SUPERFAMILY 1.75 HMM library and genome assignments server

Midkine superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   Midkine [ 57287]
Superfamily:   Midkine [ 57288] (2)
Families:   Midkine, a heparin-binding growth factor, N-terminal domain [ 57289]
  Midkine, a heparin-binding growth factor, C-terminal domain [ 57292]

Superfamily statistics
Genomes (76) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 345 374 2
Proteins 184 200 2

Functional annotation
General category Regulation
Detailed category Other regulatory function

Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) developmental process 0.0000000003003 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.000000001679 Least Informative Direct
Biological Process (BP) response to stimulus 0.0000002181 Least Informative Direct
Biological Process (BP) multi-organism process 0.0008302 Moderately Informative Direct
Biological Process (BP) system process 0.02615 Moderately Informative Inherited
Biological Process (BP) tissue development 0.001623 Moderately Informative Inherited
Biological Process (BP) organ development 0.02852 Moderately Informative Inherited
Biological Process (BP) single-organism behavior 0.0000000004944 Informative Direct
Biological Process (BP) response to bacterium 0.0000004591 Informative Direct
Biological Process (BP) learning or memory 0.000000000000348 Highly Informative Direct
Biological Process (BP) ossification 0.0000001744 Highly Informative Direct
Molecular Function (MF) binding 0.1259 Least Informative Inherited
Molecular Function (MF) anion binding 0.000000575 Moderately Informative Direct
Molecular Function (MF) sulfur compound binding 0.0000000000006087 Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.000000000002301 Informative Direct
Molecular Function (MF) heparin binding 0.00000000000002888 Highly Informative Direct
Cellular Component (CC) extracellular region part 0.0000004038 Moderately Informative Direct
Cellular Component (CC) extracellular matrix 0.0000000002287 Informative Direct
Cellular Component (CC) proteinaceous extracellular matrix 0.000003979 Highly Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation0.0000000006678Moderately InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
DomainSignal3.091e-16Least InformativeDirect
Molecular functionHeparin-binding0InformativeDirect
Post-translational modificationDevelopmental protein0.000000000000006125Moderately InformativeDirect
Post-translational modificationGrowth factor0InformativeDirect
Post-translational modificationAntimicrobial0.000000000006777InformativeDirect
Post-translational modificationMitogen0Highly InformativeDirect
Post-translational modificationAntibiotic0.00000000000007282Highly InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR000762 SSF57288 Protein matches
Abstract Several extracellular heparin-binding proteins involved in regulation of growth and differentiation belong to a new family of growth factors. These growth factors are highly related proteins of about 140 amino acids that contain 10 conserved cysteines probably involved in disulphide bonds, and include pleiotrophin [PubMed15121180] (also known as heparin-binding growth-associated molecule HB-GAM, heparin-binding growth factor 8 HBGF-8, heparin-binding neutrophic factor HBNF and osteoblast specific protein OSF-1); midkine (MK) [PubMed15047154]; retinoic acid-induced heparin-binding protein (RIHB) [PubMed7796887]; and pleiotrophic factors alpha-1and -2 and beta-1 and -2 from Xenopus laevis, the homologs of midkine and pleiotrophin respectively. Pleiotrophin is a heparin-binding protein that has neurotrophic activity and has mitogenic activity towards fibroblasts. It is highly expressed in brain and uterus tissues, but is also found in gut, muscle and skin. It is thought to possess an important brain-specific function. Midkine is a regulator of differentiation whose expression is regulated by retinoic acid, and, like pleiotrophin, is a heparin-binding growth/differentiation factor that acts on fibroblasts and nerve cells.

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 · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) ]

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 2 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 Midkine 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 2 hidden Markov models representing the Midkine 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 · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · Internal database links ]