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 (3,158) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 12,319 76,077 12
Proteins 12,226 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 process0.00011990.000278Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process0.0000010830.0001325Least InformativeDirect
Biological Process (BP)localization0.00056880.02761Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.0027380.1912Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.70330.2357Least InformativeInherited
Biological Process (BP)gene expression0.00000013380.0000000005774Moderately InformativeDirect
Biological Process (BP)macromolecule localization0.0000060110.00004261Moderately InformativeDirect
Biological Process (BP)cellular localization0.000080180.00005758Moderately InformativeDirect
Biological Process (BP)organic substance transport0.00030480.00006433Moderately InformativeDirect
Biological Process (BP)peptide metabolic process0.000018490.00000005096InformativeDirect
Biological Process (BP)mitochondrion organization0.000000021590.0000001506InformativeDirect
Biological Process (BP)protein transport0.000000000078440.0000000124InformativeDirect
Biological Process (BP)cytoplasmic transport0.000000000022060.000000003533InformativeDirect
Biological Process (BP)protein localization to organelle0.00000000000061870.0000000001281InformativeDirect
Biological Process (BP)protein maturation0.000000000017910InformativeDirect
Biological Process (BP)single-organism cellular localization0.000000000015520.00000005526InformativeDirect
Biological Process (BP)single-organism intracellular transport0.0000000017240.0000003505InformativeDirect
Biological Process (BP)mitochondrial transport0.00058610.000006234Highly InformativeDirect
Biological Process (BP)protein localization to mitochondrion0.0013520.000014Highly InformativeInherited
Molecular Function (MF)hydrolase activity0.00024370.000001318Least InformativeDirect
Molecular Function (MF)peptidase activity0.0000000000018740.0000000001433InformativeDirect
Molecular Function (MF)endopeptidase activity0.000019810.000001359Highly InformativeDirect
Cellular Component (CC)membrane0.00000041320.0002386Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.000077540.0000003338Least InformativeDirect
Cellular Component (CC)cytoplasmic part0.00000090080.07638Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.00000071651Least InformativeInherited
Cellular Component (CC)protein complex0.000050040.02196Least InformativeInherited
Cellular Component (CC)endoplasmic reticulum0.0000020090.000009822Moderately InformativeDirect
Cellular Component (CC)mitochondrial part0.0014170.0007454Moderately InformativeInherited
Cellular Component (CC)organelle envelope0.0027780.000262Moderately InformativeInherited
Cellular Component (CC)membrane region0.0018110.0178Moderately InformativeInherited
Cellular Component (CC)bounding membrane of organelle0.55531Moderately InformativeInherited
Cellular Component (CC)endoplasmic reticulum membrane0.00025770.0004966InformativeDirect
Cellular Component (CC)mitochondrial membrane part0.000040170.0000002651InformativeDirect

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 0.000278 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0001325 Least Informative Direct
Biological Process (BP) localization 0.02761 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.1912 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.2357 Least Informative Inherited
Biological Process (BP) gene expression 0.0000000005774 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.00004261 Moderately Informative Direct
Biological Process (BP) cellular localization 0.00005758 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.00006433 Moderately Informative Direct
Biological Process (BP) peptide metabolic process 0.00000005096 Informative Direct
Biological Process (BP) mitochondrion organization 0.0000001506 Informative Direct
Biological Process (BP) protein transport 0.0000000124 Informative Direct
Biological Process (BP) cytoplasmic transport 0.000000003533 Informative Direct
Biological Process (BP) protein localization to organelle 0.0000000001281 Informative Direct
Biological Process (BP) protein maturation 0 Informative Direct
Biological Process (BP) single-organism cellular localization 0.00000005526 Informative Direct
Biological Process (BP) single-organism intracellular transport 0.0000003505 Informative Direct
Biological Process (BP) mitochondrial transport 0.000006234 Highly Informative Direct
Biological Process (BP) protein localization to mitochondrion 0.000014 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.000001318 Least Informative Direct
Molecular Function (MF) peptidase activity 0.0000000001433 Informative Direct
Molecular Function (MF) endopeptidase activity 0.000001359 Highly Informative Direct
Cellular Component (CC) membrane 0.0002386 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0000003338 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.07638 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.02196 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.7084 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.000009822 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.000262 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.0007454 Moderately Informative Direct
Cellular Component (CC) membrane region 0.0178 Moderately Informative Inherited
Cellular Component (CC) bounding membrane of organelle 1 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.000002585 Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0.0004966 Informative Direct
Cellular Component (CC) mitochondrial membrane part 0.0000002651 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 processConjugation0.000000000151Highly InformativeDirect
Cellular componentMembrane0.000000003768Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainSignal-anchor0InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationProtease0.0000003328Moderately 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 ]