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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 (3,070) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 25,630 143,796 31
Proteins 25,516 143,456 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 process0.000014990.0000008491Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process0.000071290.000005108Least InformativeDirect
Biological Process (BP)single-organism metabolic process00Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.0000056130.0000001754Least InformativeDirect
Biological Process (BP)organonitrogen compound metabolic process0.86210.9425Least InformativeInherited
Biological Process (BP)single-organism cellular process0.0015950.0006409Least InformativeInherited
Biological Process (BP)biosynthetic process0.18060.0003224Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.0011670.00005911Least InformativeInherited
Biological Process (BP)primary metabolic process0.89661Least InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.000000000002050Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.00000000022050.00000000000007786Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process0.00000000000060830.00000000000002436Moderately InformativeDirect
Biological Process (BP)monocarboxylic acid metabolic process0.00021190.000008901Moderately InformativeDirect
Biological Process (BP)purine-containing compound metabolic process0.0000000020680.000000000006724Moderately InformativeDirect
Biological Process (BP)organophosphate biosynthetic process0.0000018620.00001463Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process0.000000018970.00000000002657Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process0.46980.3975Moderately InformativeInherited
Biological Process (BP)single-organism catabolic process0.3020.288Moderately InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.020360.000000532Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.0020650.000000395Moderately InformativeInherited
Biological Process (BP)nucleoside phosphate metabolic process0.84340.1726Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.27610.00711Moderately InformativeInherited
Biological Process (BP)generation of precursor metabolites and energy0.43450.2531Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.0040620.00005109Moderately InformativeInherited
Biological Process (BP)monosaccharide metabolic process0.00016150.00005622InformativeDirect
Biological Process (BP)cellular aldehyde metabolic process0.00000000010910.00000000000002436InformativeDirect
Biological Process (BP)carbohydrate catabolic process0.00026490.00004916InformativeDirect
Biological Process (BP)cellular metabolic compound salvage0.00000000058640.00000000000004411InformativeDirect
Biological Process (BP)cellular carbohydrate metabolic process0.000013020.0000006204InformativeDirect
Biological Process (BP)sulfur compound biosynthetic process0.00037450.000000002903InformativeDirect
Biological Process (BP)purine-containing compound biosynthetic process0.000012840.00004981InformativeDirect
Biological Process (BP)pyridine-containing compound metabolic process0.0000000000021450InformativeDirect
Biological Process (BP)pyrimidine-containing compound biosynthetic process0.0000084410InformativeDirect
Biological Process (BP)organic hydroxy compound biosynthetic process0.0000067970.0002081InformativeDirect
Biological Process (BP)oxidoreduction coenzyme metabolic process0.11830.1915InformativeInherited
Biological Process (BP)glycosyl compound metabolic process0.09340.01893InformativeInherited
Biological Process (BP)coenzyme biosynthetic process0.14810.1325InformativeInherited
Biological Process (BP)water-soluble vitamin biosynthetic process0.014060.0001989InformativeInherited
Biological Process (BP)ATP metabolic process0.82850.8342InformativeInherited
Biological Process (BP)phosphorylation0.34071InformativeInherited
Biological Process (BP)thiamine biosynthetic process00Highly InformativeDirect
Biological Process (BP)glyceraldehyde-3-phosphate metabolic process0.000016780.00001074Highly InformativeDirect
Biological Process (BP)vitamin B6 metabolic process0.00000000031620Highly InformativeDirect
Biological Process (BP)purine ribonucleoside metabolic process0.0000004340.0000001035Highly InformativeDirect
Biological Process (BP)pyridine-containing compound biosynthetic process0.0000035290.00000004536Highly InformativeDirect
Molecular Function (MF)transferase activity00Least InformativeDirect
Molecular Function (MF)binding0.87721Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups00Moderately InformativeDirect
Molecular Function (MF)small molecule binding0.0001220.001617Moderately InformativeInherited
Molecular Function (MF)anion binding0.046880.1903Moderately InformativeInherited
Molecular Function (MF)carbohydrate derivative binding0.000080930.001439Moderately InformativeInherited
Molecular Function (MF)kinase activity0.000000023740.0000201InformativeDirect
Molecular Function (MF)phosphotransferase activity, alcohol group as acceptor0.000000000068210.0003621InformativeDirect
Molecular Function (MF)purine nucleotide binding0.0000042980.00007282InformativeDirect
Molecular Function (MF)ribonucleotide binding0.000008240.00009004InformativeDirect
Molecular Function (MF)purine ribonucleoside triphosphate binding0.000073020.00002043InformativeDirect
Molecular Function (MF)ATP binding0.00000000023490.0000007009Highly InformativeDirect
Molecular Function (MF)nucleobase-containing compound kinase activity0.61410.0001408Highly InformativeInherited
Molecular Function (MF)phosphotransferase activity, phosphate group as acceptor10.01653Highly InformativeInherited
Cellular Component (CC)cytoplasmic part0.18740.0571Least 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 0.0000008491 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0003224 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.000005108 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0006409 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0000001754 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00005911 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.9425 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 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 0.000000532 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.00000000000007786 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.00000000000002436 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 0.000008901 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.00005109 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0.000000000006724 Moderately Informative Direct
Biological Process (BP) organophosphate biosynthetic process 0.00001463 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.000000395 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.00000000002657 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.3975 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.288 Moderately Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 0.1726 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.00711 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) generation of precursor metabolites and energy 0.2531 Moderately Informative Inherited
Biological Process (BP) monosaccharide metabolic process 0.00005622 Informative Direct
Biological Process (BP) cellular aldehyde metabolic process 0.00000000000002436 Informative Direct
Biological Process (BP) carbohydrate catabolic process 0.00004916 Informative Direct
Biological Process (BP) water-soluble vitamin biosynthetic process 0.0001989 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 0.00000000000004411 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 0.0000006204 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0.000000002903 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0.00004981 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 0 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 0.0002081 Informative Direct
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.1915 Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 0.1325 Informative Inherited
Biological Process (BP) glycosyl compound metabolic process 0.01893 Informative Inherited
Biological Process (BP) liposaccharide metabolic process 0.02665 Informative Inherited
Biological Process (BP) ATP metabolic process 0.8342 Informative Inherited
Biological Process (BP) phosphorylation 1 Informative Inherited
Biological Process (BP) polysaccharide metabolic process 0.02156 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 0.2191 Informative Inherited
Biological Process (BP) nucleoside biosynthetic process 0.0003584 Highly Informative Direct
Biological Process (BP) thiamine biosynthetic process 0 Highly Informative Direct
Biological Process (BP) glyceraldehyde-3-phosphate metabolic process 0.00001074 Highly Informative Direct
Biological Process (BP) cellular polysaccharide biosynthetic process 0.00005595 Highly Informative Direct
Biological Process (BP) vitamin B6 metabolic process 0 Highly Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.0000001035 Highly Informative Direct
Biological Process (BP) pyridine-containing compound biosynthetic process 0.00000004536 Highly Informative Direct
Biological Process (BP) lipopolysaccharide metabolic process 0.001056 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) small molecule binding 0.001617 Moderately Informative Inherited
Molecular Function (MF) lyase activity 0.6744 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.1903 Moderately Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.001439 Moderately Informative Inherited
Molecular Function (MF) kinase activity 0.0000201 Informative Direct
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.0003621 Informative Direct
Molecular Function (MF) hydro-lyase activity 0.0002749 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.00007282 Informative Direct
Molecular Function (MF) ribonucleotide binding 0.00009004 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.00002043 Informative Direct
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 0.3938 Informative Inherited
Molecular Function (MF) ATP binding 0.0000007009 Highly Informative Direct
Molecular Function (MF) nucleobase-containing compound kinase activity 0.0001408 Highly Informative Direct
Molecular Function (MF) phosphotransferase activity, phosphate group as acceptor 0.01653 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.0571 Least Informative Inherited
Cellular Component (CC) plastid 0.0006529 Informative Direct
Cellular Component (CC) chloroplast stroma 0.0003063 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCarbohydrate metabolism0Moderately InformativeDirect
Biological processThiamine biosynthesis0Highly InformativeDirect
Biological processLipopolysaccharide biosynthesis0.0000000143Highly InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionNADP0.00000002384Moderately InformativeDirect
Molecular functionNAD0.00005099Moderately InformativeDirect
Molecular functionPotassium0.000000000001352InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0.000000003326Moderately InformativeDirect
Post-translational modificationLyase0.000001107Moderately InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · 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 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) · UniProtKB KeyWords (KW) · Internal database links ]