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alpha/beta knot superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   alpha/beta knot [ 75216]
Superfamily:   alpha/beta knot [ 75217] (8)
Families:   YbeA-like [ 82371] (4)
  tRNA(m1G37)-methyltransferase TrmD [ 89629]
  SpoU-like RNA 2'-O ribose methyltransferase [ 75218] (4)
  Hypothetical protein MTH1 (MT0001), dimerisation domain [ 75221]
  YggJ C-terminal domain-like [ 89632] (3)
  EMG1/NEP1-like [ 159513] (2)
  AF1056-like [ 159518] (2)
  AF0751-like [ 159523]


Superfamily statistics
Genomes (3,245) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 20,140 113,818 21
Proteins 20,014 113,607 21


Functional annotation
General category Other
Detailed category Unknown function

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)cellular aromatic compound metabolic process0.000000018620.00000004191Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process0.00000012930.0000005351Least InformativeDirect
Biological Process (BP)macromolecule metabolic process0.00000060170.0008494Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.000000019510.00000003244Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.000000086150.0000002298Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.02640.2329Least InformativeInherited
Biological Process (BP)primary metabolic process0.00093580.07464Least InformativeInherited
Biological Process (BP)gene expression0.0000000000000030420.000000000005207Moderately InformativeDirect
Biological Process (BP)RNA metabolic process00Moderately InformativeDirect
Biological Process (BP)RNA modification0.0000000000000015570InformativeDirect
Biological Process (BP)ribonucleoprotein complex biogenesis0.00000066040.00000000000001746InformativeDirect
Biological Process (BP)ncRNA processing00.0000000001709InformativeDirect
Biological Process (BP)tRNA metabolic process0.37230.6609InformativeInherited
Biological Process (BP)macromolecule methylation0.0000000000038590Highly InformativeDirect
Biological Process (BP)tRNA modification0.14280.7712Highly InformativeInherited
Molecular Function (MF)transferase activity0.000000012680.0000000005523Least InformativeDirect
Molecular Function (MF)transferase activity, transferring one-carbon groups00InformativeDirect
Molecular Function (MF)S-adenosylmethionine-dependent methyltransferase activity0.050120.1291Highly 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) cellular aromatic compound metabolic process 0.00000004191 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.0000005351 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0008494 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00000003244 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0000002298 Least Informative Direct
Biological Process (BP) primary metabolic process 0.07464 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.2329 Least Informative Inherited
Biological Process (BP) gene expression 0.000000000005207 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) RNA modification 0 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.00000000000001746 Informative Direct
Biological Process (BP) ncRNA processing 0.0000000001709 Informative Direct
Biological Process (BP) tRNA metabolic process 0.6609 Informative Inherited
Biological Process (BP) macromolecule methylation 0 Highly Informative Direct
Biological Process (BP) tRNA modification 0.7712 Highly Informative Inherited
Biological Process (BP) rRNA metabolic process 0.01091 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.0000000005523 Least Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0 Informative Direct
Molecular Function (MF) S-adenosylmethionine-dependent methyltransferase activity 0.1291 Highly Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring one-carbon groups0Least InformativeDirect
Enzyme Commission (EC)Methyltransferases0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)general pace of development variant0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval growth 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)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least 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)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring one-carbon groups0Moderately InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processrRNA processing0InformativeDirect
Biological processtRNA processing0InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionS-adenosyl-L-methionine0InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationMethyltransferase0InformativeDirect

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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 20 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 alpha/beta knot 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 20 hidden Markov models representing the alpha/beta knot 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) · Internal database links ]