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Galactose-binding domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Galactose-binding domain-like [ 49784]
Superfamily:   Galactose-binding domain-like [ 49785] (32)
Families:   Galactose-binding domain [ 49786] (2)
  Discoidin domain (FA58C, coagulation factor 5/8 C-terminal domain) [ 49791] (3)
  APC10-like [ 69210] (2)
  delta-Endotoxin, C-terminal domain [ 49796]
  Ephrin receptor ligand binding domain [ 49800] (2)
  beta-Galactosidase/glucuronidase, N-terminal domain [ 49803] (4)
  Chondroitin ABC lyase I, N-terminal domain [ 89236]
  CBM4/9 [ 74893] (3)
  Family 6 carbohydrate binding module, CBM6 [ 69213] (4)
  CBM15 [ 69216]
  Family 17 carbohydrate binding module, CBM17 [ 69219]
  CBM22 [ 49811]
  Family 27 carbohydrate binding module, CBM27 [ 89241] (2)
  Family 29 carbohydrate binding module, CBM29 [ 89244]
  Fucose binding lectin [ 74896]
  N-terminal domain of xrcc1 [ 49814]
  F-box associated region, FBA [ 101585]
  Allantoicase repeat [ 101588]
  PepX C-terminal domain-like [ 69222] (3)
  PA-IL, galactose-binding lectin 1 [ 82022]
  Proprotein convertase P-domain [ 89249] (3)
  Family 28 carbohydrate binding module, CBM28 [ 110122]
  Family 30 carbohydrate binding module, CBM30 (PKD repeat) [ 110125]
  Rhamnogalacturonase B, RhgB, C-terminal domain [ 110128]
  Hypothetical protein AT3g04780/F7O18 27 [ 117108]
  Beta-galactosidase LacA, domains 4 and 5 [ 117111]
  Family 36 carbohydrate binding module, CBM36 [ 117114]
  Extended PAW domain [ 141113]
  CBM11 [ 141116]
  beta-mannanase CBM [ 141119]
  YxiM N-terminal domain-like [ 158963]
  NPCBM-like [ 158966] (2)


Superfamily statistics
Genomes (2,327) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 37,571 225,221 111
Proteins 31,214 190,586 104


Functional annotation
General category Metabolism
Detailed category Carbohydrate metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0.0161Least InformativeInherited
Enzyme Commission (EC)Glycosidases, i.e. enzymes hydrolyzing O- and S-gl0Moderately InformativeDirect
Enzyme Commission (EC)In linear amides1Moderately InformativeInherited
Enzyme Commission (EC)Serine endopeptidases0.734Moderately InformativeInherited
Enzyme Commission (EC)Dipeptidyl-peptidases and tripeptidyl-peptidases0InformativeDirect
Enzyme Commission (EC)Receptor protein-tyrosine kinase0InformativeDirect
Enzyme Commission (EC)Beta-galactosidase0InformativeDirect
Enzyme Commission (EC)Acting on polysaccharides0.000000000000003708InformativeDirect
Enzyme Commission (EC)In linear amidines0Highly InformativeDirect
Enzyme Commission (EC)Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagin0Highly InformativeDirect
Enzyme Commission (EC)Furin4.713e-16Highly InformativeDirect
Enzyme Commission (EC)Rhamnogalacturonan endolyase0.000000000000005085Highly InformativeDirect
Enzyme Commission (EC)Proprotein convertase 20.000000000001228Highly InformativeDirect
Enzyme Commission (EC)Proprotein convertase 10.00000000005325Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.3663Least InformativeInherited
Disease Ontology (DO)endocrine gland cancer0.006561InformativeInherited
Disease Ontology (DO)pancreatic ductal adenocarcinoma0.00002801Highly InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the skeletal system0.3495Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vertebral column0.04931Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the odontoid process0.001891Highly InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving the vertebral column0.01116Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.001582Least InformativeInherited
Mammalian Phenotype (MP)growth/size/body region phenotype0.07856Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.1075Least InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.1405Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.2909Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.4521Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell differentiation0.01341InformativeInherited
Mammalian Phenotype (MP)abnormal spinal cord morphology0.1276InformativeInherited
Mammalian Phenotype (MP)abnormal axon guidance0.00000422Highly InformativeDirect
Mammalian Phenotype (MP)abnormal body wall morphology0.00007776Highly InformativeDirect
Mammalian Phenotype (MP)abnormal brain white matter morphology0.0002967Highly InformativeDirect
Mammalian Phenotype (MP)abnormal spinal cord white matter morphology0.03059Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.01201Least InformativeInherited
Worm Phenotype (WP)protein protein interaction variant0.0000009938Moderately InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)cavitated compound organ0.2394Least InformativeInherited
Xenopus ANatomical entity (XAN)nervous system0.3538Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.8052Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue1Least InformativeInherited
Xenopus ANatomical entity (XAN)multi-tissue structure0.1061Moderately InformativeInherited
Xenopus ANatomical entity (XAN)sensory system0.4639Moderately InformativeInherited
Xenopus ANatomical entity (XAN)brain0.7591Moderately InformativeInherited
Xenopus ANatomical entity (XAN)peripheral nervous system0.1381InformativeInherited
Xenopus ANatomical entity (XAN)hindbrain0.3617InformativeInherited
Xenopus ANatomical entity (XAN)eye0.4582InformativeInherited
Xenopus ANatomical entity (XAN)cranial nerve0.03087Highly InformativeInherited

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)leaf0.7245Least InformativeInherited
Plant ANatomical entity (PAN)fruit0.00000005538InformativeDirect
Plant ANatomical entity (PAN)rosette leaf0.00004913InformativeDirect
Plant ANatomical entity (PAN)juvenile vascular leaf0Highly InformativeDirect
Plant ANatomical entity (PAN)adult vascular leaf0Highly InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Transferring phosphorus-containing groups1Least InformativeInherited
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Glycosylases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptidases)0.004407Moderately InformativeInherited
Enzyme Commission (EC)Carbon-oxygen lyases0.3847Moderately InformativeInherited
Enzyme Commission (EC)Acyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds1Moderately InformativeInherited
Enzyme Commission (EC)Protein-tyrosine kinases0InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0.5609InformativeInherited
Enzyme Commission (EC)In linear amides1InformativeInherited
Enzyme Commission (EC)Receptor protein-tyrosine kinase0Highly InformativeDirect
Enzyme Commission (EC)Beta-galactosidase0Highly InformativeDirect
Enzyme Commission (EC)Dipeptidyl-peptidases and tripeptidyl-peptidases0Highly InformativeDirect
Enzyme Commission (EC)In linear amidines0Highly InformativeDirect
Enzyme Commission (EC)Acting on polysaccharides0Highly InformativeDirect
Enzyme Commission (EC)HECT-type E3 ubiquitin transferase0.000000000005194Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR008979 SSF49785 Protein matches
Abstract

Proteins containing a galactose-binding domain-like fold can be found in several different protein families, in both eukaryotes and prokaryotes. The common function of these domains is to bind to specific ligands, such as cell-surface-attached carbohydrate substrates for galactose oxidase and sialidase [PubMed2002850], phospholipids on the outer side of the mammalian cell membrane for coagulation factor Va [PubMed10586886], membrane-anchored ephrin for the Eph family of receptor tyrosine kinases [PubMed11780069], and a complex of broken single-stranded DNA and DNA polymerase beta for XRCC1 [PubMed10467102].

The structure of the galactose-binding domain-like members consists of a beta-sandwich, in which the strands making up the sheets exhibit a jellyroll fold. There is a high degree of similarity in the beta-sandwich and in the loops between different family members, despite an often low level of sequence similarity.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 111 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Galactose-binding domain-like domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 111 hidden Markov models representing the Galactose-binding domain-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]