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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 (3,065) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 25,576 163,746 31
Proteins 25,463 163,601 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 process0.00042920.00003135Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.0000000000000030420Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.000067950.000002976Least InformativeDirect
Biological Process (BP)biosynthetic process0.55450.00548Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process0.0011770.0001637Least InformativeInherited
Biological Process (BP)single-organism cellular process0.061680.09503Least InformativeInherited
Biological Process (BP)primary metabolic process0.97941Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.0046930.0003472Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.012090.0000004293Least InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.0000000000011440Moderately InformativeDirect
Biological Process (BP)monocarboxylic acid metabolic process0.00088070.00078Moderately InformativeDirect
Biological Process (BP)purine-containing compound metabolic process0.00000085910.0000003682Moderately InformativeDirect
Biological Process (BP)organophosphate biosynthetic process0.0000054350.00003511Moderately InformativeDirect
Biological Process (BP)cofactor metabolic process0.024380.001646Moderately InformativeInherited
Biological Process (BP)glycosyl compound metabolic process0.046220.007861Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process0.34560.3405Moderately InformativeInherited
Biological Process (BP)single-organism catabolic process0.25010.2773Moderately InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.027930.0000007064Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.69640.07485Moderately InformativeInherited
Biological Process (BP)nucleoside phosphate metabolic process0.92490.3485Moderately InformativeInherited
Biological Process (BP)generation of precursor metabolites and energy0.35940.3369Moderately InformativeInherited
Biological Process (BP)ribose phosphate metabolic process0.44580.2195Moderately InformativeInherited
Biological Process (BP)monosaccharide metabolic process0.000027640.00002818InformativeDirect
Biological Process (BP)cellular aldehyde metabolic process0.0000000014790.000000000002027InformativeDirect
Biological Process (BP)carbohydrate catabolic process0.00013040.00005066InformativeDirect
Biological Process (BP)cellular metabolic compound salvage0.0000000064110.0000000002136InformativeDirect
Biological Process (BP)cellular carbohydrate metabolic process0.0000045820.000000176InformativeDirect
Biological Process (BP)sulfur compound biosynthetic process0.00028030.000000001394InformativeDirect
Biological Process (BP)purine-containing compound biosynthetic process0.000030540.0001592InformativeDirect
Biological Process (BP)pyridine-containing compound metabolic process0.0000000015850.00000000005268InformativeDirect
Biological Process (BP)pyrimidine-containing compound metabolic process0.000070730.000000000000005508InformativeDirect
Biological Process (BP)organic hydroxy compound biosynthetic process0.0000041070.000206InformativeDirect
Biological Process (BP)phosphorylation0.19751InformativeInherited
Biological Process (BP)oxidoreduction coenzyme metabolic process0.16110.2992InformativeInherited
Biological Process (BP)coenzyme biosynthetic process0.23290.1741InformativeInherited
Biological Process (BP)water-soluble vitamin biosynthetic process0.15850.003995InformativeInherited
Biological Process (BP)ATP metabolic process0.97421InformativeInherited
Biological Process (BP)nucleoside diphosphate metabolic process0.28390.1024InformativeInherited
Biological Process (BP)thiamine biosynthetic process0.0000000000000030420Highly InformativeDirect
Biological Process (BP)glyceraldehyde-3-phosphate metabolic process0.000037480.00003866Highly InformativeDirect
Biological Process (BP)vitamin B6 metabolic process0.0000049040.000000001416Highly InformativeDirect
Biological Process (BP)pyridine-containing compound biosynthetic process0.00010410.000002608Highly InformativeDirect
Molecular Function (MF)transferase activity00Least InformativeDirect
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups00Moderately InformativeDirect
Molecular Function (MF)carbohydrate derivative binding0.00033720.006092Moderately InformativeInherited
Molecular Function (MF)anion binding0.032770.1032Moderately InformativeInherited
Molecular Function (MF)small molecule binding0.00065770.007535Moderately InformativeInherited
Molecular Function (MF)purine nucleoside binding0.000021420.000175InformativeDirect
Molecular Function (MF)kinase activity0.000000038730.00004108InformativeDirect
Molecular Function (MF)phosphotransferase activity, alcohol group as acceptor0.00000000015680.0008117InformativeDirect
Molecular Function (MF)purine nucleotide binding0.000026060.0003091InformativeDirect
Molecular Function (MF)ribonucleoside binding0.000019560.0001714InformativeDirect
Molecular Function (MF)ribonucleotide binding0.000044840.0003702InformativeDirect
Molecular Function (MF)purine ribonucleoside triphosphate binding0.0000076620.0001023InformativeDirect
Molecular Function (MF)ATP binding0.0000000029190.000004915Highly InformativeDirect
Molecular Function (MF)nucleobase-containing compound kinase activity0.79950.0008638Highly InformativeInherited
Molecular Function (MF)phosphotransferase activity, phosphate group as acceptor10.01212Highly InformativeInherited
Cellular Component (CC)cytoplasmic part0.36640.06695Least 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 0.00003135 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.0001637 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.000002976 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0003472 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.0000004293 Least Informative Direct
Biological Process (BP) biosynthetic process 0.00548 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.09503 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0.0000007064 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 0.00078 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0.0000003682 Moderately Informative Direct
Biological Process (BP) organophosphate biosynthetic process 0.00003511 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.001646 Moderately Informative Inherited
Biological Process (BP) glycosyl compound metabolic process 0.007861 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.3405 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.2773 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing compound biosynthetic process 0.05087 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.9454 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.07485 Moderately Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 0.3485 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative biosynthetic process 0.04813 Moderately Informative Inherited
Biological Process (BP) generation of precursor metabolites and energy 0.3369 Moderately Informative Inherited
Biological Process (BP) ribose phosphate metabolic process 0.2195 Moderately Informative Inherited
Biological Process (BP) monosaccharide metabolic process 0.00002818 Informative Direct
Biological Process (BP) cellular aldehyde metabolic process 0.000000000002027 Informative Direct
Biological Process (BP) carbohydrate catabolic process 0.00005066 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 0.0000000002136 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 0.000000176 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0.000000001394 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0.0001592 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0.00000000005268 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0.000000000000005508 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 0.000206 Informative Direct
Biological Process (BP) phosphorylation 1 Informative Inherited
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.2992 Informative Inherited
Biological Process (BP) polysaccharide metabolic process 0.01505 Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 0.1741 Informative Inherited
Biological Process (BP) water-soluble vitamin biosynthetic process 0.003995 Informative Inherited
Biological Process (BP) liposaccharide metabolic process 0.0118 Informative Inherited
Biological Process (BP) ATP metabolic process 1 Informative Inherited
Biological Process (BP) nucleoside diphosphate metabolic process 0.1024 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 0.4095 Informative Inherited
Biological Process (BP) lipopolysaccharide metabolic process 0.000848 Highly Informative Direct
Biological Process (BP) thiamine biosynthetic process 0 Highly Informative Direct
Biological Process (BP) glyceraldehyde-3-phosphate metabolic process 0.00003866 Highly Informative Direct
Biological Process (BP) cellular polysaccharide biosynthetic process 0.00004517 Highly Informative Direct
Biological Process (BP) vitamin B6 metabolic process 0.000000001416 Highly Informative Direct
Biological Process (BP) pyridine-containing compound biosynthetic process 0.000002608 Highly Informative Direct
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 0.006092 Moderately Informative Inherited
Molecular Function (MF) lyase activity 0.6352 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.1032 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.007535 Moderately Informative Inherited
Molecular Function (MF) purine nucleoside binding 0.000175 Informative Direct
Molecular Function (MF) kinase activity 0.00004108 Informative Direct
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.0008117 Informative Direct
Molecular Function (MF) hydro-lyase activity 0.0002651 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.0003091 Informative Direct
Molecular Function (MF) ribonucleoside binding 0.0001714 Informative Direct
Molecular Function (MF) ribonucleotide binding 0.0003702 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.0001023 Informative Direct
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 0.3637 Informative Inherited
Molecular Function (MF) ATP binding 0.000004915 Highly Informative Direct
Molecular Function (MF) nucleobase-containing compound kinase activity 0.0008638 Highly Informative Direct
Molecular Function (MF) phosphotransferase activity, phosphate group as acceptor 0.01212 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.06695 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) plastid 0.00188 Informative Inherited
Cellular Component (CC) chloroplast stroma 0.0001981 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)Lyases0.2224Least InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0.000000000004031Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Isomerases1Moderately InformativeInherited
Enzyme Commission (EC)Racemases and epimerases0.000000004113InformativeDirect
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited
Enzyme Commission (EC)Phosphotransferases with a phosphate group as acceptor1InformativeInherited
Enzyme Commission (EC)Acting on other compounds0Highly InformativeDirect

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 biosynthesis0.00000001498Highly InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionMetal-binding0.0000000116Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionNAD0.00000001339Moderately InformativeDirect
Molecular functionPotassium0.000000000000001395InformativeDirect
Molecular functionNADP0.000000000001034InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0.00000001026Moderately InformativeDirect
Post-translational modificationLyase0.000004578Moderately 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 metabolism0.0000002083Moderately InformativeDirect
UniPathway (UP)organic acid metabolism0.07704Moderately 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 degradation0.0000000000008336InformativeDirect
UniPathway (UP)organic acid degradation0.009318InformativeInherited
UniPathway (UP)carbohydrate acid metabolism0.01135InformativeInherited
UniPathway (UP)myo-inositol degradation into acetyl-CoA0Highly InformativeDirect
UniPathway (UP)LPS oligosaccharide biosynthesis0Highly InformativeDirect
UniPathway (UP)aldonic acid degradation0.00000000001387Highly InformativeDirect
UniPathway (UP)LPS core biosynthesis0.0001976Highly InformativeDirect
UniPathway (UP)Lipooligosaccharide metabolism0.0002531Highly InformativeDirect
UniPathway (UP)starch biosynthesis0.0008192Highly 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 ]