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 (2,380)	Uniprot 2013_05	PDB chains (SCOP 1.75)
Domains	20,080	68,209	31
Proteins	19,987	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 term	FDR (singleton)	FDR (all)	SDFO level	Annotation (direct or inherited)
Biological Process (BP)	nitrogen compound metabolic process	0.6079	0.1382	Least Informative	Inherited
Biological Process (BP)	organic cyclic compound metabolic process	0.1505	0.02523	Least Informative	Inherited
Biological Process (BP)	single-organism metabolic process	0.2619	0.00075	Least Informative	Inherited
Biological Process (BP)	cellular aromatic compound metabolic process	0.3557	0.1244	Least Informative	Inherited
Biological Process (BP)	biosynthetic process	0.3861	0.0269	Least Informative	Inherited
Biological Process (BP)	heterocycle metabolic process	0.04109	0.003617	Least Informative	Inherited
Biological Process (BP)	carbohydrate metabolic process	3.28e-07	1.704e-07	Moderately Informative	Direct
Biological Process (BP)	phosphate-containing compound metabolic process	1.938e-07	2.011e-05	Moderately Informative	Direct
Biological Process (BP)	heterocycle biosynthetic process	0.0003711	1.373e-07	Moderately Informative	Direct
Biological Process (BP)	aromatic compound biosynthetic process	0.0008355	9.026e-07	Moderately Informative	Direct
Biological Process (BP)	cellular nitrogen compound biosynthetic process	0.0004526	2.114e-07	Moderately Informative	Direct
Biological Process (BP)	organic cyclic compound biosynthetic process	0.0003022	4.97e-07	Moderately Informative	Direct
Biological Process (BP)	organophosphate metabolic process	0.02615	0.006277	Moderately Informative	Inherited
Biological Process (BP)	nucleobase-containing small molecule metabolic process	0.0007098	0.004062	Moderately Informative	Inherited
Biological Process (BP)	carbohydrate derivative metabolic process	0.4457	0.1936	Moderately Informative	Inherited
Biological Process (BP)	organonitrogen compound biosynthetic process	0.002821	3.931e-07	Moderately Informative	Inherited
Biological Process (BP)	cofactor metabolic process	0.01801	0.01661	Moderately Informative	Inherited
Biological Process (BP)	vitamin metabolic process	0.0005816	2.838e-11	Informative	Direct
Biological Process (BP)	ribonucleoside metabolic process	0.0002124	0.0005253	Informative	Direct
Biological Process (BP)	cellular metabolic compound salvage	1.434e-09	1.888e-10	Informative	Direct
Biological Process (BP)	purine-containing compound biosynthetic process	2.894e-06	0.0003752	Informative	Direct
Biological Process (BP)	pyridine-containing compound metabolic process	1.497e-05	1.201e-05	Informative	Direct
Biological Process (BP)	glycosyl compound biosynthetic process	1.269e-05	5.623e-05	Informative	Direct
Biological Process (BP)	coenzyme biosynthetic process	0.0149	0.004767	Informative	Inherited
Biological Process (BP)	purine nucleoside metabolic process	0.614	0.468	Informative	Inherited
Biological Process (BP)	vitamin B6 metabolic process	6.882e-05	5.914e-05	Highly Informative	Direct
Molecular Function (MF)	transferase activity	0	0	Least Informative	Direct
Molecular Function (MF)	binding	1	1	Least Informative	Inherited
Molecular Function (MF)	transferase activity, transferring phosphorus-containing groups	0	0	Moderately Informative	Direct
Molecular Function (MF)	anion binding	0.04464	0.1297	Moderately Informative	Inherited
Molecular Function (MF)	organic cyclic compound binding	0.003612	0.7181	Moderately Informative	Inherited
Molecular Function (MF)	heterocyclic compound binding	0.002428	0.6903	Moderately Informative	Inherited
Molecular Function (MF)	kinase activity	0	0	Informative	Direct
Molecular Function (MF)	nucleotide binding	0.3172	0.4718	Informative	Inherited
Molecular Function (MF)	phosphotransferase activity, alcohol group as acceptor	0.2936	0.9631	Informative	Inherited
Molecular Function (MF)	ATP binding	5.558e-11	1.118e-06	Highly Informative	Direct
Molecular Function (MF)	carbohydrate kinase activity	0	0	Highly Informative	Direct
Molecular Function (MF)	nucleobase-containing compound kinase activity	0.1338	0.0004027	Highly Informative	Inherited
Cellular Component (CC)	cytoplasmic part	0.2062	0.2722	Least Informative	Inherited
Cellular Component (CC)	cytosol	0.0004268	0.000214	Moderately Informative	Direct

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	0.00075	Least Informative	Direct
Biological Process (BP)	nitrogen compound metabolic process	0.1382	Least Informative	Inherited
Biological Process (BP)	organic cyclic compound metabolic process	0.02523	Least Informative	Inherited
Biological Process (BP)	cellular aromatic compound metabolic process	0.1244	Least Informative	Inherited
Biological Process (BP)	biosynthetic process	0.0269	Least Informative	Inherited
Biological Process (BP)	heterocycle metabolic process	0.003617	Least Informative	Inherited
Biological Process (BP)	carbohydrate metabolic process	1.704e-07	Moderately Informative	Direct
Biological Process (BP)	phosphate-containing compound metabolic process	2.011e-05	Moderately Informative	Direct
Biological Process (BP)	heterocycle biosynthetic process	1.373e-07	Moderately Informative	Direct
Biological Process (BP)	aromatic compound biosynthetic process	9.026e-07	Moderately Informative	Direct
Biological Process (BP)	cellular nitrogen compound biosynthetic process	2.114e-07	Moderately Informative	Direct
Biological Process (BP)	organic cyclic compound biosynthetic process	4.97e-07	Moderately Informative	Direct
Biological Process (BP)	organonitrogen compound biosynthetic process	3.931e-07	Moderately Informative	Direct
Biological Process (BP)	organophosphate metabolic process	0.006277	Moderately Informative	Inherited
Biological Process (BP)	small molecule biosynthetic process	0.09764	Moderately Informative	Inherited
Biological Process (BP)	organic substance catabolic process	0.7691	Moderately Informative	Inherited
Biological Process (BP)	nucleobase-containing small molecule metabolic process	0.004062	Moderately Informative	Inherited
Biological Process (BP)	carbohydrate derivative metabolic process	0.1936	Moderately Informative	Inherited
Biological Process (BP)	cofactor metabolic process	0.01661	Moderately Informative	Inherited
Biological Process (BP)	vitamin metabolic process	2.838e-11	Informative	Direct
Biological Process (BP)	ribonucleoside metabolic process	0.0005253	Informative	Direct
Biological Process (BP)	carbohydrate catabolic process	0.0001281	Informative	Direct
Biological Process (BP)	cellular metabolic compound salvage	1.888e-10	Informative	Direct
Biological Process (BP)	sulfur compound biosynthetic process	9.175e-07	Informative	Direct
Biological Process (BP)	purine-containing compound biosynthetic process	0.0003752	Informative	Direct
Biological Process (BP)	pyridine-containing compound metabolic process	1.201e-05	Informative	Direct
Biological Process (BP)	pyrimidine-containing compound metabolic process	2.903e-09	Informative	Direct
Biological Process (BP)	glycosyl compound biosynthetic process	5.623e-05	Informative	Direct
Biological Process (BP)	coenzyme biosynthetic process	0.004767	Informative	Inherited
Biological Process (BP)	purine nucleoside metabolic process	0.468	Informative	Inherited
Biological Process (BP)	vitamin B6 metabolic process	5.914e-05	Highly Informative	Direct
Biological Process (BP)	pyrimidine-containing compound biosynthetic process	9.702e-09	Highly Informative	Direct
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	0.1297	Moderately Informative	Inherited
Molecular Function (MF)	organic cyclic compound binding	0.7181	Moderately Informative	Inherited
Molecular Function (MF)	heterocyclic compound binding	0.6903	Moderately Informative	Inherited
Molecular Function (MF)	kinase activity	0	Informative	Direct
Molecular Function (MF)	nucleotide binding	0.4718	Informative	Inherited
Molecular Function (MF)	phosphotransferase activity, alcohol group as acceptor	0.9631	Informative	Inherited
Molecular Function (MF)	ATP binding	1.118e-06	Highly Informative	Direct
Molecular Function (MF)	carbohydrate kinase activity	0	Highly Informative	Direct
Molecular Function (MF)	nucleobase-containing compound kinase activity	0.0004027	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	0.2722	Least Informative	Inherited
Cellular Component (CC)	cytosol	0.000214	Moderately Informative	Direct
Cellular Component (CC)	plastid	0.003109	Informative	Inherited
Cellular Component (CC)	chloroplast stroma	9.038e-05	Highly Informative	Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEO level	Annotation (direct or inherited)
Enzyme Commission (EC)	Lyases	1	Least Informative	Inherited
Enzyme Commission (EC)	Phosphotransferases with an alcohol group as accep	0	Moderately Informative	Direct
Enzyme Commission (EC)	Hydro-lyases	9.412e-05	Moderately Informative	Direct
Enzyme Commission (EC)	Transferring alkyl or aryl groups, other than meth	1	Moderately Informative	Inherited
Enzyme Commission (EC)	Phosphotransferases with a phosphate group as acce	1	Informative	Inherited

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)

	WP term	FDR (all)	SDWP level	Annotation (direct or inherited)
Worm Phenotype (WP)	growth variant	0	Least Informative	Direct
Worm Phenotype (WP)	developmental timing variant	0	Least Informative	Direct
Worm Phenotype (WP)	larval development variant	0	Least Informative	Direct

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)

	YP term	FDR (all)	SDYP level	Annotation (direct or inherited)
Yeast Phenotype (YP)	resistance to chemicals	0	Least Informative	Direct

Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)

	XA term	FDR (all)	SDXA level	Annotation (direct or inherited)
Xenopus ANatomical entity (XAN)	alimentary system	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	male genitalia	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	central nervous system	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	cell	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	head	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	viscus	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	gonad	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	sensory system	0	Moderately Informative	Direct

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)

	AP term	FDR (all)	SDAP level	Annotation (direct or inherited)
Plant ANatomical entity (PAN)	bud	0.0001187	Highly Informative	Direct

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEC level	Annotation (direct or inherited)
Enzyme Commission (EC)	Transferring phosphorous-containing groups	0	Least Informative	Direct
Enzyme Commission (EC)	Lyases	0.0007909	Least Informative	Direct
Enzyme Commission (EC)	Phosphotransferases with an alcohol group as acceptor	0	Moderately Informative	Direct
Enzyme Commission (EC)	Carbon-oxygen lyases	0	Moderately Informative	Direct
Enzyme Commission (EC)	Isomerases	1	Moderately Informative	Inherited
Enzyme Commission (EC)	Racemases and epimerases	1.51e-11	Informative	Direct
Enzyme Commission (EC)	Transferring alkyl or aryl groups, other than methyl groups	1	Informative	Inherited
Enzyme Commission (EC)	Phosphotransferases with a phosphate group as acceptor	1	Informative	Inherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)

	KW term	FDR (all)	SDKW level	Annotation (direct or inherited)
Biological process	Carbohydrate metabolism	0	Moderately Informative	Direct
Biological process	Thiamine biosynthesis	0	Highly Informative	Direct
Biological process	Lipopolysaccharide biosynthesis	6.012e-08	Highly Informative	Direct
Molecular function	Metal-binding	0	Least Informative	Direct
Molecular function	Nucleotide-binding	0	Least Informative	Direct
Molecular function	Magnesium	0	Moderately Informative	Direct
Molecular function	NAD	1.027e-08	Moderately Informative	Direct
Molecular function	NADP	5.236e-15	Informative	Direct
Molecular function	Potassium	3.328e-10	Informative	Direct
Post-translational modification	Transferase	0	Least Informative	Direct
Post-translational modification	Kinase	0	Moderately Informative	Direct
Post-translational modification	Nucleotidyltransferase	3.151e-09	Moderately Informative	Direct
Post-translational modification	Lyase	4.094e-06	Moderately Informative	Direct

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)

	UP term	FDR (all)	SDUP level	Annotation (direct or inherited)
UniPathway (UP)	biopolymer metabolism	0	Least Informative	Direct
UniPathway (UP)	cofactor metabolism	0	Least Informative	Direct
UniPathway (UP)	carbohydrate metabolism	0	Least Informative	Direct
UniPathway (UP)	lipid metabolism	0	Least Informative	Direct
UniPathway (UP)	amino-acid metabolism	1	Least Informative	Inherited
UniPathway (UP)	biopolymer biosynthesis	0	Moderately Informative	Direct
UniPathway (UP)	lipid biosynthesis	0	Moderately Informative	Direct
UniPathway (UP)	glycan metabolism	0	Moderately Informative	Direct
UniPathway (UP)	nucleotide metabolism	0	Moderately Informative	Direct
UniPathway (UP)	cellular component biogenesis	0	Moderately Informative	Direct
UniPathway (UP)	membrane lipid metabolism	0	Moderately Informative	Direct
UniPathway (UP)	alcohol metabolism	8.449e-08	Moderately Informative	Direct
UniPathway (UP)	carbohydrate degradation	1	Moderately Informative	Inherited
UniPathway (UP)	amino-acid degradation	1	Moderately Informative	Inherited
UniPathway (UP)	lipopolysaccharide biosynthesis	0	Informative	Direct
UniPathway (UP)	nucleotide-sugar biosynthesis	0	Informative	Direct
UniPathway (UP)	thiamine metabolism	0	Informative	Direct
UniPathway (UP)	alcohol degradation	6.854e-13	Informative	Direct
UniPathway (UP)	myo-inositol degradation into acetyl-CoA	0	Highly Informative	Direct
UniPathway (UP)	LPS oligosaccharide biosynthesis	0	Highly Informative	Direct
UniPathway (UP)	Lipooligosaccharide metabolism	0.0002613	Highly Informative	Direct
UniPathway (UP)	LPS core biosynthesis	0.0004408	Highly Informative	Direct

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.

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Ribokinase-like superfamily