Table 5

Examples of entry relationships in COMe

Fragment of ontology of PRX entities


complex protein PRX000001

 IsA metalloprotein PRX000002

  IsA iron protein PRX000004

   IsA iron-sulphur protein PRX000007

    IsA Fe2S2 protein PRX000053

     IsA Fe2S2 ferredoxin PRX000058

      IsA plant and mammalian-type ferredoxin PRX000963

       IsA plant-type ferredoxin domain PRX000062

        IsA plant-type ferredoxin PRX000063

Fragment of ontology of BIM entities


Fe(por)(NE.His)* BIM000025

 IsA Fe(por)(NE.His) BIM000007

 IsA Fe(por)(NE.His)(NO) BIM000018

 IsA Fe(por)(NE.His)(OH) BIM000019

 IsA Fe(por)(NE.His)(O2) BIM000021

 IsA Fe(por)(NE.His)(CO2) BIM000022

 IsA Fe(por)(NE.His)(CO) BIM000023

 IsA Fe(por)(NE.His)(O2)-BIM000024

 IsA Fe(por)(NE.His)(CN) BIM000198

Fragment of ontology of MOL entities


FAD* MOL000041

 IsA FAD MOL000039

 IsA FADH2 MOL000040

 IsA FADH. MOL000042

IsPartOf relationship


Zn(OE.Glu)2 [Fe(ND.His) k2-(OE,OE.Glu)] μ-(OE,OE.Glu)2 BIM000352

 IsPartOf [OC-6] Fe(ND.His)(OE.Glu)2 k2-(OE,OE.Glu) BIM000353

 IsPartOf [T-4] Zn(OE.Glu)4 BIM000354

IsBoundTo and IsPartOf relationships


pyridoxal 5'-phosphate protein PRX000808

 IsBoundTo pyridoxal 5'-phosphate MOL000108

 IsPartOf (C4A.Pxy)(NZ.Lys) BIM000270

IsPartOf and IsA relationships


bacterioferritin PRX000159

 IsPartOf Fe(por)(SD.Met)2 BIM000015

 IsA haem b bacterioferritin PRX001170

 IsA Fe-coproporphyrin III bacterioferritin PRX001171

IsBoundTo and IsA relationships


cytochrome b PRX000153

 IsBoundTo haem b MOL000013

 IsA haem-bis-His cytochrome b PRX000674

 IsA haem-His-Met cytochrome b PRX000675

 IsA haem b bacterioferritin PRX001170

Degtyarenko and Contrino BMC Structural Biology 2004 4:3   doi:10.1186/1472-6807-4-3

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