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 (3,116) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 12,420 22,370 30
Proteins 12,409 22,365 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 process8.602e-064.985e-06Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.00069270.0001348Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process9.842e-101.697e-11Least InformativeDirect
Biological Process (BP)heterocycle metabolic process7.22e-062.75e-06Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis2.464e-072.893e-07Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.00048980.0001293Least InformativeDirect
Biological Process (BP)regulation of metabolic process0.0068091Least InformativeInherited
Biological Process (BP)regulation of cellular process0.67281Least InformativeInherited
Biological Process (BP)biosynthetic process0.46590.09374Least InformativeInherited
Biological Process (BP)protein metabolic process0.24230.3316Least InformativeInherited
Biological Process (BP)gene expression2.745e-130Moderately InformativeDirect
Biological Process (BP)RNA metabolic process4.375e-092.339e-10Moderately InformativeDirect
Biological Process (BP)positive regulation of molecular function0.010930.07062Moderately InformativeInherited
Biological Process (BP)regulation of protein metabolic process0.00015350.005437Moderately InformativeInherited
Biological Process (BP)regulation of catalytic activity0.0021990.1661Moderately InformativeInherited
Biological Process (BP)regulation of phosphate metabolic process10.09641Moderately InformativeInherited
Biological Process (BP)positive regulation of metabolic process0.0013380.6759Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process0.016231Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.0015240.001239Moderately InformativeInherited
Biological Process (BP)negative regulation of metabolic process0.0037680.6587Moderately InformativeInherited
Biological Process (BP)negative regulation of cellular process0.013631Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.019050.000724Moderately InformativeInherited
Biological Process (BP)translation0.00023327.333e-15InformativeDirect
Biological Process (BP)RNA modification4.836e-100InformativeDirect
Biological Process (BP)ribonucleoprotein complex biogenesis00InformativeDirect
Biological Process (BP)ncRNA metabolic process1.883e-051.696e-08InformativeDirect
Biological Process (BP)regulation of kinase activity3.875e-090.0005509InformativeDirect
Biological Process (BP)regulation of protein phosphorylation8.488e-080.003544InformativeInherited
Biological Process (BP)RNA processing0.0010960.03718InformativeInherited
Biological Process (BP)positive regulation of phosphate metabolic process0.0027010.003614InformativeInherited
Biological Process (BP)positive regulation of protein metabolic process0.0024530.004314InformativeInherited
Biological Process (BP)rRNA processing5.065e-051.148e-07Highly InformativeDirect
Biological Process (BP)positive regulation of protein kinase activity0.0032480.009329Highly InformativeInherited
Molecular Function (MF)binding1.157e-050.3432Least InformativeInherited
Molecular Function (MF)nucleic acid binding07.472e-12Moderately InformativeDirect
Molecular Function (MF)structural molecule activity3.372e-059.203e-07Moderately InformativeDirect
Molecular Function (MF)RNA binding1.865e-059.651e-15InformativeDirect
Molecular Function (MF)structural constituent of ribosome1.769e-061.952e-11InformativeDirect
Cellular Component (CC)intracellular non-membrane-bounded organelle5.003e-084.696e-08Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.0590.528Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle11Least InformativeInherited
Cellular Component (CC)cytoplasmic part10.8065Least InformativeInherited
Cellular Component (CC)cytosol2.112e-051.639e-05Moderately InformativeDirect
Cellular Component (CC)ribonucleoprotein complex00Moderately InformativeDirect
Cellular Component (CC)nuclear part0.13780.5367Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.18850.7335Moderately InformativeInherited
Cellular Component (CC)nucleolus0.0011860.0006386InformativeInherited
Cellular Component (CC)small nucleolar ribonucleoprotein complex4.284e-105.927e-14Highly InformativeDirect
Cellular Component (CC)nucleolar part2.431e-051.262e-06Highly 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 4.985e-06 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0001348 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 1.697e-11 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 2.75e-06 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 2.893e-07 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0001293 Least Informative Direct
Biological Process (BP) regulation of metabolic 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 0.09374 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.3316 Least Informative Inherited
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 2.339e-10 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.000724 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 8.785e-05 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 0.07062 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.005437 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.1661 Moderately Informative Inherited
Biological Process (BP) regulation of phosphate metabolic process 0.09641 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.6759 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.001239 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.6587 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) translation 7.333e-15 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 1.696e-08 Informative Direct
Biological Process (BP) regulation of kinase activity 0.0005509 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 0.003544 Informative Inherited
Biological Process (BP) RNA processing 0.03718 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.003614 Informative Inherited
Biological Process (BP) positive regulation of protein metabolic process 0.004314 Informative Inherited
Biological Process (BP) rRNA processing 1.148e-07 Highly Informative Direct
Biological Process (BP) cellular component disassembly 2.396e-11 Highly Informative Direct
Biological Process (BP) positive regulation of protein kinase activity 0.009329 Highly Informative Inherited
Molecular Function (MF) binding 0.3432 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 7.472e-12 Moderately Informative Direct
Molecular Function (MF) structural molecule activity 9.203e-07 Moderately Informative Direct
Molecular Function (MF) RNA binding 9.651e-15 Informative Direct
Molecular Function (MF) structural constituent of ribosome 1.952e-11 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 3.201e-05 Informative Direct
Molecular Function (MF) S-adenosylmethionine-dependent methyltransferase activity 0.2349 Highly Informative Inherited
Molecular Function (MF) translation factor activity, nucleic acid binding 0.1065 Highly Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 4.696e-08 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.528 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.8065 Least Informative Inherited
Cellular Component (CC) cytosol 1.639e-05 Moderately Informative Direct
Cellular Component (CC) ribonucleoprotein complex 0 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.5367 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.7335 Moderately Informative Inherited
Cellular Component (CC) nucleolus 0.0006386 Informative Direct
Cellular Component (CC) cytosolic ribosome 0.0001335 Informative Direct
Cellular Component (CC) large ribosomal subunit 0.3239 Informative Inherited
Cellular Component (CC) small nucleolar ribonucleoprotein complex 5.927e-14 Highly Informative Direct
Cellular Component (CC) nucleolar part 1.262e-06 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 phenotype0.244Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.289Least InformativeInherited
Mammalian Phenotype (MP)renal/urinary system phenotype0.02658Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.02879Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.03739Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune cell physiology0.06214Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell-mediated immunity0.06327Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal adaptive immunity0.06545Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic system physiology0.08031Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal renal glomerulus morphology0.0008774InformativeDirect
Mammalian Phenotype (MP)autoimmune response0.001729InformativeInherited
Mammalian Phenotype (MP)abnormal kidney physiology0.001811InformativeInherited
Mammalian Phenotype (MP)abnormal humoral immune response0.004989InformativeInherited
Mammalian Phenotype (MP)abnormal B cell physiology0.006936InformativeInherited
Mammalian Phenotype (MP)increased anti-nuclear antigen antibody level2.926e-05Highly InformativeDirect
Mammalian Phenotype (MP)renal/urinary system inflammation0.0001902Highly InformativeDirect
Mammalian Phenotype (MP)increased IgG level0.0002745Highly 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 variant9.442e-07InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant1.253e-06InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant6.446e-06InformativeDirect
Worm Phenotype (WP)rachis morphology variant7.097e-06InformativeDirect
Worm Phenotype (WP)receptor mediated endocytosis defective0.0009897InformativeDirect
Worm Phenotype (WP)gonad vesiculated2.718e-07Highly InformativeDirect
Worm Phenotype (WP)oocyte number decreased1.312e-06Highly 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'-phosphomonoesters0.001918InformativeInherited
Enzyme Commission (EC)Ribonuclease P5.855e-06Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle0.01245Moderately InformativeInherited
Biological processrRNA processing0InformativeDirect
Biological processmRNA splicing8.399e-13InformativeDirect
Biological processRibosome biogenesis2.641e-12InformativeDirect
Biological processProtein biosynthesis6.389e-11InformativeDirect
Cellular componentNucleus6.556e-05Least InformativeDirect
Cellular componentCytoplasm0.0001417Least InformativeDirect
Cellular componentSpliceosome0InformativeDirect
Molecular functionRNA-binding8.402e-09Moderately InformativeDirect
Molecular functionS-adenosyl-L-methionine0InformativeDirect
Post-translational modificationHydrolase0.06405Least 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 ]