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976  structures 17002  species 76  interactions 90585  sequences 4115  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 32 families and the total number of domains in the clan is 90585. 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 32 member families:

Allantoicase ANAPC10 Bac_rhamnosid_N BetaGal_dom4_5 CBM-like CBM27 CBM60 CBM_11 CBM_15 CBM_17_28 CBM_35 CBM_4_9 CBM_6 CIA30 DUF5000 DUF642 Endotoxin_C Ephrin_lbd F5_F8_type_C FBA Glyco_hydro_2_N Laminin_N Lyase_N Muskelin_N NPCBM P_proprotein PA-IL PepX_C PITH PPC Sad1_UNC XRCC1_N

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
Glyco_hydro_2_N (PF02837) 21097 (23.3%) View
F5_F8_type_C (PF00754) 17412 (19.2%) View
PepX_C (PF08530) 13960 (15.4%) View
PPC (PF04151) 5390 (6.0%) View
Allantoicase (PF03561) 4120 (4.5%) View
CBM_4_9 (PF02018) 3770 (4.2%) View
P_proprotein (PF01483) 2904 (3.2%) View
CBM_6 (PF03422) 2631 (2.9%) View
Sad1_UNC (PF07738) 2000 (2.2%) View
Bac_rhamnosid_N (PF08531) 1934 (2.1%) View
Laminin_N (PF00055) 1862 (2.1%) View
Ephrin_lbd (PF01404) 1432 (1.6%) View
CIA30 (PF08547) 1430 (1.6%) View
BetaGal_dom4_5 (PF13364) 1322 (1.5%) View
PITH (PF06201) 1224 (1.4%) View
ANAPC10 (PF03256) 1192 (1.3%) View
NPCBM (PF08305) 1099 (1.2%) View
continued
Pfam family Num. domains Alignment
CBM_35 (PF16990) 974 (1.1%) View
DUF642 (PF04862) 914 (1.0%) View
Endotoxin_C (PF03944) 844 (0.9%) View
CBM-like (PF14683) 804 (0.9%) View
FBA (PF04300) 532 (0.6%) View
Lyase_N (PF09092) 336 (0.4%) View
XRCC1_N (PF01834) 276 (0.3%) View
Muskelin_N (PF06588) 241 (0.3%) View
PA-IL (PF07828) 228 (0.3%) View
CBM_11 (PF03425) 199 (0.2%) View
CBM60 (PF16841) 197 (0.2%) View
DUF5000 (PF16391) 115 (0.1%) View
CBM27 (PF09212) 72 (0.1%) View
CBM_17_28 (PF03424) 69 (0.1%) View
CBM_15 (PF03426) 5 (0.0%) View
Total: 32 Total: 90585 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

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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 76 interactions for this clan. More...

Interacting families
A B
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
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
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
H_lectin F5_F8_type_C
Laminin_EGF Laminin_N
Laminin_N Laminin_EGF
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
Peptidase_S15 PepX_C
Peptidase_S8 P_proprotein
PPC
PepX_C Peptidase_S15
PepX_C
PepX_N PepX_C
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

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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