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Clavaminate synthase-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Double-stranded beta-helix [ 51181] (7)
Superfamily:   Clavaminate synthase-like [ 51197] (13)
Families:   Penicillin synthase-like [ 51198] (4)
  Clavaminate synthase [ 51203]
  Gab protein (hypothetical protein YgaT) [ 63855]
  YhcH-like [ 89413]
  Type II Proline 3-hydroxylase (proline oxidase) [ 63858]
  TauD/TfdA-like [ 75038] (2)
  gamma-Butyrobetaine hydroxylase [ 89416] (2)
  Hypoxia-inducible factor HIF ihhibitor (FIH1) [ 82194]
  PhyH-like [ 141623] (2)
  AlkB-like [ 141628] (2)
  Asparaginyl hydroxylase-like [ 141633]
  YbiU-like [ 141636]
  TehB-like [ 159307] (2)


Superfamily statistics
Genomes (2,069) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 41,398 144,191 31
Proteins 40,932 143,410 31


Functional annotation
General category Metabolism
Detailed category Secondary metabolism

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 process0.000000000083530Least InformativeDirect
Biological Process (BP)biosynthetic process0.63381Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)response to stimulus0.15791Least InformativeInherited
Biological Process (BP)biological regulation11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.070591Least InformativeInherited
Biological Process (BP)single-organism cellular process0.095420.01948Least InformativeInherited
Biological Process (BP)macromolecule metabolic process10.1367Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process10.01203Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.084781Least InformativeInherited
Biological Process (BP)primary metabolic process11Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.69821Least InformativeInherited
Biological Process (BP)heterocycle biosynthetic process11Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process11Moderately InformativeInherited
Biological Process (BP)organic substance transport0.98181Moderately InformativeInherited
Biological Process (BP)lipid metabolic process0.000082720.423Moderately InformativeInherited
Biological Process (BP)cellular response to stress0.0000011840.02764Moderately InformativeInherited
Biological Process (BP)regulation of gene expression10.0000002837Moderately InformativeInherited
Biological Process (BP)regulation of macromolecule biosynthetic process10.006948Moderately InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process10.00000002143Moderately InformativeInherited
Biological Process (BP)regulation of cellular biosynthetic process10.0007992Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.46361Moderately InformativeInherited
Biological Process (BP)single-organism catabolic process0.65661Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process0.87071Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process0.29610.2736Moderately InformativeInherited
Biological Process (BP)oxidation-reduction process0.00000000076630.004142Moderately InformativeInherited
Biological Process (BP)cellular protein modification process10Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.53490.2925Moderately InformativeInherited
Biological Process (BP)response to abiotic stimulus0.0000039410.2135Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.0050441Moderately InformativeInherited
Biological Process (BP)nitrogen compound transport0.76431Moderately InformativeInherited
Biological Process (BP)gene expression0.29121Moderately InformativeInherited
Biological Process (BP)cellular localization0.34761Moderately InformativeInherited
Biological Process (BP)macromolecule localization0.61081Moderately InformativeInherited
Biological Process (BP)isoprenoid metabolic process0.00000000019020.0000000000004846InformativeDirect
Biological Process (BP)RNA modification0.0000004480.00009435InformativeDirect
Biological Process (BP)carboxylic acid catabolic process0.053850.03884InformativeInherited
Biological Process (BP)protein transport0.11051InformativeInherited
Biological Process (BP)secondary metabolic process0.0092210.5543InformativeInherited
Biological Process (BP)regulation of transcription from RNA polymerase II promoter0.34631InformativeInherited
Biological Process (BP)peptidyl-amino acid modification0.53840.8325InformativeInherited
Biological Process (BP)response to radiation0.47730.1245InformativeInherited
Biological Process (BP)intracellular transport0.08461InformativeInherited
Biological Process (BP)cellular response to DNA damage stimulus0.002220.00001993InformativeInherited
Biological Process (BP)DNA metabolic process0.0000087140.9786InformativeInherited
Biological Process (BP)isoprenoid biosynthetic process0.000000034690.0000001884Highly InformativeDirect
Biological Process (BP)response to red or far red light0.00005860.0001202Highly InformativeDirect
Biological Process (BP)flavonoid biosynthetic process0.000000004570.000000008695Highly InformativeDirect
Biological Process (BP)diterpenoid metabolic process0.00070310.0001098Highly InformativeDirect
Biological Process (BP)regulation of transcription from RNA polymerase II promoter in response to stress0.00089850.0000949Highly InformativeDirect
Biological Process (BP)secondary metabolite biosynthetic process0.00045890.000244Highly InformativeDirect
Biological Process (BP)demethylation00Highly InformativeDirect
Biological Process (BP)ribonucleoprotein complex localization0.000000036530.000114Highly InformativeDirect
Biological Process (BP)lactone biosynthetic process0.00000038360.0000004163Highly InformativeDirect
Biological Process (BP)DNA methylation or demethylation0.45750.4506Highly InformativeInherited
Biological Process (BP)nucleobase-containing compound transport0.000051810.0104Highly InformativeInherited
Biological Process (BP)establishment of RNA localization0.00000047180.001649Highly InformativeInherited
Biological Process (BP)nuclear export0.00000058080.001725Highly InformativeInherited
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)oxidoreductase activity00Moderately InformativeDirect
Molecular Function (MF)metal ion binding0.000090550Moderately InformativeDirect
Molecular Function (MF)nucleic acid binding0.78960.5812Moderately InformativeInherited
Molecular Function (MF)RNA binding0.26010.3683InformativeInherited
Molecular Function (MF)iron ion binding00Highly InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxyge00Highly InformativeDirect
Molecular Function (MF)dioxygenase activity00Highly InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on the CH-NH2 group of donors0.000000043510.05822Highly InformativeInherited

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 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.01948 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.1367 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.01203 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.003117 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) cellular protein modification process 0 Moderately Informative Direct
Biological Process (BP) organelle organization 0.000000000000001925 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.000001177 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0000002837 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.00000002143 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.0007992 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.006948 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 1 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.7705 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.03856 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.423 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 1 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.2736 Moderately Informative Inherited
Biological Process (BP) oxidation-reduction process 0.004142 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) animal organ development 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.7874 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.2925 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.2135 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.02764 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) isoprenoid metabolic process 0.0000000000004846 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.00001993 Informative Direct
Biological Process (BP) RNA modification 0.00009435 Informative Direct
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.0001526 Informative Direct
Biological Process (BP) negative regulation of cellular biosynthetic process 0.0002107 Informative Direct
Biological Process (BP) regulation of organelle organization 0.0004258 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.00001329 Informative Direct
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) ammonium ion metabolic process 0.0003002 Informative Direct
Biological Process (BP) glycosyl compound metabolic process 0.2243 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.03884 Informative Inherited
Biological Process (BP) protein transport 1 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 1 Informative Inherited
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 1 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.02891 Informative Inherited
Biological Process (BP) negative regulation of cell communication 1 Informative Inherited
Biological Process (BP) negative regulation of signaling 1 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 1 Informative Inherited
Biological Process (BP) regulation of cell differentiation 1 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.3603 Informative Inherited
Biological Process (BP) cell cycle process 0.6463 Informative Inherited
Biological Process (BP) secondary metabolic process 0.5543 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 1 Informative Inherited
Biological Process (BP) DNA metabolic process 0.9786 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 1 Informative Inherited
Biological Process (BP) positive regulation of gene expression 0.7132 Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 0.2431 Informative Inherited
Biological Process (BP) regulation of protein modification process 0.3077 Informative Inherited
Biological Process (BP) central nervous system development 0.1796 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.8325 Informative Inherited
Biological Process (BP) response to radiation 0.1245 Informative Inherited
Biological Process (BP) tRNA metabolic process 0.004251 Informative Inherited
Biological Process (BP) ncRNA processing 0.1063 Informative Inherited
Biological Process (BP) intracellular transport 1 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) circulatory system development 0.2777 Informative Inherited
Biological Process (BP) isoprenoid biosynthetic process 0.0000001884 Highly Informative Direct
Biological Process (BP) response to red or far red light 0.0001202 Highly Informative Direct
Biological Process (BP) flavonoid biosynthetic process 0.000000008695 Highly Informative Direct
Biological Process (BP) diterpenoid metabolic process 0.0001098 Highly Informative Direct
Biological Process (BP) histone modification 0 Highly Informative Direct
Biological Process (BP) antibiotic biosynthetic process 0.000997 Highly Informative Direct
Biological Process (BP) negative regulation of protein modification process 0.000008353 Highly Informative Direct
Biological Process (BP) regulation of chromosome organization 0 Highly Informative Direct
Biological Process (BP) regulation of transcription from RNA polymerase II promoter in response to stress 0.0000949 Highly Informative Direct
Biological Process (BP) secondary metabolite biosynthetic process 0.000244 Highly Informative Direct
Biological Process (BP) mitotic cell cycle phase transition 0.000008148 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 0.00003037 Highly Informative Direct
Biological Process (BP) demethylation 0 Highly Informative Direct
Biological Process (BP) ribonucleoprotein complex localization 0.000114 Highly Informative Direct
Biological Process (BP) lactone biosynthetic process 0.0000004163 Highly Informative Direct
Biological Process (BP) DNA methylation or demethylation 0.4506 Highly Informative Inherited
Biological Process (BP) cellular response to abiotic stimulus 0.5889 Highly Informative Inherited
Biological Process (BP) nucleobase-containing compound transport 0.0104 Highly Informative Inherited
Biological Process (BP) establishment of RNA localization 0.001649 Highly Informative Inherited
Biological Process (BP) nuclear export 0.001725 Highly Informative Inherited
Biological Process (BP) regulation of gene expression, epigenetic 0.01055 Highly Informative Inherited
Biological Process (BP) peptidyl-lysine modification 0.002857 Highly Informative Inherited
Biological Process (BP) angiogenesis 0.04323 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) metal ion binding 0 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.5812 Moderately Informative Inherited
Molecular Function (MF) receptor binding 1 Informative Inherited
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.51 Informative Inherited
Molecular Function (MF) RNA binding 0.3683 Informative Inherited
Molecular Function (MF) chromatin binding 0.0000002417 Highly Informative Direct
Molecular Function (MF) iron ion binding 0 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxyge 0 Highly Informative Direct
Molecular Function (MF) dioxygenase activity 0 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH2 group of donors 0.05822 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.2267 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) nuclear part 0.00009206 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.00002649 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.3494 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.0001833 Informative Direct
Cellular Component (CC) nucleoplasm part 0.07023 Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.8245Least InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases0.6674Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups1Least InformativeInherited
Enzyme Commission (EC)Acting on paired donors, with incorporation or red0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0.008223Moderately InformativeInherited
Enzyme Commission (EC)Methyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)RNA-directed RNA polymerase0.00000000001846InformativeDirect
Enzyme Commission (EC)With 2-oxoglutarate as one donor, and incorporatio0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processDifferentiation0.000000256Moderately InformativeDirect
Biological processViral RNA replication0.0000000001739InformativeDirect
Biological processBiological rhythms0.0000002663InformativeDirect
Biological processPlant defense0.00004645InformativeDirect
Biological processAntibiotic biosynthesis0Highly InformativeDirect
Biological processAlkaloid metabolism0.000000000002537Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationRepressor0.00000000000002388Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase1Moderately InformativeInherited
Post-translational modificationChromatin regulator0InformativeDirect
Post-translational modificationDioxygenase0Highly InformativeDirect
Post-translational modificationRNA-directed RNA polymerase0.00000000006218Highly InformativeDirect
Post-translational modificationPhosphoprotein0.0001989Least InformativeDirect
Post-translational modificationHydroxylation0.0000927InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

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 21 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 Clavaminate synthase-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 21 hidden Markov models representing the Clavaminate synthase-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) · UniProtKB KeyWords (KW) · Internal database links ]