909 (0.6%) View
G3P_antiterm (PF04309) 7377 (0.6%) View
UxuA (PF03786) 6813 (0.5%) View
Tagatose_6_P_K (PF08013) 5909 (0.4%) View
DAHP_synth_2 (PF01474) 5763 (0.4%) View
PcrB (PF01884) 5243 (0.4%) View
NeuB (PF03102) 4356 (0.3%) View
RhaA (PF06134) 4245 (0.3%) View
DUF1341 (PF07071) 3783 (0.3%) View
BtpA (PF03437) 2514 (0.2%) View
DUF692 (PF05114) 2502 (0.2%) View
DUF2090 (PF09863) 1680 (0.1%) View
UvdE (PF03851) 1169 (0.1%) View
CdhD (PF03599) 1007 (0.1%) View
DUF993 (PF06187) 696 (0.1%) View
Lys-AminoMut_A (PF09043) 601 (0.0%) View
OAM_alpha (PF16552) 400 (0.0%) View
DUF556 (PF04476) 228 (0.0%) View
DUF561 (PF04481) 210 (0.0%) View
MtrH (PF02007) 148 (0.0%) View
Total: 57 Total: 1335500 Clan alignment
 

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Family relationships

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

We could not retrieve a family relationship diagram for this clan.

Species distribution

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

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Interactions

There are 128 interactions for this clan. More...

Interacting families
A B
AcetDehyd-dimer HMGL-like
Ala_racemase_C Ala_racemase_N
Ala_racemase_N Ala_racemase_C
Ala_racemase_N
D-ser_dehydrat
ALAD ALAD
Aldolase Aldolase
AP_endonuc_2 AP_endonuc_2
AP_endonuc_2_N
AP_endonuc_2_N AP_endonuc_2
B12-binding Lys-AminoMut_A
Biotin_lipoyl HMGL-like
CdhD CdhD
CutC CutC
Cyt-b5 FMN_dh
D-ser_dehydrat Ala_racemase_N
DAHP_synth_1 DAHP_synth_1
DAHP_synth_2 CM_2
DAHP_synth_2
DeoC DeoC
DHDPS DHDPS
DHO_dh DHO_dh
DHODB_Fe-S_bind
FAD_binding_6
Fer4_20
Fer4_21
NAD_binding_8
DHquinase_I DHquinase_I
Shikimate_dh_N
DmpG_comm HMGL-like
DUF1341 DUF1341
Dus Dus
F_bP_aldolase F_bP_aldolase
Fer4_12 Radical_SAM
Fer4_20 DHO_dh
Fer4_21 DHO_dh
FeS CdhD
FMN_dh Cyt-b5
FMN_dh
G3P_antiterm G3P_antiterm
GATase His_biosynth
GATase_2 Glu_syn_central
Glu_synthase
Glu_syn_central Fer4_20
GATase_2
Glu_synthase
GXGXG
Glu_synthase Fer4_20
GATase_2
GXGXG
GXGXG Glu_syn_central
Glu_synthase
His_biosynth GATase
His_biosynth
HMGL-like AcetDehyd-dimer
Biotin_lipoyl
DmpG_comm
HMGL-like
PYC_OADA
Semialdhyde_dh
HPPK Pterin_bind
IGPS IGPS
PRAI
IMPDH CBS
IMPDH
LAM_C Radical_SAM
LeuA_dimer HMGL-like
Lys-AminoMut_A B12-binding
Lys-AminoMut_A
MHC_II_alpha TIM
MHC_II_beta TIM
NanE NanE
NAPRTase NAPRTase
NeuB NeuB
SAF
NMO NMO
OMPdecase OMPdecase
Pribosyltran
Orn_Arg_deC_N Orn_Arg_deC_N
Orn_DAP_Arg_deC
Orn_DAP_Arg_deC Orn_Arg_deC_N
Oxidored_FMN NAD_binding_8
Oxidored_FMN
Pyr_redox_2
PALP Trp_syntA
PcrB PcrB
PdxJ PdxJ
PRAI PRAI
Pterin_bind CdhD
FeS
Pterin_bind
PYC_OADA HMGL-like
Pyr_redox_2 Oxidored_FMN
QRPTase_C QRPTase_C
QRPTase_N
QRPTase_N QRPTase_C
Radical_SAM BATS
Fer4_12
Fer4_14
LAM_C
Mob_synth_C
Radical_SAM
SPASM
Wyosine_form
Response_reg His_biosynth
RhaA RhaA
Ribul_P_3_epim Ribul_P_3_epim
S-methyl_trans Pterin_bind
SAF NeuB
Semialdhyde_dh HMGL-like
SOR_SNZ SNO
SOR_SNZ
ThiG
Tagatose_6_P_K Tagatose_6_P_K
ThiC-associated ThiC_Rad_SAM
ThiC_Rad_SAM ThiC_Rad_SAM
ThiG SOR_SNZ
ThiG
ThiS
ThiS ThiG
TIM TIM
TMP-TENI HK
TMP-TENI
Transaldolase Transaldolase
Trp_syntA PALP
Trp_syntA
UPF0004 Radical_SAM
UxuA UxuA

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 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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