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 (3,063) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 25,536 163,746 31
Proteins 25,423 163,601 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)nitrogen compound metabolic process0.22040.03621Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.073590.01522Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.22820.00395Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.12950.04567Least InformativeInherited
Biological Process (BP)biosynthetic process0.11230.001903Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.074250.01949Least InformativeInherited
Biological Process (BP)carbohydrate metabolic process2.51e-092.661e-09Moderately InformativeDirect
Biological Process (BP)phosphate-containing compound metabolic process00Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process8.605e-062.533e-10Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process6.334e-075.535e-10Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process4.612e-061.302e-10Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process1.93e-053.238e-09Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process9.949e-057.261e-11Moderately InformativeDirect
Biological Process (BP)organophosphate metabolic process0.0030170.002706Moderately InformativeInherited
Biological Process (BP)single-organism biosynthetic process0.019828.789e-07Moderately InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.037336.894e-08Moderately InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process0.00046190.006213Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.61910.4511Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.0045640.002391Moderately InformativeInherited
Biological Process (BP)vitamin metabolic process1.601e-060InformativeDirect
Biological Process (BP)phosphorylation6.858e-080.0001704InformativeDirect
Biological Process (BP)cellular metabolic compound salvage3.959e-131.091e-14InformativeDirect
Biological Process (BP)cellular carbohydrate metabolic process00InformativeDirect
Biological Process (BP)purine-containing compound biosynthetic process2.196e-060.0002041InformativeDirect
Biological Process (BP)pyridine-containing compound metabolic process1.015e-054.849e-06InformativeDirect
Biological Process (BP)pyrimidine-containing compound metabolic process0.00094123.468e-14InformativeDirect
Biological Process (BP)glycosyl compound biosynthetic process1.476e-053.278e-05InformativeDirect
Biological Process (BP)coenzyme biosynthetic process0.019420.004624InformativeInherited
Biological Process (BP)sulfur compound biosynthetic process0.001692.221e-10InformativeInherited
Biological Process (BP)purine ribonucleoside metabolic process5.201e-050.002036InformativeInherited
Biological Process (BP)hexose metabolic process11InformativeInherited
Biological Process (BP)thiamine-containing compound metabolic process8.921e-070Highly InformativeDirect
Biological Process (BP)carbohydrate phosphorylation00Highly InformativeDirect
Biological Process (BP)pyrimidine-containing compound biosynthetic process0.000161.305e-13Highly InformativeDirect
Biological Process (BP)pentose metabolic process0.037420.04358Highly InformativeInherited
Molecular Function (MF)transferase activity00Least InformativeDirect
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups00Moderately InformativeDirect
Molecular Function (MF)anion binding0.057610.1214Moderately InformativeInherited
Molecular Function (MF)kinase activity00InformativeDirect
Molecular Function (MF)purine ribonucleoside binding1.26e-057.332e-05InformativeDirect
Molecular Function (MF)purine ribonucleoside triphosphate binding5.813e-064.733e-05InformativeDirect
Molecular Function (MF)nucleotide binding0.33950.4568InformativeInherited
Molecular Function (MF)phosphotransferase activity, alcohol group as acceptor0.019920.548InformativeInherited
Molecular Function (MF)ATP binding7.428e-101.741e-06Highly InformativeDirect
Molecular Function (MF)carbohydrate kinase activity00Highly InformativeDirect
Molecular Function (MF)nucleobase-containing compound kinase activity0.30030.0009267Highly InformativeInherited
Cellular Component (CC)cytoplasmic part0.16260.2328Least InformativeInherited
Cellular Component (CC)cytosol0.00031499.818e-05Moderately 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) nitrogen compound metabolic process 0.03621 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.01522 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.00395 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.04567 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.001903 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.01949 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 2.661e-09 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 6.894e-08 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 2.533e-10 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 5.535e-10 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 1.302e-10 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 8.789e-07 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 3.238e-09 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 7.261e-11 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.002706 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.006213 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.4511 Moderately Informative Inherited
Biological Process (BP) cofactor metabolic process 0.002391 Moderately Informative Inherited
Biological Process (BP) vitamin metabolic process 0 Informative Direct
Biological Process (BP) phosphorylation 0.0001704 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 1.091e-14 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 0 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 2.221e-10 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0.0002041 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 4.849e-06 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 3.468e-14 Informative Direct
Biological Process (BP) glycosyl compound biosynthetic process 3.278e-05 Informative Direct
Biological Process (BP) coenzyme biosynthetic process 0.004624 Informative Inherited
Biological Process (BP) purine ribonucleoside metabolic process 0.002036 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 0.0003751 Highly Informative Direct
Biological Process (BP) carbohydrate phosphorylation 0 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 1.305e-13 Highly Informative Direct
Biological Process (BP) pentose metabolic process 0.04358 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) anion binding 0.1214 Moderately Informative Inherited
Molecular Function (MF) kinase activity 0 Informative Direct
Molecular Function (MF) purine ribonucleoside binding 7.332e-05 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 4.733e-05 Informative Direct
Molecular Function (MF) nucleotide binding 0.4568 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.548 Informative Inherited
Molecular Function (MF) ATP binding 1.741e-06 Highly Informative Direct
Molecular Function (MF) carbohydrate kinase activity 0 Highly Informative Direct
Molecular Function (MF) nucleobase-containing compound kinase activity 0.0009267 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 0.2328 Least Informative Inherited
Cellular Component (CC) cytosol 9.818e-05 Moderately Informative Direct
Cellular Component (CC) plastid 0.0009765 Informative Direct
Cellular Component (CC) chloroplast stroma 0.0001286 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-lyases9.412e-05Moderately 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)bud8.074e-05Highly 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)Lyases0.1733Least InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases7.668e-12Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Isomerases1Moderately InformativeInherited
Enzyme Commission (EC)Racemases and epimerases2.793e-09InformativeDirect
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 biosynthesis1.26e-08Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionNAD1.361e-08Moderately InformativeDirect
Molecular functionNADP1.588e-14InformativeDirect
Molecular functionPotassium1.977e-09InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase1.023e-08Moderately InformativeDirect
Post-translational modificationLyase2.959e-06Moderately 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 metabolism1.164e-07Moderately InformativeDirect
UniPathway (UP)organic acid metabolism0.05149Moderately 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 degradation7.786e-14InformativeDirect
UniPathway (UP)organic acid degradation0.006199InformativeInherited
UniPathway (UP)carbohydrate acid metabolism0.0113InformativeInherited
UniPathway (UP)myo-inositol degradation into acetyl-CoA0Highly InformativeDirect
UniPathway (UP)ADP-L-glycero-beta-D-manno-heptose biosynthesis0Highly InformativeDirect
UniPathway (UP)aldonic acid degradation1.124e-11Highly InformativeDirect
UniPathway (UP)LPS core biosynthesis0.0001768Highly InformativeDirect
UniPathway (UP)Lipooligosaccharide metabolism0.0002613Highly 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 ]