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Ribokinase-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Ribokinase-like [ 53612] (3)
Superfamily:   Ribokinase-like [ 53613] (5)
Families:   Thiamin biosynthesis kinases [ 53620] (2)
  YjeF C-terminal domain-like [ 75292] (2)
  PfkB-like kinase [ 82515] (2)
  Ribokinase-like [ 53614] (9)
  ADP-specific Phosphofructokinase/Glucokinase [ 64147] (2)


Superfamily statistics
Genomes (3,066) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 25,604 163,746 31
Proteins 25,491 163,601 31


Functional annotation
General category Metabolism
Detailed category Other enzymes

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 process0.000037060.000004132Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process0.0003320.00007067Least InformativeDirect
Biological Process (BP)single-organism metabolic process00Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.000013810.0000009058Least InformativeDirect
Biological Process (BP)organic substance biosynthetic process0.13580.00009887Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.0035620.00000006266Least InformativeInherited
Biological Process (BP)primary metabolic process0.9141Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.0019850.0001833Least InformativeInherited
Biological Process (BP)single-organism cellular process0.0014120.0007134Least InformativeInherited
Biological Process (BP)cellular biosynthetic process0.18550.0001237Least InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.0000000000013240Moderately InformativeDirect
Biological Process (BP)monocarboxylic acid metabolic process0.00019960.00004121Moderately InformativeDirect
Biological Process (BP)purine-containing compound metabolic process0.00000014070.00000004404Moderately InformativeDirect
Biological Process (BP)organophosphate biosynthetic process0.00000067550.000006104Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process0.46520.4674Moderately InformativeInherited
Biological Process (BP)single-organism catabolic process0.3870.4254Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.29750.006787Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.004260.0001469Moderately InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.043540.000001772Moderately InformativeInherited
Biological Process (BP)nucleoside phosphate metabolic process0.84280.2267Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.0017090.0000006696Moderately InformativeInherited
Biological Process (BP)generation of precursor metabolites and energy0.41830.4065Moderately InformativeInherited
Biological Process (BP)monosaccharide metabolic process0.00012520.0001357InformativeDirect
Biological Process (BP)cellular aldehyde metabolic process0.000000000092270.00000000000002425InformativeDirect
Biological Process (BP)carbohydrate catabolic process0.00024760.0001402InformativeDirect
Biological Process (BP)cellular metabolic compound salvage0.000000005520.0000000000008137InformativeDirect
Biological Process (BP)cellular carbohydrate metabolic process0.000010010.0000004302InformativeDirect
Biological Process (BP)purine-containing compound biosynthetic process0.000013240.00006958InformativeDirect
Biological Process (BP)pyridine-containing compound metabolic process0.00000000014020.000000000003917InformativeDirect
Biological Process (BP)pyrimidine-containing compound biosynthetic process0.000056550.00000000000001416InformativeDirect
Biological Process (BP)organic hydroxy compound biosynthetic process0.0000026850.0001305InformativeDirect
Biological Process (BP)oxidoreduction coenzyme metabolic process0.11340.2602InformativeInherited
Biological Process (BP)glycosyl compound metabolic process0.094650.02094InformativeInherited
Biological Process (BP)coenzyme biosynthetic process0.14580.09123InformativeInherited
Biological Process (BP)water-soluble vitamin biosynthetic process0.017230.0002547InformativeInherited
Biological Process (BP)sulfur compound biosynthetic process0.0012630.00000001153InformativeInherited
Biological Process (BP)phosphorylation0.25181InformativeInherited
Biological Process (BP)ATP metabolic process0.84460.9447InformativeInherited
Biological Process (BP)nucleoside diphosphate metabolic process0.46170.2232InformativeInherited
Biological Process (BP)thiamine biosynthetic process0.0000000000000015710Highly InformativeDirect
Biological Process (BP)glyceraldehyde-3-phosphate metabolic process0.00001880.00001122Highly InformativeDirect
Biological Process (BP)vitamin B6 metabolic process0.00000000028050Highly InformativeDirect
Biological Process (BP)purine ribonucleoside metabolic process0.00000033470.000000066Highly InformativeDirect
Biological Process (BP)pyridine-containing compound biosynthetic process0.0000045760.00000007362Highly InformativeDirect
Molecular Function (MF)transferase activity00Least InformativeDirect
Molecular Function (MF)binding0.90521Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups00Moderately InformativeDirect
Molecular Function (MF)carbohydrate derivative binding0.000013230.0006343Moderately InformativeDirect
Molecular Function (MF)small molecule binding0.000094390.001394Moderately InformativeInherited
Molecular Function (MF)anion binding0.029120.1119Moderately InformativeInherited
Molecular Function (MF)kinase activity0.000000033220.0000288InformativeDirect
Molecular Function (MF)phosphotransferase activity, alcohol group as acceptor0.000000000097740.000459InformativeDirect
Molecular Function (MF)purine nucleotide binding0.00000047480.00001476InformativeDirect
Molecular Function (MF)ribonucleotide binding0.00000096620.00001864InformativeDirect
Molecular Function (MF)purine ribonucleoside triphosphate binding0.00000010880.000003708InformativeDirect
Molecular Function (MF)ATP binding0.0000000000081890.00000008798Highly InformativeDirect
Molecular Function (MF)nucleobase-containing compound kinase activity0.61310.0001271Highly InformativeInherited
Molecular Function (MF)phosphotransferase activity, phosphate group as acceptor10.01697Highly InformativeInherited
Cellular Component (CC)cytoplasmic part0.23180.04329Least 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 0.000004132 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.00007067 Least Informative Direct
Biological Process (BP) cellular biosynthetic process 0.0001237 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0007134 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0000009058 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0001833 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.00000006266 Least Informative Direct
Biological Process (BP) organic substance biosynthetic process 0.00009887 Least Informative Direct
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0.000001772 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 0.00004121 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.0001469 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0.00000004404 Moderately Informative Direct
Biological Process (BP) organophosphate biosynthetic process 0.000006104 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0000006696 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.4674 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.4254 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing compound biosynthetic process 0.01591 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.006787 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 0.2267 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) generation of precursor metabolites and energy 0.4065 Moderately Informative Inherited
Biological Process (BP) monosaccharide metabolic process 0.0001357 Informative Direct
Biological Process (BP) cellular aldehyde metabolic process 0.00000000000002425 Informative Direct
Biological Process (BP) carbohydrate catabolic process 0.0001402 Informative Direct
Biological Process (BP) water-soluble vitamin biosynthetic process 0.0002547 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 0.0000000000008137 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 0.0000004302 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0.00000001153 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0.00006958 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0.000000000003917 Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 0.00000000000001416 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 0.0001305 Informative Direct
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.2602 Informative Inherited
Biological Process (BP) glycosyl compound metabolic process 0.02094 Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 0.09123 Informative Inherited
Biological Process (BP) polysaccharide metabolic process 0.01896 Informative Inherited
Biological Process (BP) liposaccharide metabolic process 0.02383 Informative Inherited
Biological Process (BP) phosphorylation 1 Informative Inherited
Biological Process (BP) ATP metabolic process 0.9447 Informative Inherited
Biological Process (BP) nucleoside diphosphate metabolic process 0.2232 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 0.1853 Informative Inherited
Biological Process (BP) thiamine biosynthetic process 0 Highly Informative Direct
Biological Process (BP) glyceraldehyde-3-phosphate metabolic process 0.00001122 Highly Informative Direct
Biological Process (BP) cellular polysaccharide biosynthetic process 0.00004796 Highly Informative Direct
Biological Process (BP) vitamin B6 metabolic process 0 Highly Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.000000066 Highly Informative Direct
Biological Process (BP) pyridine-containing compound biosynthetic process 0.00000007362 Highly Informative Direct
Biological Process (BP) lipopolysaccharide metabolic process 0.001049 Highly Informative Inherited
Molecular Function (MF) transferase activity 0 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.0006343 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.001394 Moderately Informative Inherited
Molecular Function (MF) lyase activity 0.6752 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.1119 Moderately Informative Inherited
Molecular Function (MF) kinase activity 0.0000288 Informative Direct
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.000459 Informative Direct
Molecular Function (MF) hydro-lyase activity 0.0002649 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.00001476 Informative Direct
Molecular Function (MF) ribonucleotide binding 0.00001864 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.000003708 Informative Direct
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 0.3879 Informative Inherited
Molecular Function (MF) ATP binding 0.00000008798 Highly Informative Direct
Molecular Function (MF) nucleobase-containing compound kinase activity 0.0001271 Highly Informative Direct
Molecular Function (MF) phosphotransferase activity, phosphate group as acceptor 0.01697 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.04329 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) plastid 0.0006775 Informative Direct
Cellular Component (CC) chloroplast stroma 0.0003064 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)Lyases1Least InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as accep0Moderately InformativeDirect
Enzyme Commission (EC)Hydro-lyases0.00009412Moderately InformativeDirect
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than meth1Moderately InformativeInherited
Enzyme Commission (EC)Phosphotransferases with a phosphate group as acce1InformativeInherited

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)general pace of development variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval growth variant0Least InformativeDirect
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)bud0.00008416Highly InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Lyases0.247Least InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0.000000000002977Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Isomerases1Moderately InformativeInherited
Enzyme Commission (EC)Racemases and epimerases0.000000003608InformativeDirect
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited
Enzyme Commission (EC)Phosphotransferases with a phosphate group as acceptor1InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCarbohydrate metabolism0Moderately InformativeDirect
Biological processThiamine biosynthesis0Highly InformativeDirect
Biological processLipopolysaccharide biosynthesis0.00000001444Highly InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionNADP0.00000002451Moderately InformativeDirect
Molecular functionNAD0.00005285Moderately InformativeDirect
Molecular functionPotassium0.000000000001177InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0.000000003898Moderately InformativeDirect
Post-translational modificationLyase0.0000009809Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)cofactor metabolism0Least InformativeDirect
UniPathway (UP)carbohydrate metabolism0Least InformativeDirect
UniPathway (UP)lipid metabolism0Least InformativeDirect
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)biopolymer biosynthesis0Moderately InformativeDirect
UniPathway (UP)lipid biosynthesis0Moderately InformativeDirect
UniPathway (UP)glycan metabolism0Moderately InformativeDirect
UniPathway (UP)nucleotide metabolism0Moderately InformativeDirect
UniPathway (UP)cellular component biogenesis0Moderately InformativeDirect
UniPathway (UP)membrane lipid metabolism0Moderately InformativeDirect
UniPathway (UP)alcohol metabolism0.000000256Moderately InformativeDirect
UniPathway (UP)organic acid metabolism0.08191Moderately InformativeInherited
UniPathway (UP)carbohydrate degradation1Moderately InformativeInherited
UniPathway (UP)amino-acid degradation1Moderately InformativeInherited
UniPathway (UP)lipopolysaccharide biosynthesis0InformativeDirect
UniPathway (UP)nucleotide-sugar biosynthesis0InformativeDirect
UniPathway (UP)thiamine metabolism0InformativeDirect
UniPathway (UP)alcohol degradation0.0000000000009417InformativeDirect
UniPathway (UP)organic acid degradation0.009208InformativeInherited
UniPathway (UP)carbohydrate acid metabolism0.01129InformativeInherited
UniPathway (UP)myo-inositol degradation into acetyl-CoA0Highly InformativeDirect
UniPathway (UP)LPS oligosaccharide biosynthesis0Highly InformativeDirect
UniPathway (UP)aldonic acid degradation0.00000000001369Highly InformativeDirect
UniPathway (UP)LPS core biosynthesis0.0002168Highly InformativeDirect
UniPathway (UP)Lipooligosaccharide metabolism0.0002519Highly InformativeDirect
UniPathway (UP)starch biosynthesis0.0008032Highly InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 25 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 Ribokinase-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 25 hidden Markov models representing the Ribokinase-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 · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]