SUPERFAMILY 1.75 HMM library and genome assignments server


LexA/Signal peptidase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   LexA/Signal peptidase [ 51305]
Superfamily:   LexA/Signal peptidase [ 51306] (2)
Families:   LexA-related [ 51307] (3)
  Type 1 signal peptidase [ 51312]


Superfamily statistics
Genomes (3,157) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 12,317 76,077 12
Proteins 12,224 75,668 12


Functional annotation
General category Information
Detailed category Transcription

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)protein metabolic process0.00012060.0002676Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process1.069e-060.000129Least InformativeDirect
Biological Process (BP)single-organism cellular process0.0063680.6172Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.69550.2362Least InformativeInherited
Biological Process (BP)localization0.00044370.0233Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.032020.4358Least InformativeInherited
Biological Process (BP)gene expression8.603e-083.269e-10Moderately InformativeDirect
Biological Process (BP)macromolecule localization8.243e-065.931e-05Moderately InformativeDirect
Biological Process (BP)cellular localization5.722e-063.349e-05Moderately InformativeDirect
Biological Process (BP)organic substance transport0.00040098.178e-05Moderately InformativeDirect
Biological Process (BP)organelle organization0.010360.02447Moderately InformativeInherited
Biological Process (BP)peptide metabolic process1.351e-053.108e-08InformativeDirect
Biological Process (BP)mitochondrion organization2.05e-082.029e-07InformativeDirect
Biological Process (BP)protein transport7.687e-111.195e-08InformativeDirect
Biological Process (BP)cytoplasmic transport1.512e-112.144e-09InformativeDirect
Biological Process (BP)protein localization to organelle4.901e-131.153e-10InformativeDirect
Biological Process (BP)mitochondrial transport2.835e-071.67e-09Highly InformativeDirect
Biological Process (BP)establishment of protein localization to organelle1.688e-152.793e-14Highly InformativeDirect
Biological Process (BP)protein processing00.07883Highly InformativeInherited
Biological Process (BP)protein localization to mitochondrion0.0015931.533e-05Highly InformativeInherited
Molecular Function (MF)hydrolase activity0.00024861.331e-06Least InformativeDirect
Molecular Function (MF)peptidase activity1.873e-121.354e-10InformativeDirect
Molecular Function (MF)endopeptidase activity1.979e-051.328e-06Highly InformativeDirect
Cellular Component (CC)membrane4.09e-070.000237Least InformativeDirect
Cellular Component (CC)intracellular organelle part7.582e-054.334e-07Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle1.075e-061Least InformativeInherited
Cellular Component (CC)cytoplasmic part9.884e-070.06945Least InformativeInherited
Cellular Component (CC)protein complex5.163e-050.02289Least InformativeInherited
Cellular Component (CC)endoplasmic reticulum5.114e-073.19e-06Moderately InformativeDirect
Cellular Component (CC)endomembrane system2.683e-074.919e-05Moderately InformativeDirect
Cellular Component (CC)organelle membrane4.1e-111.17e-08Moderately InformativeDirect
Cellular Component (CC)mitochondrial part0.0013690.000688Moderately InformativeInherited
Cellular Component (CC)organelle envelope0.0026610.0002454Moderately InformativeInherited
Cellular Component (CC)endoplasmic reticulum membrane0.00027260.0005675InformativeDirect
Cellular Component (CC)mitochondrial membrane part4.296e-052.963e-07InformativeDirect

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) protein metabolic process 0.0002676 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.000129 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.6172 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.2362 Least Informative Inherited
Biological Process (BP) localization 0.0233 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.4358 Least Informative Inherited
Biological Process (BP) gene expression 3.269e-10 Moderately Informative Direct
Biological Process (BP) macromolecule localization 5.931e-05 Moderately Informative Direct
Biological Process (BP) cellular localization 3.349e-05 Moderately Informative Direct
Biological Process (BP) organic substance transport 8.178e-05 Moderately Informative Direct
Biological Process (BP) organelle organization 0.02447 Moderately Informative Inherited
Biological Process (BP) peptide metabolic process 3.108e-08 Informative Direct
Biological Process (BP) mitochondrion organization 2.029e-07 Informative Direct
Biological Process (BP) protein transport 1.195e-08 Informative Direct
Biological Process (BP) cytoplasmic transport 2.144e-09 Informative Direct
Biological Process (BP) protein localization to organelle 1.153e-10 Informative Direct
Biological Process (BP) mitochondrial transport 1.67e-09 Highly Informative Direct
Biological Process (BP) protein localization to mitochondrion 1.533e-05 Highly Informative Direct
Biological Process (BP) establishment of protein localization to organelle 2.793e-14 Highly Informative Direct
Biological Process (BP) protein processing 0.07883 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 1.331e-06 Least Informative Direct
Molecular Function (MF) peptidase activity 1.354e-10 Informative Direct
Molecular Function (MF) endopeptidase activity 1.328e-06 Highly Informative Direct
Cellular Component (CC) membrane 0.000237 Least Informative Direct
Cellular Component (CC) intracellular organelle part 4.334e-07 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.06945 Least Informative Inherited
Cellular Component (CC) protein complex 0.02289 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.6994 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 3.19e-06 Moderately Informative Direct
Cellular Component (CC) endomembrane system 4.919e-05 Moderately Informative Direct
Cellular Component (CC) organelle membrane 1.17e-08 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.0002454 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.000688 Moderately Informative Direct
Cellular Component (CC) chromosome 2.613e-06 Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0.0005675 Informative Direct
Cellular Component (CC) mitochondrial membrane part 2.963e-07 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0Moderately InformativeDirect

Document: EC 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)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately 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

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Moderately InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Biological processTranscription regulation0Moderately InformativeDirect
Biological processDNA replication0InformativeDirect
Biological processSOS response0Highly InformativeDirect
Biological processConjugation1.51e-10Highly InformativeDirect
Cellular componentMembrane3.768e-09Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainSignal-anchor0InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationProtease3.328e-07Moderately InformativeDirect
Post-translational modificationAutocatalytic cleavage0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR015927 SSF51306 Protein matches
Abstract

This signature is associated with serine peptidases belong to MEROPS peptidase families: S24 (LexA family, clan SF); S26A (signal peptidase I), S26B (signalase) and S26C TraF peptidase.

The S26 family includes Escherichia coli signal peptidase, SPase, which is a membrane-bound endopeptidase, with two N-terminal transmembrane segments and a C-terminal catalytic region [PubMed9823901]. SPase functions to release proteins that have been translocated into the inner membrane from the cell interior, by cleaving off their signal peptides.

The S24 family includes:

  • the lambda repressor CI/C2 family and related bacterial prophage repressor proteins [PubMed10892750].
  • LexA, the repressor of genes in the cellular SOS response to DNA damage [PubMed11551506].
  • MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage [PubMed8994967].
  • RulA, a component of the rulAB locus that confers resistance to UV.

All of these proteins, with the possible exception of RulA, interact with RecA, which activates self cleavage either derepressing transcription in the case of CI and LexA [PubMed10692372] or activating the lesion-bypass polymerase in the case of UmuD and MucA. UmuD'2, is the homodimeric component of DNA pol V, which is produced from UmuD by RecA-facilitated self-cleavage. The first 24 N-terminal residues of UmuD are removed; UmuD'2 is a DNA lesion bypass polymerase [PubMed10692372, PubMed11483531]. MucA [PubMed9925794, PubMed11016960], like UmuD, is a plasmid encoded a DNA polymerase (pol RI) which is converted into the active lesion-bypass polymerase by a self-cleavage reaction involving RecA [PubMed11114935]

This group of proteins also contains proteins not recognised as peptidases as well as those classified as non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for catalytic activity.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · 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 4 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 LexA/Signal peptidase 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 4 hidden Markov models representing the LexA/Signal peptidase 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]