SUPERFAMILY 1.75 HMM library and genome assignments server

L30e-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Bacillus chorismate mutase-like [ 55297] (9)
Superfamily:   L30e-like [ 55315] (3)
Families:   L30e/L7ae ribosomal proteins [ 55316] (4)
  RNA 2'-O ribose methyltransferase substrate binding domain [ 75480] (2)
  ERF1/Dom34 C-terminal domain-like [ 55323] (3)


Superfamily statistics
Genomes (3,158) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 12,921 51,469 30
Proteins 12,906 51,458 30


Functional annotation
General category Information
Detailed category Translation

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 process0.000029210.00005465Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process0.00000000029140.0000000000008831Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.000025990.00003225Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.00000056060.00000148Least InformativeDirect
Biological Process (BP)regulation of metabolic process0.013891Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.0015590.0008891Least InformativeInherited
Biological Process (BP)positive regulation of biological process0.11281Least InformativeInherited
Biological Process (BP)regulation of cellular process0.72761Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.0011010.00089Least InformativeInherited
Biological Process (BP)biosynthetic process0.37110.02353Least InformativeInherited
Biological Process (BP)protein metabolic process0.17440.1652Least InformativeInherited
Biological Process (BP)gene expression0.00000000000043670Moderately InformativeDirect
Biological Process (BP)RNA metabolic process0.000000012990.000000004232Moderately InformativeDirect
Biological Process (BP)regulation of catalytic activity0.0013220.1996Moderately InformativeInherited
Biological Process (BP)positive regulation of metabolic process0.0098591Moderately InformativeInherited
Biological Process (BP)regulation of phosphorus metabolic process0.00025860.2138Moderately InformativeInherited
Biological Process (BP)regulation of signal transduction0.0012130.7531Moderately InformativeInherited
Biological Process (BP)positive regulation of response to stimulus0.00069040.3461Moderately InformativeInherited
Biological Process (BP)regulation of protein metabolic process0.00071650.001844Moderately InformativeInherited
Biological Process (BP)positive regulation of molecular function0.020910.1407Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process0.040941Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.0011790.00146Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.0095030.00005147Moderately InformativeInherited
Biological Process (BP)RNA modification0.00000000044540InformativeDirect
Biological Process (BP)ribonucleoprotein complex biogenesis00InformativeDirect
Biological Process (BP)ncRNA metabolic process0.000019560.00000002434InformativeDirect
Biological Process (BP)regulation of protein phosphorylation0.00000017480.005722InformativeInherited
Biological Process (BP)regulation of transferase activity0.000000022990.001501InformativeInherited
Biological Process (BP)positive regulation of phosphate metabolic process0.071950.08605InformativeInherited
Biological Process (BP)regulation of MAPK cascade0.00022160.002612InformativeInherited
Biological Process (BP)positive regulation of intracellular signal transduction0.0000025260.009569InformativeInherited
Biological Process (BP)positive regulation of cellular protein metabolic process0.00043780.008188InformativeInherited
Biological Process (BP)RNA processing0.00089760.05091InformativeInherited
Biological Process (BP)rRNA processing0.000027060.00000007585Highly InformativeDirect
Biological Process (BP)positive regulation of MAPK cascade0.000000012080.0003275Highly InformativeDirect
Biological Process (BP)positive regulation of protein kinase activity0.0028370.007982Highly InformativeInherited
Molecular Function (MF)binding0.000020370.2754Least InformativeInherited
Molecular Function (MF)nucleic acid binding00.0000000000007202Moderately InformativeDirect
Molecular Function (MF)structural molecule activity0.0000042940.00000003269Moderately InformativeDirect
Molecular Function (MF)RNA binding0.000035830.000000000000006187InformativeDirect
Molecular Function (MF)structural constituent of ribosome0.00000017970.0000000000002208InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle0.0000000037570.00000001846Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle11Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.012560.2812Least InformativeInherited
Cellular Component (CC)cytoplasmic part11Least InformativeInherited
Cellular Component (CC)cytosol0.00010260.00001756Moderately InformativeDirect
Cellular Component (CC)ribonucleoprotein complex00Moderately InformativeDirect
Cellular Component (CC)nuclear part0.012490.08479Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.02570.1957Moderately InformativeInherited
Cellular Component (CC)small nucleolar ribonucleoprotein complex0.00000000030810.00000000000004363Highly InformativeDirect
Cellular Component (CC)nucleolar part0.00011270.00001165Highly 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 0.00005465 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0008891 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0000000000008831 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00003225 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.00000148 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00089 Least Informative Direct
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.02353 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.1652 Least Informative Inherited
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.000000004232 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00005147 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.1996 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of phosphorus metabolic process 0.2138 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.7531 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.3461 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.002514 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.001844 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.1407 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.00146 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) RNA modification 0 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.0003405 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0 Informative Direct
Biological Process (BP) ncRNA metabolic process 0.00000002434 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 0.005722 Informative Inherited
Biological Process (BP) regulation of transferase activity 0.001501 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.08605 Informative Inherited
Biological Process (BP) regulation of MAPK cascade 0.002612 Informative Inherited
Biological Process (BP) positive regulation of intracellular signal transduction 0.009569 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 0.008188 Informative Inherited
Biological Process (BP) RNA processing 0.05091 Informative Inherited
Biological Process (BP) rRNA processing 0.00000007585 Highly Informative Direct
Biological Process (BP) regulation of translation 0.00002165 Highly Informative Direct
Biological Process (BP) cellular component disassembly 0.00000000004123 Highly Informative Direct
Biological Process (BP) positive regulation of MAPK cascade 0.0003275 Highly Informative Direct
Biological Process (BP) positive regulation of protein kinase activity 0.007982 Highly Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) binding 0.2754 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.0000000000007202 Moderately Informative Direct
Molecular Function (MF) structural molecule activity 0.00000003269 Moderately Informative Direct
Molecular Function (MF) RNA binding 0.000000000000006187 Informative Direct
Molecular Function (MF) structural constituent of ribosome 0.0000000000002208 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.00004867 Informative Direct
Molecular Function (MF) methyltransferase activity 0.00002619 Highly Informative Direct
Molecular Function (MF) translation factor activity, nucleic acid binding 0.08849 Highly Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.00000001846 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.2812 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) cytosol 0.00001756 Moderately Informative Direct
Cellular Component (CC) ribonucleoprotein complex 0 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.08479 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.1957 Moderately Informative Inherited
Cellular Component (CC) cytosolic ribosome 0.0001744 Informative Direct
Cellular Component (CC) large ribosomal subunit 0.1884 Informative Inherited
Cellular Component (CC) small nucleolar ribonucleoprotein complex 0.00000000000004363 Highly Informative Direct
Cellular Component (CC) nucleolar part 0.00001165 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)hematopoietic system phenotype0.2466Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.2904Least InformativeInherited
Mammalian Phenotype (MP)renal/urinary system phenotype0.02664Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.02974Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.03839Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune cell physiology0.06144Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell-mediated immunity0.06255Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal adaptive immunity0.06494Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell physiology0.06919Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal renal glomerulus morphology0.0008863InformativeDirect
Mammalian Phenotype (MP)autoimmune response0.001788InformativeInherited
Mammalian Phenotype (MP)abnormal kidney physiology0.001788InformativeInherited
Mammalian Phenotype (MP)abnormal humoral immune response0.005085InformativeInherited
Mammalian Phenotype (MP)abnormal B cell physiology0.007128InformativeInherited
Mammalian Phenotype (MP)increased anti-nuclear antigen antibody level0.00003508Highly InformativeDirect
Mammalian Phenotype (MP)renal/urinary system inflammation0.0001974Highly InformativeDirect
Mammalian Phenotype (MP)abnormal IgG1 level0.0003484Highly InformativeDirect
Mammalian Phenotype (MP)increased immunoglobulin level0.0007619Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.02751Least InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.0002519Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.0002589Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.001696Moderately InformativeInherited
Worm Phenotype (WP)endocytic transport defect0.004996Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.1506Moderately InformativeInherited
Worm Phenotype (WP)pachytene progression during oogenesis variant0.0000009442InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant0.000001253InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.000006446InformativeDirect
Worm Phenotype (WP)rachis morphology variant0.000007097InformativeDirect
Worm Phenotype (WP)receptor mediated endocytosis defective0.0009897InformativeDirect
Worm Phenotype (WP)gonad vesiculated0.0000002718Highly InformativeDirect
Worm Phenotype (WP)oocyte number decreased0.000001312Highly InformativeDirect
Worm Phenotype (WP)nuclear appearance variant0.007363Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)alimentary system0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups0Moderately InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0.0001893InformativeDirect
Enzyme Commission (EC)Ribonuclease P0.0000001234Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle0.01155Moderately InformativeInherited
Biological processrRNA processing0InformativeDirect
Biological processtRNA processing0.0000000000002908InformativeDirect
Biological processmRNA splicing0.000000000001137InformativeDirect
Biological processRibosome biogenesis0.000000000002787InformativeDirect
Biological processProtein biosynthesis0.00000000006471InformativeDirect
Cellular componentCytoplasm0.000000000000001914Least InformativeDirect
Cellular componentNucleus0.00003983Least InformativeDirect
Cellular componentSpliceosome0InformativeDirect
Molecular functionRNA-binding0.000000009599Moderately InformativeDirect
Molecular functionS-adenosyl-L-methionine0InformativeDirect
Post-translational modificationHydrolase0.03292Least InformativeInherited
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationEndonuclease0InformativeDirect
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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · 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 18 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 L30e-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 18 hidden Markov models representing the L30e-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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]