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807  structures 4159  species 28  interactions 38880  sequences 2917  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 27 families and the total number of domains in the clan is 38880. 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 27 member families:

Allantoicase APC10 Bac_rhamnosid_N BetaGal_dom4_5 CBM_11 CBM_15 CBM_17_28 CBM_4_9 CBM_6 CIA30 Cleaved_Adhesin DUF642 Endotoxin_C Ephrin_lbd F5_F8_type_C FBA Glyco_hydro_2_N Laminin_N Lyase_N MAM Muskelin_N P_proprotein PA-IL PepX_C PITH 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
F5_F8_type_C (PF00754) 10300 (26.5%) View
Glyco_hydro_2_N (PF02837) 7272 (18.7%) View
MAM (PF00629) 3415 (8.8%) View
PepX_C (PF08530) 2418 (6.2%) View
CBM_6 (PF03422) 1755 (4.5%) View
CBM_4_9 (PF02018) 1727 (4.4%) View
P_proprotein (PF01483) 1577 (4.1%) View
Laminin_N (PF00055) 1311 (3.4%) View
Allantoicase (PF03561) 1158 (3.0%) View
Sad1_UNC (PF07738) 1140 (2.9%) View
Ephrin_lbd (PF01404) 1131 (2.9%) View
Bac_rhamnosid_N (PF08531) 876 (2.3%) View
CIA30 (PF08547) 768 (2.0%) View
APC10 (PF03256) 646 (1.7%) View
continued
Pfam family Num. domains Alignment
PITH (PF06201) 613 (1.6%) View
BetaGal_dom4_5 (PF13364) 562 (1.4%) View
Endotoxin_C (PF03944) 512 (1.3%) View
DUF642 (PF04862) 419 (1.1%) View
FBA (PF04300) 396 (1.0%) View
Cleaved_Adhesin (PF07675) 203 (0.5%) View
XRCC1_N (PF01834) 182 (0.5%) View
CBM_11 (PF03425) 149 (0.4%) View
Muskelin_N (PF06588) 139 (0.4%) View
Lyase_N (PF09092) 133 (0.3%) View
CBM_17_28 (PF03424) 48 (0.1%) View
PA-IL (PF07828) 27 (0.1%) View
CBM_15 (PF03426) 3 (0.0%) View
Total: 27 Total: 38880 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 28 interactions for this clan. More...

Interacting families
A B
PepX_C Peptidase_S15
PepX_C
PepX_N
CBM_6 Glyco_hydro_11
CBM_6
Lyase_N Lyase_catalyt
CBM_17_28 CBM_17_28
Bac_rhamnosid_N Bac_rhamnosid
Bac_rhamnosid_N
FBA RnaseA
F-box
Skp1
P_proprotein Peptidase_S8
P_proprotein
Glyco_hydro_2_N Glyco_hydro_2
Glyco_hydro_2_C
Bgal_small_N
Endotoxin_C Endotoxin_M
Endotoxin_N
Endotoxin_mid
CBM_15 Glyco_hydro_10
Allantoicase Allantoicase
APC10 APC10
PA-IL PA-IL
Ephrin_lbd Ephrin_lbd
MAM ig
F5_F8_type_C CUB
F5_F8_type_C

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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