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 (3,019) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 24,936 68,209 31
Proteins 24,841 68,131 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 process0.27830.05068Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.15870.0384Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.27830.006228Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.17890.06388Least InformativeInherited
Biological Process (BP)biosynthetic process0.098390.003314Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.10480.02846Least InformativeInherited
Biological Process (BP)carbohydrate metabolic process4.069e-094.76e-09Moderately InformativeDirect
Biological Process (BP)phosphate-containing compound metabolic process00Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process1.09e-052.573e-09Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process8.605e-078.632e-10Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process5.453e-061.265e-09Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process1.252e-051.223e-08Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process0.00010616.99e-10Moderately InformativeDirect
Biological Process (BP)organophosphate metabolic process0.0041540.004028Moderately InformativeInherited
Biological Process (BP)single-organism biosynthetic process0.029567.339e-06Moderately InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.073962.593e-07Moderately InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process0.00058110.00841Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.53920.3904Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.008590.005718Moderately InformativeInherited
Biological Process (BP)vitamin metabolic process5.33e-060InformativeDirect
Biological Process (BP)phosphorylation4.703e-080.0002492InformativeDirect
Biological Process (BP)cellular metabolic compound salvage1.942e-137.333e-15InformativeDirect
Biological Process (BP)cellular carbohydrate metabolic process00InformativeDirect
Biological Process (BP)purine-containing compound biosynthetic process1.104e-069.815e-05InformativeDirect
Biological Process (BP)pyridine-containing compound metabolic process3.939e-052.326e-05InformativeDirect
Biological Process (BP)glycosyl compound biosynthetic process8.399e-062.036e-05InformativeDirect
Biological Process (BP)coenzyme biosynthetic process0.0036830.0007971InformativeInherited
Biological Process (BP)pyrimidine-containing compound metabolic process0.0025171.808e-13InformativeInherited
Biological Process (BP)sulfur compound biosynthetic process0.0060529.818e-10InformativeInherited
Biological Process (BP)purine ribonucleoside metabolic process2.798e-050.001354InformativeInherited
Biological Process (BP)hexose metabolic process11InformativeInherited
Biological Process (BP)thiamine-containing compound metabolic process8.5e-060Highly InformativeDirect
Biological Process (BP)vitamin B6 metabolic process0.0005470.0001751Highly InformativeDirect
Biological Process (BP)carbohydrate phosphorylation00Highly InformativeDirect
Biological Process (BP)pyrimidine-containing compound biosynthetic process0.00073335.865e-13Highly InformativeDirect
Biological Process (BP)pentose metabolic process0.037530.04407Highly InformativeInherited
Molecular Function (MF)binding0.96861Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups00Moderately InformativeDirect
Molecular Function (MF)anion binding0.054590.1722Moderately InformativeInherited
Molecular Function (MF)kinase activity00InformativeDirect
Molecular Function (MF)purine ribonucleoside binding5.953e-060.0001883InformativeDirect
Molecular Function (MF)purine ribonucleoside triphosphate binding2.621e-060.0001248InformativeDirect
Molecular Function (MF)nucleotide binding0.32280.4898InformativeInherited
Molecular Function (MF)phosphotransferase activity, alcohol group as acceptor0.026680.5846InformativeInherited
Molecular Function (MF)ATP binding2.653e-106.311e-06Highly InformativeDirect
Molecular Function (MF)carbohydrate kinase activity00Highly InformativeDirect
Molecular Function (MF)nucleobase-containing compound kinase activity0.25920.000692Highly InformativeInherited
Cellular Component (CC)cytoplasmic part0.096570.2465Least InformativeInherited
Cellular Component (CC)cytosol0.00035270.0002066Moderately 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 0.05068 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.0384 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.006228 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.06388 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.003314 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.02846 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 4.76e-09 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 2.593e-07 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 2.573e-09 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 8.632e-10 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 1.265e-09 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 7.339e-06 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 1.223e-08 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 6.99e-10 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.004028 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.00841 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.3904 Moderately Informative Inherited
Biological Process (BP) cofactor metabolic process 0.005718 Moderately Informative Inherited
Biological Process (BP) vitamin metabolic process 0 Informative Direct
Biological Process (BP) coenzyme biosynthetic process 0.0007971 Informative Direct
Biological Process (BP) phosphorylation 0.0002492 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 7.333e-15 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 0 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 9.818e-10 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 9.815e-05 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 2.326e-05 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 1.808e-13 Informative Direct
Biological Process (BP) glycosyl compound biosynthetic process 2.036e-05 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.001354 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 0.0001751 Highly Informative Direct
Biological Process (BP) carbohydrate phosphorylation 0 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 5.865e-13 Highly Informative Direct
Biological Process (BP) pentose metabolic process 0.04407 Highly Informative Inherited
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 0.1722 Moderately Informative Inherited
Molecular Function (MF) kinase activity 0 Informative Direct
Molecular Function (MF) purine ribonucleoside binding 0.0001883 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.0001248 Informative Direct
Molecular Function (MF) nucleotide binding 0.4898 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.5846 Informative Inherited
Molecular Function (MF) ATP binding 6.311e-06 Highly Informative Direct
Molecular Function (MF) carbohydrate kinase activity 0 Highly Informative Direct
Molecular Function (MF) nucleobase-containing compound kinase activity 0.000692 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 0.2465 Least Informative Inherited
Cellular Component (CC) cytosol 0.0002066 Moderately Informative Direct
Cellular Component (CC) plastid 0.003689 Informative Inherited
Cellular Component (CC) chloroplast stroma 0.0001057 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)Lyases0.1743Least InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases7.811e-12Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Isomerases1Moderately InformativeInherited
Enzyme Commission (EC)Racemases and epimerases3.398e-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 biosynthesis1.328e-08Highly InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionNAD1.456e-08Moderately InformativeDirect
Molecular functionNADP1.587e-14InformativeDirect
Molecular functionPotassium2.172e-09InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase1.005e-08Moderately InformativeDirect
Post-translational modificationLyase2.238e-06Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)aromatic compound metabolism1.475e-07Least InformativeDirect
UniPathway (UP)carbohydrate metabolism3.944e-05Least InformativeDirect
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)nucleotide metabolism6.126e-14Moderately InformativeDirect
UniPathway (UP)carbohydrate degradation5.051e-09Moderately InformativeDirect
UniPathway (UP)heterocycle metabolism2.116e-06Moderately InformativeDirect
UniPathway (UP)amino-acid degradation0.002281Moderately InformativeInherited
UniPathway (UP)purine nucleotide metabolism0InformativeDirect
UniPathway (UP)purine biosynthesis1InformativeInherited
UniPathway (UP)purine biosynthesis via salvage pathway0Highly InformativeDirect
UniPathway (UP)AMP biosynthesis0Highly InformativeDirect
UniPathway (UP)fructoselysine degradation2.142e-08Highly 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 ]