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 (3,116) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 12,084 31,526 12
Proteins 11,993 31,297 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 process0.00029940.000948Least InformativeDirect
Biological Process (BP)single-organism cellular process0.002230.5415Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process3.054e-060.001279Least InformativeInherited
Biological Process (BP)localization0.00029590.01089Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.023460.3032Least InformativeInherited
Biological Process (BP)gene expression2.398e-073.143e-09Moderately InformativeDirect
Biological Process (BP)macromolecule localization7.072e-065.809e-05Moderately InformativeDirect
Biological Process (BP)cellular localization4.919e-061.177e-05Moderately InformativeDirect
Biological Process (BP)organic substance transport0.00040079.037e-05Moderately InformativeDirect
Biological Process (BP)organelle organization0.010070.01361Moderately InformativeInherited
Biological Process (BP)mitochondrion organization1.047e-082.127e-07InformativeDirect
Biological Process (BP)protein transport3.15e-114.589e-09InformativeDirect
Biological Process (BP)cytoplasmic transport7.23e-128.088e-10InformativeDirect
Biological Process (BP)protein localization to organelle2.272e-134.412e-11InformativeDirect
Biological Process (BP)mitochondrial transport2.034e-071.591e-09Highly InformativeDirect
Biological Process (BP)protein processing00.1373Highly InformativeInherited
Biological Process (BP)establishment of protein localization to mitochondrion0.020770.001988Highly InformativeInherited
Molecular Function (MF)hydrolase activity0.00065773.446e-06Least InformativeDirect
Molecular Function (MF)peptidase activity2.693e-114.996e-10InformativeDirect
Molecular Function (MF)endopeptidase activity1.406e-051.09e-05Highly InformativeDirect
Cellular Component (CC)membrane4.898e-087.789e-05Least InformativeDirect
Cellular Component (CC)intracellular organelle part5.567e-055.323e-08Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle1.225e-071Least InformativeInherited
Cellular Component (CC)cytoplasmic part1.775e-070.05068Least InformativeInherited
Cellular Component (CC)protein complex2.694e-050.01195Least InformativeInherited
Cellular Component (CC)endoplasmic reticulum5.339e-073.585e-06Moderately InformativeDirect
Cellular Component (CC)endomembrane system1.578e-050.0004774Moderately InformativeDirect
Cellular Component (CC)organelle membrane8.332e-119.77e-09Moderately InformativeDirect
Cellular Component (CC)mitochondrial part0.0017620.0009932Moderately InformativeInherited
Cellular Component (CC)organelle envelope0.0033590.0002878Moderately InformativeInherited
Cellular Component (CC)endoplasmic reticulum membrane0.0002090.0003388InformativeDirect
Cellular Component (CC)mitochondrial membrane part3.917e-051.496e-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 0.000948 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.5415 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.001279 Least Informative Inherited
Biological Process (BP) localization 0.01089 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.3032 Least Informative Inherited
Biological Process (BP) gene expression 3.143e-09 Moderately Informative Direct
Biological Process (BP) macromolecule localization 5.809e-05 Moderately Informative Direct
Biological Process (BP) cellular localization 1.177e-05 Moderately Informative Direct
Biological Process (BP) organic substance transport 9.037e-05 Moderately Informative Direct
Biological Process (BP) organelle organization 0.01361 Moderately Informative Inherited
Biological Process (BP) mitochondrion organization 2.127e-07 Informative Direct
Biological Process (BP) protein transport 4.589e-09 Informative Direct
Biological Process (BP) cytoplasmic transport 8.088e-10 Informative Direct
Biological Process (BP) protein localization to organelle 4.412e-11 Informative Direct
Biological Process (BP) mitochondrial transport 1.591e-09 Highly Informative Direct
Biological Process (BP) protein processing 0.1373 Highly Informative Inherited
Biological Process (BP) establishment of protein localization to mitochondrion 0.001988 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 3.446e-06 Least Informative Direct
Molecular Function (MF) peptidase activity 4.996e-10 Informative Direct
Molecular Function (MF) endopeptidase activity 1.09e-05 Highly Informative Direct
Cellular Component (CC) membrane 7.789e-05 Least Informative Direct
Cellular Component (CC) intracellular organelle part 5.323e-08 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.05068 Least Informative Inherited
Cellular Component (CC) protein complex 0.01195 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.4919 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 3.585e-06 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0.0004774 Moderately Informative Direct
Cellular Component (CC) organelle membrane 9.77e-09 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.0002878 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.0009932 Moderately Informative Direct
Cellular Component (CC) chromosome 1.006e-06 Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0.0003388 Informative Direct
Cellular Component (CC) mitochondrial membrane part 1.496e-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 processConjugation1.574e-10Highly InformativeDirect
Cellular componentMembrane3.64e-09Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainSignal-anchor0InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationProtease3.617e-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 ]