SUPERFAMILY 1.75 HMM library and genome assignments server


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 (3,202) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 20,038 49,948 21
Proteins 19,896 49,810 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 process9.391e-094.208e-08Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process4.339e-072.452e-06Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process8.34e-087.543e-05Least InformativeDirect
Biological Process (BP)heterocycle metabolic process8.24e-092.7e-08Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process4.398e-082.504e-07Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.0026430.02048Least InformativeInherited
Biological Process (BP)gene expression06.196e-12Moderately InformativeDirect
Biological Process (BP)RNA metabolic process00Moderately InformativeDirect
Biological Process (BP)cellular component biogenesis1.445e-074.071e-08Moderately InformativeDirect
Biological Process (BP)RNA processing02.96e-09InformativeDirect
Biological Process (BP)RNA modification00InformativeDirect
Biological Process (BP)ribonucleoprotein complex biogenesis2.522e-080InformativeDirect
Biological Process (BP)ncRNA metabolic process09.074e-13InformativeDirect
Biological Process (BP)RNA methylation3.854e-069.973e-12Highly InformativeDirect
Biological Process (BP)rRNA processing0.14790.04092Highly InformativeInherited
Molecular Function (MF)transferase activity, transferring one-carbon groups00InformativeDirect
Molecular Function (MF)S-adenosylmethionine-dependent methyltransferase activity0.19190.2831Highly 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 4.208e-08 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 2.452e-06 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 7.543e-05 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 2.7e-08 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 2.504e-07 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.02048 Least Informative Inherited
Biological Process (BP) gene expression 6.196e-12 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 4.071e-08 Moderately Informative Direct
Biological Process (BP) RNA processing 2.96e-09 Informative Direct
Biological Process (BP) RNA modification 0 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0 Informative Direct
Biological Process (BP) ncRNA metabolic process 9.074e-13 Informative Direct
Biological Process (BP) RNA methylation 9.973e-12 Highly Informative Direct
Biological Process (BP) rRNA processing 0.04092 Highly Informative Inherited
Molecular Function (MF) transporter activity 0.2482 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring one-carbon groups 0 Informative Direct
Molecular Function (MF) S-adenosylmethionine-dependent methyltransferase activity 0.2831 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

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0Least InformativeDirect

Document: MP 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

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) · Mouse Phenotype (MP) · Yeast Phenotype (YP) · 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) · Mouse Phenotype (MP) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]