SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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 (3,166) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 12,343 76,629 12
Proteins 12,250 75,761 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)macromolecule metabolic process0.00000000057130.007448Least InformativeInherited
Biological Process (BP)primary metabolic process0.0000036380.2074Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.0002870.01232Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.015821Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process0.65980.2904Least InformativeInherited
Biological Process (BP)macromolecule localization0.00000000000081710.00001157Moderately InformativeDirect
Biological Process (BP)nitrogen compound transport0.0000000000038470.0000004537Moderately InformativeDirect
Biological Process (BP)organic substance transport0.000000000067040.000007316Moderately InformativeDirect
Biological Process (BP)gene expression0.00070110.00000534Moderately InformativeDirect
Biological Process (BP)cellular localization0.020610.1015Moderately InformativeInherited
Biological Process (BP)single-organism transport0.98670.9075Moderately InformativeInherited
Biological Process (BP)organelle organization0.00042540.4568Moderately InformativeInherited
Biological Process (BP)peptide metabolic process0.0061770.0001245Moderately InformativeInherited
Biological Process (BP)proteolysis00.000000000001349InformativeDirect
Biological Process (BP)protein transport00.000000002377InformativeDirect
Biological Process (BP)protein localization to organelle0.00000000043630.000015InformativeDirect
Biological Process (BP)mitochondrion organization0.0000000087950.00001674InformativeDirect
Biological Process (BP)secretion by cell0.0000010990.0002977InformativeDirect
Biological Process (BP)intracellular transport0.0068350.0219InformativeInherited
Biological Process (BP)protein maturation0.00000000000044070Highly InformativeDirect
Biological Process (BP)protein targeting0.0000000000036150.00000001654Highly InformativeDirect
Biological Process (BP)mitochondrial transport0.000045930.00000191Highly InformativeDirect
Biological Process (BP)establishment of protein localization to mitochondrion0.00038690.00005471Highly InformativeDirect
Molecular Function (MF)hydrolase activity0.0000011490.0001812Least InformativeDirect
Molecular Function (MF)peptidase activity, acting on L-amino acid peptides11InformativeInherited
Cellular Component (CC)membrane0.000000016930.2967Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.00025490.1962Least InformativeInherited
Cellular Component (CC)protein complex0.0098231Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.0017120.3172Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.0000000011370.6503Least InformativeInherited
Cellular Component (CC)membrane protein complex0.0000026130.0000002263Moderately InformativeDirect
Cellular Component (CC)mitochondrial protein complex0.000031770.000001163Moderately InformativeDirect
Cellular Component (CC)organelle inner membrane0.00007360.00007339Moderately InformativeDirect
Cellular Component (CC)endomembrane system0.000023180.02916Moderately InformativeInherited
Cellular Component (CC)mitochondrial envelope0.0000027510.006463Moderately InformativeInherited
Cellular Component (CC)endoplasmic reticulum membrane0.00000036440.000002452InformativeDirect
Cellular Component (CC)inner mitochondrial membrane protein complex0.0061690.0008811InformativeInherited
Cellular Component (CC)peptidase complex0.0020590.00001606Highly InformativeInherited

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) biological regulation 0.00674 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.007448 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.2074 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.01232 Least Informative Inherited
Biological Process (BP) response to stimulus 0.5376 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.2904 Least Informative Inherited
Biological Process (BP) macromolecule localization 0.00001157 Moderately Informative Direct
Biological Process (BP) nitrogen compound transport 0.0000004537 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.000007316 Moderately Informative Direct
Biological Process (BP) gene expression 0.00000534 Moderately Informative Direct
Biological Process (BP) peptide metabolic process 0.0001245 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.00000001528 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.00000000000001079 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0000000002353 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.000001086 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.000005724 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.0001351 Moderately Informative Direct
Biological Process (BP) response to external stimulus 0.0001791 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0002657 Moderately Informative Direct
Biological Process (BP) cellular localization 0.1015 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.9075 Moderately Informative Inherited
Biological Process (BP) cell communication 0.005095 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.4568 Moderately Informative Inherited
Biological Process (BP) proteolysis 0.000000000001349 Informative Direct
Biological Process (BP) protein transport 0.000000002377 Informative Direct
Biological Process (BP) protein localization to organelle 0.000015 Informative Direct
Biological Process (BP) mitochondrion organization 0.00001674 Informative Direct
Biological Process (BP) secretion by cell 0.0002977 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.00000000000001763 Informative Direct
Biological Process (BP) response to extracellular stimulus 0.0000000000009475 Informative Direct
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.000000000004409 Informative Direct
Biological Process (BP) negative regulation of cellular biosynthetic process 0.00000000001641 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.00000000005004 Informative Direct
Biological Process (BP) intracellular transport 0.0219 Informative Inherited
Biological Process (BP) protein maturation 0 Highly Informative Direct
Biological Process (BP) protein targeting 0.00000001654 Highly Informative Direct
Biological Process (BP) mitochondrial transport 0.00000191 Highly Informative Direct
Biological Process (BP) establishment of protein localization to mitochondrion 0.00005471 Highly Informative Direct
Biological Process (BP) cellular response to extracellular stimulus 0 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 0.00000000000002102 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.0001812 Least Informative Direct
Molecular Function (MF) binding 0.001301 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) transcription factor activity, sequence-specific DNA binding 0 Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) peptidase activity, acting on L-amino acid peptides 1 Informative Inherited
Molecular Function (MF) transcription regulatory region DNA binding 0 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding 0.0000002781 Highly Informative Direct
Molecular Function (MF) double-stranded DNA binding 0.00002976 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.1962 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) membrane 0.2967 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.3172 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.6503 Least Informative Inherited
Cellular Component (CC) membrane protein complex 0.0000002263 Moderately Informative Direct
Cellular Component (CC) mitochondrial protein complex 0.000001163 Moderately Informative Direct
Cellular Component (CC) organelle inner membrane 0.00007339 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0.02916 Moderately Informative Inherited
Cellular Component (CC) mitochondrial envelope 0.006463 Moderately Informative Inherited
Cellular Component (CC) endoplasmic reticulum membrane 0.000002452 Informative Direct
Cellular Component (CC) inner mitochondrial membrane protein complex 0.0008811 Informative Direct
Cellular Component (CC) protein-DNA complex 0 Informative Direct
Cellular Component (CC) peptidase complex 0.00001606 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)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0Moderately InformativeDirect

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 repair0InformativeDirect
Biological processDNA replication0InformativeDirect
Biological processSOS response0Highly InformativeDirect
Biological processConjugation0.0000000001442Highly InformativeDirect
Cellular componentMembrane0.00000004712Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainSignal-anchor0InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationProtease0.0000006401Moderately 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) · 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) · UniProtKB KeyWords (KW) · Internal database links ]