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 (3,062) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 25,531 163,746 31
Proteins 25,418 163,601 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 process0.22450.03669Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.075720.01519Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.25140.004649Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.12890.0446Least InformativeInherited
Biological Process (BP)biosynthetic process0.12110.002106Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.075020.01916Least InformativeInherited
Biological Process (BP)carbohydrate metabolic process2.665e-092.572e-09Moderately InformativeDirect
Biological Process (BP)phosphate-containing compound metabolic process00Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process9.126e-062.649e-10Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process6.58e-075.755e-10Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process4.936e-061.378e-10Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process2.023e-053.354e-09Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process0.0001119.251e-11Moderately InformativeDirect
Biological Process (BP)organophosphate metabolic process0.0035120.002876Moderately InformativeInherited
Biological Process (BP)single-organism biosynthetic process0.021611.035e-06Moderately InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.041978.51e-08Moderately InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process0.00050530.006423Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.63580.4603Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.0056070.002658Moderately InformativeInherited
Biological Process (BP)vitamin metabolic process1.548e-060InformativeDirect
Biological Process (BP)phosphorylation4.958e-080.000127InformativeDirect
Biological Process (BP)cellular metabolic compound salvage3.571e-131.083e-14InformativeDirect
Biological Process (BP)cellular carbohydrate metabolic process00InformativeDirect
Biological Process (BP)purine-containing compound biosynthetic process2.192e-060.0002132InformativeDirect
Biological Process (BP)pyridine-containing compound metabolic process9.868e-064.731e-06InformativeDirect
Biological Process (BP)pyrimidine-containing compound metabolic process0.00096794.112e-14InformativeDirect
Biological Process (BP)glycosyl compound biosynthetic process1.623e-053.89e-05InformativeDirect
Biological Process (BP)coenzyme biosynthetic process0.019720.005016InformativeInherited
Biological Process (BP)sulfur compound biosynthetic process0.0019012.593e-10InformativeInherited
Biological Process (BP)purine ribonucleoside metabolic process5.321e-050.001971InformativeInherited
Biological Process (BP)hexose metabolic process11InformativeInherited
Biological Process (BP)thiamine-containing compound metabolic process7.969e-070Highly InformativeDirect
Biological Process (BP)carbohydrate phosphorylation00Highly InformativeDirect
Biological Process (BP)pyrimidine-containing compound biosynthetic process0.00016271.607e-13Highly InformativeDirect
Biological Process (BP)pentose metabolic process0.038070.04406Highly InformativeInherited
Molecular Function (MF)transferase activity00Least InformativeDirect
Molecular Function (MF)binding0.98261Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups00Moderately InformativeDirect
Molecular Function (MF)anion binding0.032340.08034Moderately InformativeInherited
Molecular Function (MF)kinase activity00InformativeDirect
Molecular Function (MF)purine ribonucleoside binding1.406e-061.063e-05InformativeDirect
Molecular Function (MF)purine ribonucleoside triphosphate binding5.899e-076.463e-06InformativeDirect
Molecular Function (MF)nucleotide binding0.29870.4094InformativeInherited
Molecular Function (MF)phosphotransferase activity, alcohol group as acceptor0.027960.6194InformativeInherited
Molecular Function (MF)ATP binding3.428e-111.614e-07Highly InformativeDirect
Molecular Function (MF)carbohydrate kinase activity00Highly InformativeDirect
Molecular Function (MF)nucleobase-containing compound kinase activity0.240.0003419Highly InformativeInherited
Cellular Component (CC)cytoplasmic part0.1350.1938Least InformativeInherited
Cellular Component (CC)cytosol0.00024497.494e-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 0.03669 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.01519 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.004649 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.0446 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.002106 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.01916 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 2.572e-09 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 8.51e-08 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 2.649e-10 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 5.755e-10 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 1.378e-10 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 1.035e-06 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 3.354e-09 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 9.251e-11 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.002876 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.006423 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.4603 Moderately Informative Inherited
Biological Process (BP) cofactor metabolic process 0.002658 Moderately Informative Inherited
Biological Process (BP) vitamin metabolic process 0 Informative Direct
Biological Process (BP) phosphorylation 0.000127 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 1.083e-14 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 0 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 2.593e-10 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0.0002132 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 4.731e-06 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 4.112e-14 Informative Direct
Biological Process (BP) glycosyl compound biosynthetic process 3.89e-05 Informative Direct
Biological Process (BP) coenzyme biosynthetic process 0.005016 Informative Inherited
Biological Process (BP) purine ribonucleoside metabolic process 0.001971 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 0.0003489 Highly Informative Direct
Biological Process (BP) carbohydrate phosphorylation 0 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 1.607e-13 Highly Informative Direct
Biological Process (BP) pentose metabolic process 0.04406 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 0.08034 Moderately Informative Inherited
Molecular Function (MF) kinase activity 0 Informative Direct
Molecular Function (MF) purine ribonucleoside binding 1.063e-05 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 6.463e-06 Informative Direct
Molecular Function (MF) nucleotide binding 0.4094 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.6194 Informative Inherited
Molecular Function (MF) ATP binding 1.614e-07 Highly Informative Direct
Molecular Function (MF) carbohydrate kinase activity 0 Highly Informative Direct
Molecular Function (MF) nucleobase-containing compound kinase activity 0.0003419 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 0.1938 Least Informative Inherited
Cellular Component (CC) cytosol 7.494e-05 Moderately Informative Direct
Cellular Component (CC) plastid 0.0008618 Informative Direct
Cellular Component (CC) chloroplast stroma 0.0001164 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)Lyases0.1845Least InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases7.596e-12Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Isomerases1Moderately InformativeInherited
Enzyme Commission (EC)Racemases and epimerases2.753e-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)heterocycle metabolism2.806e-10Moderately InformativeDirect
UniPathway (UP)carbohydrate metabolism0.003828Moderately InformativeInherited
UniPathway (UP)purine nucleotide biosynthesis1InformativeInherited
UniPathway (UP)AMP biosynthesis via salvage pathway0Highly InformativeDirect
UniPathway (UP)glycolysis2.613e-07Highly 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 ]