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 (3,244) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 20,138 113,818 21
Proteins 20,011 113,607 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 process0.000000020750.000000052Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.00000088740.000003362Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process0.00000012520.00008685Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.000000018970.00000003358Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.00000009530.0000003137Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.0050350.04227Least InformativeInherited
Biological Process (BP)gene expression0.0000000000000032510.000000000005931Moderately InformativeDirect
Biological Process (BP)RNA metabolic process00Moderately InformativeDirect
Biological Process (BP)cellular component biogenesis0.00000020150.0000000278Moderately InformativeDirect
Biological Process (BP)RNA processing00.0000000003477InformativeDirect
Biological Process (BP)RNA modification00InformativeDirect
Biological Process (BP)ribonucleoprotein complex biogenesis0.000000018340InformativeDirect
Biological Process (BP)ncRNA metabolic process00.000000000009001InformativeDirect
Biological Process (BP)RNA methylation0.0000035240.000000000002713Highly InformativeDirect
Biological Process (BP)rRNA processing0.11490.03425Highly InformativeInherited
Molecular Function (MF)transferase activity0.0000013170.000000005146Least InformativeDirect
Molecular Function (MF)transferase activity, transferring one-carbon groups00InformativeDirect
Molecular Function (MF)methyltransferase activity00Highly InformativeDirect

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 0.000000052 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.000003362 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.00008685 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00000003358 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0000003137 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.04227 Least Informative Inherited
Biological Process (BP) gene expression 0.000000000005931 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.0000000278 Moderately Informative Direct
Biological Process (BP) RNA processing 0.0000000003477 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 0.000000000009001 Informative Direct
Biological Process (BP) RNA methylation 0.000000000002713 Highly Informative Direct
Biological Process (BP) rRNA processing 0.03425 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.000000005146 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transporter activity 0.2826 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.1851 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.0006559 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0 Informative Direct
Molecular Function (MF) methyltransferase activity 0 Highly Informative Direct

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)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence 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 ]