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 (3,151) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 12,270 76,077 12
Proteins 12,178 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 process0.0001410.0002848Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process0.0000091610.0002306Least InformativeDirect
Biological Process (BP)single-organism cellular process0.01820.8135Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.68810.2357Least InformativeInherited
Biological Process (BP)localization0.001070.02991Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.045260.4644Least InformativeInherited
Biological Process (BP)gene expression0.000000080550.0000000003163Moderately InformativeDirect
Biological Process (BP)macromolecule localization0.0000082740.00005811Moderately InformativeDirect
Biological Process (BP)cellular localization0.000005730.00004543Moderately InformativeDirect
Biological Process (BP)organic substance transport0.00042980.00008864Moderately InformativeDirect
Biological Process (BP)organelle organization0.010490.02911Moderately InformativeInherited
Biological Process (BP)mitochondrion organization0.000000061910.0000002085InformativeDirect
Biological Process (BP)protein transport0.00000000040130.00000001747InformativeDirect
Biological Process (BP)cytoplasmic transport0.000000000080090.000000003052InformativeDirect
Biological Process (BP)protein localization to organelle0.0000000000031130.0000000001735InformativeDirect
Biological Process (BP)cellular amide metabolic process0.00067890.000003939InformativeDirect
Biological Process (BP)mitochondrial transport0.00000028510.000000001657Highly InformativeDirect
Biological Process (BP)establishment of protein localization to organelle0.000000000000012670.00000000000004724Highly InformativeDirect
Biological Process (BP)protein processing00.0751Highly InformativeInherited
Biological Process (BP)protein localization to mitochondrion0.0015420.00001445Highly InformativeInherited
Molecular Function (MF)hydrolase activity0.00026660.000002087Least InformativeDirect
Molecular Function (MF)peptidase activity0.000000000012820.0000000001334InformativeDirect
Molecular Function (MF)endopeptidase activity0.000041350.000001633Highly InformativeDirect
Cellular Component (CC)membrane0.0000028480.0008492Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.000077640.0000005012Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.000024681Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.000020440.06362Least InformativeInherited
Cellular Component (CC)protein complex0.0002080.02925Least InformativeInherited
Cellular Component (CC)endoplasmic reticulum0.00000045450.000003084Moderately InformativeDirect
Cellular Component (CC)endomembrane system0.000017380.0006492Moderately InformativeDirect
Cellular Component (CC)organelle membrane0.000000000053640.000000007432Moderately InformativeDirect
Cellular Component (CC)mitochondrial part0.0014230.0007074Moderately InformativeInherited
Cellular Component (CC)organelle envelope0.0027560.0002489Moderately InformativeInherited
Cellular Component (CC)endoplasmic reticulum membrane0.00025060.0003563InformativeDirect
Cellular Component (CC)mitochondrial membrane part0.000040690.0000001383InformativeDirect

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 0.0002848 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0002306 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.8135 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.2357 Least Informative Inherited
Biological Process (BP) localization 0.02991 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.4644 Least Informative Inherited
Biological Process (BP) gene expression 0.0000000003163 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.00005811 Moderately Informative Direct
Biological Process (BP) cellular localization 0.00004543 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.00008864 Moderately Informative Direct
Biological Process (BP) organelle organization 0.02911 Moderately Informative Inherited
Biological Process (BP) mitochondrion organization 0.0000002085 Informative Direct
Biological Process (BP) protein transport 0.00000001747 Informative Direct
Biological Process (BP) cytoplasmic transport 0.000000003052 Informative Direct
Biological Process (BP) protein localization to organelle 0.0000000001735 Informative Direct
Biological Process (BP) cellular amide metabolic process 0.000003939 Informative Direct
Biological Process (BP) mitochondrial transport 0.000000001657 Highly Informative Direct
Biological Process (BP) protein localization to mitochondrion 0.00001445 Highly Informative Direct
Biological Process (BP) establishment of protein localization to organelle 0.00000000000004724 Highly Informative Direct
Biological Process (BP) protein processing 0.0751 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.000002087 Least Informative Direct
Molecular Function (MF) peptidase activity 0.0000000001334 Informative Direct
Molecular Function (MF) endopeptidase activity 0.000001633 Highly Informative Direct
Cellular Component (CC) membrane 0.0008492 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0000005012 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.06362 Least Informative Inherited
Cellular Component (CC) protein complex 0.02925 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.6999 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.000003084 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0.0006492 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0.000000007432 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.0002489 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.0007074 Moderately Informative Direct
Cellular Component (CC) chromosome 0.000003326 Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0.0003563 Informative Direct
Cellular Component (CC) mitochondrial membrane part 0.0000001383 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 processConjugation0.0000000001403Highly InformativeDirect
Cellular componentMembrane0.000000005593Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainSignal-anchor0InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationProtease0.000000665Moderately 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 ]