SUPERFAMILY 1.75 HMM library and genome assignments server


Nucleoside diphosphate kinase, NDK superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ferredoxin-like [ 54861] (59)
Superfamily:   Nucleoside diphosphate kinase, NDK [ 54919]
Families:   Nucleoside diphosphate kinase, NDK [ 54920]


Superfamily statistics
Genomes (2,225) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 4,424 8,696 34
Proteins 3,869 8,248 34


Functional annotation
General category Metabolism
Detailed category Nucleotide metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)cellular aromatic compound metabolic process1.741e-060.0007282Least InformativeDirect
Biological Process (BP)heterocycle metabolic process1.435e-060.0004978Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process6.491e-060.0009004Least InformativeDirect
Biological Process (BP)multicellular organismal process0.13060.1839Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process4.968e-050.003077Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.0012230.001253Least InformativeInherited
Biological Process (BP)biosynthetic process0.0021410.00583Least InformativeInherited
Biological Process (BP)regulation of cellular process0.0024720.02419Least InformativeInherited
Biological Process (BP)single-organism cellular process0.38810.7426Least InformativeInherited
Biological Process (BP)response to stimulus0.23590.2509Least InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process3.407e-067.769e-05Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process1.203e-056.723e-05Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process2.128e-066.134e-05Moderately InformativeDirect
Biological Process (BP)organophosphate metabolic process1.251e-071.256e-07Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process1.463e-058.516e-05Moderately InformativeDirect
Biological Process (BP)nucleobase-containing small molecule metabolic process3.208e-109.122e-12Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process2.333e-050.0001001Moderately InformativeDirect
Biological Process (BP)positive regulation of cellular process0.00014520.312Moderately InformativeInherited
Biological Process (BP)reproduction0.018120.0713Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.051310.06711Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.0015230.0004861Moderately InformativeInherited
Biological Process (BP)signal transduction0.066890.005373Moderately InformativeInherited
Biological Process (BP)regulation of apoptotic process7.487e-065.663e-05InformativeDirect
Biological Process (BP)multicellular organismal reproductive process0.0004540.0008032InformativeDirect
Biological Process (BP)purine-containing compound biosynthetic process1.539e-053.462e-05InformativeDirect
Biological Process (BP)glycosyl compound biosynthetic process5.981e-055.141e-05InformativeDirect
Biological Process (BP)purine nucleoside metabolic process0.53340.6725InformativeInherited
Biological Process (BP)ribonucleoside metabolic process0.87681InformativeInherited
Biological Process (BP)regulation of cell proliferation0.0094770.1167InformativeInherited
Biological Process (BP)nucleoside triphosphate metabolic process0.0097210.002439InformativeInherited
Biological Process (BP)purine nucleotide metabolic process0.30720.3497InformativeInherited
Biological Process (BP)ribose phosphate metabolic process0.043890.07101InformativeInherited
Biological Process (BP)nucleotide biosynthetic process0.00030430.002509InformativeInherited
Biological Process (BP)nucleoside diphosphate metabolic process6.629e-084.368e-10Highly InformativeDirect
Biological Process (BP)nucleoside triphosphate biosynthetic process7.445e-111.639e-11Highly InformativeDirect
Biological Process (BP)positive regulation of epithelial cell proliferation8.411e-091.445e-06Highly InformativeDirect
Biological Process (BP)guanosine-containing compound metabolic process1.141e-053.612e-06Highly InformativeDirect
Biological Process (BP)purine ribonucleoside triphosphate metabolic process0.85461Highly InformativeInherited
Molecular Function (MF)transferase activity1.821e-081.467e-07Least InformativeDirect
Molecular Function (MF)binding0.02120.5809Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups3.816e-157.403e-12Moderately InformativeDirect
Molecular Function (MF)organic cyclic compound binding0.0021670.1637Moderately InformativeInherited
Molecular Function (MF)heterocyclic compound binding0.0014730.1517Moderately InformativeInherited
Molecular Function (MF)anion binding7.544e-060.07536Moderately InformativeInherited
Molecular Function (MF)nucleotide binding2.716e-069.82e-05InformativeDirect
Molecular Function (MF)kinase activity03.487e-13InformativeDirect
Molecular Function (MF)ATP binding1.013e-104.93e-07Highly InformativeDirect
Molecular Function (MF)nucleobase-containing compound kinase activity00Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.073020.3216Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.36750.1588Least InformativeInherited
Cellular Component (CC)cell projection4.187e-050.001775Moderately InformativeInherited
Cellular Component (CC)cell leading edge5.392e-101.685e-07InformativeDirect
Cellular Component (CC)cell junction7.26e-070.001279InformativeInherited
Cellular Component (CC)ruffle1.787e-094.338e-09Highly InformativeDirect
Cellular Component (CC)lamellipodium3.553e-082.742e-08Highly InformativeDirect
Cellular Component (CC)cell-substrate junction2.199e-141.315e-08Highly InformativeDirect
Cellular Component (CC)adherens junction11.221e-06Highly InformativeInherited

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular aromatic compound metabolic process 0.0007282 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0004978 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0009004 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.003077 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.001253 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.05831 Least Informative Inherited
Biological Process (BP) localization 0.2497 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.00583 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.1839 Least Informative Inherited
Biological Process (BP) developmental process 0.1396 Least Informative Inherited
Biological Process (BP) response to stimulus 0.2509 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.02419 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.7426 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 7.769e-05 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 6.723e-05 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 6.134e-05 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 1.256e-07 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 8.516e-05 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 9.122e-12 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0004861 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.0001001 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.14 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.3564 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.312 Moderately Informative Inherited
Biological Process (BP) reproduction 0.0713 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.2919 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.06711 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.06147 Moderately Informative Inherited
Biological Process (BP) organ development 0.08641 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.0307 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.005373 Moderately Informative Inherited
Biological Process (BP) cellular component movement 0.0002554 Informative Direct
Biological Process (BP) microtubule-based process 2.6e-06 Informative Direct
Biological Process (BP) central nervous system development 0.000293 Informative Direct
Biological Process (BP) regulation of apoptotic process 5.663e-05 Informative Direct
Biological Process (BP) multicellular organismal reproductive process 0.0008032 Informative Direct
Biological Process (BP) negative regulation of cell death 0.0002335 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 3.462e-05 Informative Direct
Biological Process (BP) glycosyl compound biosynthetic process 5.141e-05 Informative Direct
Biological Process (BP) purine nucleoside metabolic process 0.6725 Informative Inherited
Biological Process (BP) ribonucleoside metabolic process 1 Informative Inherited
Biological Process (BP) cellular membrane organization 0.001847 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.1167 Informative Inherited
Biological Process (BP) cell projection organization 0.001537 Informative Inherited
Biological Process (BP) nucleoside triphosphate metabolic process 0.002439 Informative Inherited
Biological Process (BP) purine nucleotide metabolic process 0.3497 Informative Inherited
Biological Process (BP) ribose phosphate metabolic process 0.07101 Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 0.002509 Informative Inherited
Biological Process (BP) microtubule-based movement 7.463e-08 Highly Informative Direct
Biological Process (BP) nucleoside diphosphate metabolic process 4.368e-10 Highly Informative Direct
Biological Process (BP) nucleoside triphosphate biosynthetic process 1.639e-11 Highly Informative Direct
Biological Process (BP) positive regulation of epithelial cell proliferation 1.445e-06 Highly Informative Direct
Biological Process (BP) protein localization to membrane 8.393e-08 Highly Informative Direct
Biological Process (BP) guanosine-containing compound metabolic process 3.612e-06 Highly Informative Direct
Biological Process (BP) purine ribonucleoside triphosphate metabolic process 1 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.00161 Highly Informative Inherited
Molecular Function (MF) transferase activity 1.467e-07 Least Informative Direct
Molecular Function (MF) binding 0.5809 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 7.403e-12 Moderately Informative Direct
Molecular Function (MF) organic cyclic compound binding 0.1637 Moderately Informative Inherited
Molecular Function (MF) heterocyclic compound binding 0.1517 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.07536 Moderately Informative Inherited
Molecular Function (MF) nucleotide binding 9.82e-05 Informative Direct
Molecular Function (MF) kinase activity 3.487e-13 Informative Direct
Molecular Function (MF) ATP binding 4.93e-07 Highly Informative Direct
Molecular Function (MF) nucleobase-containing compound kinase activity 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.3216 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1588 Least Informative Inherited
Cellular Component (CC) cell projection 0.001775 Moderately Informative Inherited
Cellular Component (CC) cell leading edge 1.685e-07 Informative Direct
Cellular Component (CC) cell junction 0.001279 Informative Inherited
Cellular Component (CC) ruffle 4.338e-09 Highly Informative Direct
Cellular Component (CC) adherens junction 1.221e-06 Highly Informative Direct
Cellular Component (CC) lamellipodium 2.742e-08 Highly Informative Direct
Cellular Component (CC) cell-substrate junction 1.315e-08 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Phosphotransferases with a phosphate group as acce0InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)shoot apex0Least InformativeDirect
Plant ANatomical entity (PAN)shoot internode0Least InformativeDirect
Plant ANatomical entity (PAN)plant cell0Least InformativeDirect
Plant ANatomical entity (PAN)root0Least InformativeDirect
Plant ANatomical entity (PAN)plant embryo0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)vascular leaf0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)sepal0Least InformativeDirect
Plant ANatomical entity (PAN)petal0Least InformativeDirect
Plant ANatomical entity (PAN)stem0Least InformativeDirect
Plant ANatomical entity (PAN)pedicel0Least InformativeDirect
Plant ANatomical entity (PAN)androecium0Least InformativeDirect
Plant ANatomical entity (PAN)gynoecium0Least InformativeDirect
Plant ANatomical entity (PAN)leaf lamina0Least InformativeDirect
Plant ANatomical entity (PAN)collective leaf structure0Least InformativeDirect
Plant ANatomical entity (PAN)stalk0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)phyllome apex0Least InformativeDirect
Plant ANatomical entity (PAN)microgametophyte0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell7.876e-05Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Phosphotransferases with a phosphate group as acceptor0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation0.005407Moderately InformativeInherited
Biological processNucleotide metabolism0Highly InformativeDirect
Biological processSpermatogenesis0.0009723Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001564 SSF54919 Protein matches
Abstract

Nucleoside diphosphate kinases (NDK) are enzymes required for the synthesis of nucleoside triphosphates (NTP) other than ATP. They provide NTPs for nucleic acid synthesis, CTP for lipid synthesis, UTP for polysaccharide synthesis and GTP for protein elongation, signal transduction and microtubule polymerization.

In eukaryotes, there seems to be a small family of NDK isozymes each of which acts in a different subcellular compartment and/or has a distinct biological function. Eukaryotic NDK isozymes are hexamers of two highly related chains (A and B) [PubMed1851158]. By random association (A6, A5B...AB5, B6), these two kinds of chain form isoenzymes differing in their isoelectric point.

NDK are proteins of 17 Kd that act via a ping-pong mechanism in which a histidine residue is phosphorylated, by transfer of the terminal phosphate group from ATP. In the presence of magnesium, the phosphoenzyme can transfer its phosphate group to any NDP, to produce an NTP.

NDK isozymes have been sequenced from prokaryotic and eukaryotic sources. It has also been shown [PubMed2175255] that the Drosophila awd (abnormal wing discs) protein, is a microtubule-associated NDK. Mammalian NDK is also known as metastasis inhibition factor nm23. The sequence of NDK has been highly conserved through evolution. There is a single histidine residue conserved in all known NDK isozymes, which is involved in the catalytic mechanism [PubMed1851158]. Our signature pattern contains this residue.


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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · 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 20 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 Nucleoside diphosphate kinase, NDK 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 20 hidden Markov models representing the Nucleoside diphosphate kinase, NDK 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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]