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  Home > SCOP hierarchy > Clavaminate synthase-like superfamily


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 (2,071) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 41,535 193,323 31
Proteins 41,066 192,391 31

 Functional annotation
General category Metabolism
Detailed category Secondary metabolism

Document: Function annotation of SCOP domain superfamilies

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

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Mode of Inheritance (MI)Gonosomal inheritance0.0001362InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.07118Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.5755Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal testis morphology0.003517InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cardiovascular system phenotype0.1266Least InformativeInherited
Mammalian Phenotype (MP)abnormal muscle morphology0.1482Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.2828Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart layer morphology0.1487InformativeInherited
Mammalian Phenotype (MP)abnormal cardiac muscle tissue morphology0.05466Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.5984Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.7331Least InformativeInherited
Worm Phenotype (WP)metabolic pathway variant0.1717Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.2512Moderately InformativeInherited
Worm Phenotype (WP)protein expression variant0.2541Moderately InformativeInherited
Worm Phenotype (WP)life span variant0.0000002115InformativeDirect
Worm Phenotype (WP)protein modification variant0.001863InformativeInherited
Worm Phenotype (WP)transgenerational loss of fertility0.0000001473Highly InformativeDirect
Worm Phenotype (WP)protein methylation variant0.000004554Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)urogenital system0.2809Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.2894Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.3776Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.3995Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.5578Least InformativeInherited
Xenopus ANatomical entity (XAN)multi-tissue structure0.8121Moderately InformativeInherited
Xenopus ANatomical entity (XAN)anatomical space0.08619InformativeInherited
Xenopus ANatomical entity (XAN)urinary system0.3848InformativeInherited
Xenopus ANatomical entity (XAN)pronephric tubule0.03646Highly InformativeInherited

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant1Least InformativeInherited
Plant ANatomical entity (PAN)flower1Least InformativeInherited
Plant ANatomical entity (PAN)plant ovule0.2547Highly InformativeInherited

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Transferring phosphorus-containing groups1Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides0.6437Moderately InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups1Moderately InformativeInherited
Enzyme Commission (EC)Transferring groups other than amino-acyl groups1Moderately InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen. The oxygen incorporate0InformativeDirect
Enzyme Commission (EC)RNA-directed RNA polymerase0.0000000000746InformativeDirect
Enzyme Commission (EC)RNA helicase0.0001701InformativeDirect
Enzyme Commission (EC)Acting on single donors with incorporation of molecular oxygen (oxygenases). The oxygen incorporated0.9953InformativeInherited
Enzyme Commission (EC)With 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors0Highly InformativeDirect
Enzyme Commission (EC)With incorporation of one atom of oxygen (internal monooxygenases or internal mixed function oxidase0.000000003879Highly InformativeDirect

Document: EC annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

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 48 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 48 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 · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.