SUPERFAMILY 1.75 HMM library and genome assignments server

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 (3,064) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 25,571 163,746 31
Proteins 25,458 163,601 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)single-organism metabolic process0.000000000038740.00000000008227Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.062930.00626Least InformativeInherited
Biological Process (BP)single-organism cellular process0.91991Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.01660.004313Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.015120.002871Least InformativeInherited
Biological Process (BP)biosynthetic process0.10710.001653Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.013770.002155Least InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.0000000024540.000000002421Moderately InformativeDirect
Biological Process (BP)phosphate-containing compound metabolic process00Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.0000000053330.00000000000007887Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process0.000000000010810.00000000000001587Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process0.0000000023980.00000000000003411Moderately InformativeDirect
Biological Process (BP)nucleobase-containing small molecule metabolic process0.000001520.00002235Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process0.000000019910.00000000000195Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process0.000000090010.000000000000007248Moderately InformativeDirect
Biological Process (BP)organophosphate metabolic process0.0048330.003605Moderately InformativeInherited
Biological Process (BP)organic hydroxy compound metabolic process0.0080820.02593Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.0079390.003226Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.68630.5086Moderately InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.062320.0000006619Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.14780.000319Moderately InformativeInherited
Biological Process (BP)cellular aldehyde metabolic process0.0000059360.00000003868InformativeDirect
Biological Process (BP)vitamin metabolic process0.0000023810InformativeDirect
Biological Process (BP)phosphorylation0.00000077650.0006956InformativeDirect
Biological Process (BP)cellular metabolic compound salvage0.00000000000083430.00000000000002089InformativeDirect
Biological Process (BP)cellular carbohydrate metabolic process00InformativeDirect
Biological Process (BP)purine-containing compound biosynthetic process0.000010230.0004266InformativeDirect
Biological Process (BP)pyridine-containing compound metabolic process0.000000027970.000000009137InformativeDirect
Biological Process (BP)glycosyl compound biosynthetic process0.000013450.00003348InformativeDirect
Biological Process (BP)purine ribonucleoside metabolic process0.00012040.003323InformativeInherited
Biological Process (BP)coenzyme biosynthetic process0.027550.006905InformativeInherited
Biological Process (BP)organic hydroxy compound biosynthetic process0.000024490.001195InformativeInherited
Biological Process (BP)pyrimidine-containing compound metabolic process0.0017780.0000000000001439InformativeInherited
Biological Process (BP)sulfur compound biosynthetic process0.0025980.00000000131InformativeInherited
Biological Process (BP)hexose metabolic process11InformativeInherited
Biological Process (BP)thiamine-containing compound metabolic process0.0000000056430Highly InformativeDirect
Biological Process (BP)vitamin B6 metabolic process0.000000014860.000000000002256Highly InformativeDirect
Biological Process (BP)carbohydrate phosphorylation00Highly InformativeDirect
Biological Process (BP)pyridine-containing compound biosynthetic process0.0000071050.00000005268Highly InformativeDirect
Biological Process (BP)pentose metabolic process0.037140.03338Highly InformativeInherited
Molecular Function (MF)transferase activity00Least InformativeDirect
Molecular Function (MF)binding0.94961Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups00Moderately InformativeDirect
Molecular Function (MF)small molecule binding0.000040240.0005744Moderately InformativeDirect
Molecular Function (MF)carbohydrate derivative binding0.000025260.0007078Moderately InformativeDirect
Molecular Function (MF)anion binding0.032370.08156Moderately InformativeInherited
Molecular Function (MF)kinase activity0.000029330.00003908InformativeDirect
Molecular Function (MF)purine ribonucleoside binding0.0000013950.00001055InformativeDirect
Molecular Function (MF)purine ribonucleoside triphosphate binding0.00000059390.000006464InformativeDirect
Molecular Function (MF)nucleotide binding0.057140.09263InformativeInherited
Molecular Function (MF)phosphotransferase activity, alcohol group as acceptor0.023890.5885InformativeInherited
Molecular Function (MF)ATP binding0.000000000033820.0000001621Highly InformativeDirect
Molecular Function (MF)carbohydrate kinase activity00Highly InformativeDirect
Molecular Function (MF)nucleobase-containing compound kinase activity0.24070.0003475Highly InformativeInherited
Cellular Component (CC)cytoplasmic part0.12970.2014Least InformativeInherited
Cellular Component (CC)cytosol0.00024040.00008634Moderately InformativeDirect

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) single-organism metabolic process 0.00000000008227 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.00626 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.004313 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.002871 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.001653 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.002155 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.000000002421 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0.0000006619 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.00000000000007887 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.00000000000001587 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.00000000000003411 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.000319 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.00002235 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.00000000000195 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.000000000000007248 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.003605 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.02593 Moderately Informative Inherited
Biological Process (BP) cofactor metabolic process 0.003226 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.5086 Moderately Informative Inherited
Biological Process (BP) cellular aldehyde metabolic process 0.00000003868 Informative Direct
Biological Process (BP) vitamin metabolic process 0 Informative Direct
Biological Process (BP) phosphorylation 0.0006956 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 0.00000000000002089 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 0 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0.00000000131 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0.0004266 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0.000000009137 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0.0000000000001439 Informative Direct
Biological Process (BP) glycosyl compound biosynthetic process 0.00003348 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.003323 Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 0.006905 Informative Inherited
Biological Process (BP) organic hydroxy compound biosynthetic process 0.001195 Informative Inherited
Biological Process (BP) hexose metabolic process 1 Informative Inherited
Biological Process (BP) thiamine-containing compound metabolic process 0 Highly Informative Direct
Biological Process (BP) vitamin B6 metabolic process 0.000000000002256 Highly Informative Direct
Biological Process (BP) carbohydrate phosphorylation 0 Highly Informative Direct
Biological Process (BP) pyridine-containing compound biosynthetic process 0.00000005268 Highly Informative Direct
Biological Process (BP) pentose metabolic process 0.03338 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 0.0005744 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.0007078 Moderately Informative Direct
Molecular Function (MF) anion binding 0.08156 Moderately Informative Inherited
Molecular Function (MF) kinase activity 0.00003908 Informative Direct
Molecular Function (MF) purine ribonucleoside binding 0.00001055 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.000006464 Informative Direct
Molecular Function (MF) nucleotide binding 0.09263 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.5885 Informative Inherited
Molecular Function (MF) ATP binding 0.0000001621 Highly Informative Direct
Molecular Function (MF) carbohydrate kinase activity 0 Highly Informative Direct
Molecular Function (MF) nucleobase-containing compound kinase activity 0.0003475 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.2014 Least Informative Inherited
Cellular Component (CC) cytosol 0.00008634 Moderately Informative Direct
Cellular Component (CC) plastid 0.0008475 Informative Direct
Cellular Component (CC) chloroplast stroma 0.0001155 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)growth variant0Least InformativeDirect
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least 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)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)alimentary system0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)visual system0Moderately 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)bud0.00008074Highly 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)Lyases0.1843Least InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0.000000000007642Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Isomerases1Moderately InformativeInherited
Enzyme Commission (EC)Racemases and epimerases0.000000002753InformativeDirect
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 biosynthesis0.00000001253Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionNAD0.0000000133Moderately InformativeDirect
Molecular functionNADP0.0000000000000154InformativeDirect
Molecular functionPotassium0.000000001937InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0.000000009484Moderately InformativeDirect
Post-translational modificationLyase0.000003417Moderately 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 metabolism0.0000001153Moderately InformativeDirect
UniPathway (UP)organic acid metabolism0.05127Moderately 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)polyol degradation0.00000000000007682InformativeDirect
UniPathway (UP)organic acid degradation0.00618InformativeInherited
UniPathway (UP)carbohydrate acid metabolism0.01129InformativeInherited
UniPathway (UP)myo-inositol degradation into acetyl-CoA0Highly InformativeDirect
UniPathway (UP)ADP-L-glycero-beta-D-manno-heptose biosynthesis0Highly InformativeDirect
UniPathway (UP)aldonic acid degradation0.0000000000112Highly InformativeDirect
UniPathway (UP)LPS core biosynthesis0.0001772Highly InformativeDirect
UniPathway (UP)Lipooligosaccharide metabolism0.0002618Highly 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 ]