SUPERFAMILY 1.75 HMM library and genome assignments server

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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 (3,250) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 20,152 111,974 21
Proteins 20,025 111,504 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 process0.000000022410.000000004894Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process0.00000015170.00000007818Least InformativeDirect
Biological Process (BP)macromolecule metabolic process0.00000076470.0002996Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.000000023450.000000003575Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.00000011370.00000003313Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.033440.1398Least InformativeInherited
Biological Process (BP)primary metabolic process0.001190.05Least InformativeInherited
Biological Process (BP)gene expression0.0000000000000031190.0000000000004523Moderately InformativeDirect
Biological Process (BP)RNA metabolic process00Moderately InformativeDirect
Biological Process (BP)RNA modification0.0000000000000016070InformativeDirect
Biological Process (BP)ncRNA processing00.00000000003204InformativeDirect
Biological Process (BP)ribosome biogenesis0.0000000034940InformativeDirect
Biological Process (BP)tRNA metabolic process0.43790.8477InformativeInherited
Biological Process (BP)macromolecule methylation0.000000000010290Highly InformativeDirect
Biological Process (BP)tRNA modification0.14650.9141Highly InformativeInherited
Molecular Function (MF)transferase activity0.000000013340.00000000004772Least InformativeDirect
Molecular Function (MF)transferase activity, transferring one-carbon groups00InformativeDirect
Molecular Function (MF)S-adenosylmethionine-dependent methyltransferase activity0.060850.1143Highly 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 0.000000004894 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.00000007818 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0002996 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.000000003575 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00000003313 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.1398 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.05 Least Informative Inherited
Biological Process (BP) gene expression 0.0000000000004523 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) RNA modification 0 Informative Direct
Biological Process (BP) ncRNA processing 0.00000000003204 Informative Direct
Biological Process (BP) ribosome biogenesis 0 Informative Direct
Biological Process (BP) tRNA metabolic process 0.8477 Informative Inherited
Biological Process (BP) macromolecule methylation 0 Highly Informative Direct
Biological Process (BP) tRNA modification 0.9141 Highly Informative Inherited
Biological Process (BP) rRNA metabolic process 0.008198 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.00000000004772 Least Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0 Informative Direct
Molecular Function (MF) S-adenosylmethionine-dependent methyltransferase activity 0.1143 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 ]