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1350  structures 4050  species 87  interactions 61721  sequences 5108  architectures

Clan: GBD (CL0202)

Summary

Galactose-binding domain-like superfamily Add an annotation

This large superfamily contains beta sandwich domains with a jelly roll topology. Many of these families are involved in carbohydrate recognition. Despite sharing little sequence similarity they do share a weak sequence motif, with a conserved bulge in the C-terminal beta sheet. The probable role of this bulge is in bending of the beta sheet that contains the bulge. This enables the curvature of the sheet forming the sugar binding site [1].

This clan contains 49 families and the total number of domains in the clan is 61721. The clan was built by A Bateman.

Literature references

  1. Murzin AG, Bateman A; , Proteins 1997;1:105-112.: Distant homology recognition using structural classification of proteins. PUBMED:9485501 EPMC:9485501

Members

This clan contains the following 49 member families:

7TMR-DISMED2 Allantoicase ANAPC10 Arabino_trans_C Bac_rhamnosid_N BcsB BetaGal_dom4_5 Calpain_III CBM-like CBM27 CBM60 CBM_11 CBM_15 CBM_17_28 CBM_26 CBM_35 CBM_4_9 CBM_6 CIA30 Clenterotox DUF4465 DUF4627 DUF5000 DUF5077 DUF642 Endotoxin_C Ephrin_lbd F5_F8_type_C FBA FlhE Glyco_hydro_2_N GxDLY Laminin_B Laminin_N Lipl32 Lyase_N Muskelin_N NPCBM P_proprotein PA-IL PAW PCMD PepX_C PINIT PITH PPC Sad1_UNC XRCC1_N YpM

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
F5_F8_type_C (PF00754) 11133 (18.0%) View
Glyco_hydro_2_N (PF02837) 6508 (10.5%) View
PepX_C (PF08530) 3430 (5.6%) View
Calpain_III (PF01067) 2788 (4.5%) View
P_proprotein (PF01483) 2721 (4.4%) View
Sad1_UNC (PF07738) 2690 (4.4%) View
CBM_4_9 (PF02018) 2393 (3.9%) View
Laminin_N (PF00055) 2350 (3.8%) View
Laminin_B (PF00052) 2204 (3.6%) View
BetaGal_dom4_5 (PF13364) 2074 (3.4%) View
CBM_6 (PF03422) 2019 (3.3%) View
Allantoicase (PF03561) 1861 (3.0%) View
PPC (PF04151) 1757 (2.8%) View
CIA30 (PF08547) 1713 (2.8%) View
PITH (PF06201) 1614 (2.6%) View
Bac_rhamnosid_N (PF08531) 1568 (2.5%) View
Ephrin_lbd (PF01404) 1482 (2.4%) View
ANAPC10 (PF03256) 1472 (2.4%) View
DUF642 (PF04862) 1247 (2.0%) View
7TMR-DISMED2 (PF07696) 1184 (1.9%) View
CBM-like (PF14683) 1118 (1.8%) View
PINIT (PF14324) 973 (1.6%) View
NPCBM (PF08305) 787 (1.3%) View
BcsB (PF03170) 592 (1.0%) View
CBM_35 (PF16990) 592 (1.0%) View
continued
Pfam family Num. domains Alignment
FBA (PF04300) 554 (0.9%) View
Arabino_trans_C (PF14896) 374 (0.6%) View
PCMD (PF13201) 349 (0.6%) View
Muskelin_N (PF06588) 318 (0.5%) View
XRCC1_N (PF01834) 300 (0.5%) View
PAW (PF04721) 249 (0.4%) View
CBM_11 (PF03425) 200 (0.3%) View
GxDLY (PF14607) 173 (0.3%) View
CBM60 (PF16841) 164 (0.3%) View
DUF4465 (PF14717) 130 (0.2%) View
DUF5077 (PF16871) 128 (0.2%) View
Lyase_N (PF09092) 115 (0.2%) View
FlhE (PF06366) 102 (0.2%) View
DUF5000 (PF16391) 101 (0.2%) View
CBM_26 (PF16824) 41 (0.1%) View
CBM27 (PF09212) 28 (0.0%) View
Lipl32 (PF12103) 26 (0.0%) View
CBM_17_28 (PF03424) 26 (0.0%) View
DUF4627 (PF15425) 25 (0.0%) View
PA-IL (PF07828) 19 (0.0%) View
Endotoxin_C (PF03944) 16 (0.0%) View
Clenterotox (PF03505) 10 (0.0%) View
CBM_15 (PF03426) 3 (0.0%) View
YpM (PF09144) 0 (0.0%) View
Total: 49 Total: 61721
No alignment ℹ
 

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Family relationships

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

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 87 interactions for this clan. More...

Interacting families
A B
7TMR-DISMED2 7TMR-DISMED2
Allantoicase Allantoicase
Alpha_L_fucos F5_F8_type_C
ANAPC10 ANAPC10
Bac_rhamnosid Bac_rhamnosid_N
Bac_rhamnosid_N Bac_rhamnosid
Bac_rhamnosid_N
BetaGal_dom4_5 BetaGal_dom4_5
Bgal_small_N Glyco_hydro_2_N
Calpain_III Calpain_inhib
EF-hand_8
CBM-like RhgB_N
CBM27 CBM27
CBM_15 Glyco_hydro_10
CBM_17_28 CBM_17_28
CBM_4_9 CBM_4_9
CelD_N
Glyco_hydro_10
CBM_6 CBM_6
Glyco_hydro_11
Cellulase CBM_17_28
CBM_6
Clenterotox Clenterotox
Cu-oxidase_2 F5_F8_type_C
Cu-oxidase_3 F5_F8_type_C
CUB F5_F8_type_C
Endotoxin_C Endotoxin_M
Endotoxin_M Endotoxin_C
Endotoxin_mid Endotoxin_C
Endotoxin_N Endotoxin_C
Ephrin Ephrin_lbd
Ephrin_lbd Ephrin
Ephrin_lbd
F-box FBA
F5_F8_type_C CUB
F5_F8_type_C
H_lectin
NAGLU
NAGLU_C
Sialidase
VEGF_C
FBA RnaseA
Skp1
fn3_3 CBM-like
Glyco_hydro_11 CBM_6
Glyco_hydro_2 Glyco_hydro_2_N
Glyco_hydro_2_C Glyco_hydro_2_N
Glyco_hydro_2_N Bgal_small_N
Glyco_hydro_2
Glyco_hydro_2_C
Glyco_hydro_2_N
Glyco_hydro_31 CBM_6
Glyco_hydro_35 BetaGal_dom4_5
Glyco_hydro_43 CBM_6
GxDLY Lipase_GDSL_3
H_lectin F5_F8_type_C
Laminin_EGF Laminin_N
Laminin_N Laminin_EGF
Lipl32 Lipl32
LRR_1 Laminin_N
LRR_5 Laminin_N
LRR_8 Laminin_N
Lyase_N Lyase_catalyt
NPCBM Glyco_hydro_98M
NPCBM
NPCBM_assoc F5_F8_type_C
P_proprotein P_proprotein
Peptidase_S8
PA-IL PA-IL
PAW PAW
PCMD PCMD
Peptidase_C2 Calpain_III
Peptidase_S15 PepX_C
Peptidase_S8 P_proprotein
PPC
PepX_C Peptidase_S15
PepX_C
PepX_N PepX_C
PINIT zf-MIZ
PPC PPC
RhgB_N CBM-like
Sad1_UNC KASH
SLT PPC
VEGF_C F5_F8_type_C
XRCC1_N DNA_pol_B_thumb
XRCC1_N
YpM YpM

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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