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Conserved domains on  [gi|1550395606|gb|RVQ58772|]
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helix-turn-helix transcriptional regulator [Sinorhizobium meliloti]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 11459250)

helix-turn-helix (HTH) transcriptional regulator similar to phage repressor protein CI and Pseudomonas aeruginosa HTH-type transcriptional regulator PrtR, which represses the expression of various pyocin genes

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 118-215 2.79e-30

Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: prophages, transposons];


:

Pssm-ID: 442176  Cd Length: 121  Bit Score: 108.13  E-value: 2.79e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550395606 118 DTIEFPtpERRQGGTYALEVQGDSMLPLYRDGDVLIVDPSA-QVRRNDRVVVKTrGGEVMAKVLARQTPRGIELVSLNPD 196
Cdd:COG2932    23 DKLEFP--GLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDtEIRDGGIYVVRT-DGELLVKRLQRRPDGKLRLISDNPA 99

                          90       100
                  ....*....|....*....|..
gi 1550395606 197 HPNRNF---EMNDVEWIARIIW 215
Cdd:COG2932   100 YPPIEIppeDADEIEIIGRVVW 121
 
Name Accession Description Interval E-value
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 118-215 2.79e-30

Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: prophages, transposons];


Pssm-ID: 442176  Cd Length: 121  Bit Score: 108.13  E-value: 2.79e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550395606 118 DTIEFPtpERRQGGTYALEVQGDSMLPLYRDGDVLIVDPSA-QVRRNDRVVVKTrGGEVMAKVLARQTPRGIELVSLNPD 196
Cdd:COG2932    23 DKLEFP--GLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDtEIRDGGIYVVRT-DGELLVKRLQRRPDGKLRLISDNPA 99

                          90       100
                  ....*....|....*....|..
gi 1550395606 197 HPNRNF---EMNDVEWIARIIW 215
Cdd:COG2932   100 YPPIEIppeDADEIEIIGRVVW 121
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 133-214 2.21e-25

Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the protein. In the presence of single-stranded DNA, the LexA, UmuD and MucA proteins interact with RecA, activating self cleavage, thus either derepressing transcription in the case of LexA or activating the lesion-bypass polymerase in the case of UmuD and MucA. The LexA proteins are serine proteases that carry out catalysis using a serine/lysine dyad instead of the prototypical serine/histidine/aspartic acid triad found in most serine proteases. LexA sequence homologs are found in almost all of the bacterial genomes sequenced to date, covering a large number of phyla, suggesting both, an ancient origin and a widespread distribution of lexA and the SOS response.


Pssm-ID: 119397 [Multi-domain]  Cd Length: 81  Bit Score: 94.55  E-value: 2.21e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550395606 133 YALEVQGDSMLPLYRDGDVLIVDPSAQVRRNDRVVVKTrGGEVMAKVLARQTPRGIELVSLNPDHPNRNFEMNDVEWIAR 212
Cdd:cd06529     1 FALRVKGDSMEPTIPDGDLVLVDPSDTPRDGDIVVARL-DGELTVKRLQRRGGGRLRLISDNPAYPPIEIDEEELEIVGV 79


                  ..
gi 1550395606 213 II 214
Cdd:cd06529    80 VG 81
Peptidase_S24 pfam00717
Peptidase S24-like;
127-214 2.34e-25

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 95.35  E-value: 2.34e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550395606 127 RRQGGTYALEVQGDSMLPLYRDGDVLIVDPSAQVRRNDRVVVKTrGGEVMAKVLARQtPRGIELVSLNPDHPNRNFEMND 206
Cdd:pfam00717  30 SPPGNLFALRVKGDSMEPGIPDGDLVLVDPSREARNGDIVVARL-DGEATVKRLYRD-GGGIRLISLNPEYPPIELPAED 107


                  ....*....
gi 1550395606 207 -VEWIARII 214
Cdd:pfam00717 108 dVEIIGRVV 116
PRK10276 PRK10276
translesion error-prone DNA polymerase V autoproteolytic subunit;
130-197 4.96e-05

translesion error-prone DNA polymerase V autoproteolytic subunit;


Pssm-ID: 182350  Cd Length: 139  Bit Score: 41.71  E-value: 4.96e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1550395606 130 GGTYALEVQGDSMLPL-YRDGDVLIVDPSAQVRRNDrVVVKTRGGEVMAKVLaRQTPRgIELVSLNPDH 197
Cdd:PRK10276   49 SATYFVKASGDSMIDAgISDGDLLIVDSAITASHGD-IVIAAVDGEFTVKKL-QLRPT-VQLIPMNSAY 114
 
Name Accession Description Interval E-value
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 118-215 2.79e-30

Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: prophages, transposons];


Pssm-ID: 442176  Cd Length: 121  Bit Score: 108.13  E-value: 2.79e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550395606 118 DTIEFPtpERRQGGTYALEVQGDSMLPLYRDGDVLIVDPSA-QVRRNDRVVVKTrGGEVMAKVLARQTPRGIELVSLNPD 196
Cdd:COG2932    23 DKLEFP--GLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDtEIRDGGIYVVRT-DGELLVKRLQRRPDGKLRLISDNPA 99

                          90       100
                  ....*....|....*....|..
gi 1550395606 197 HPNRNF---EMNDVEWIARIIW 215
Cdd:COG2932   100 YPPIEIppeDADEIEIIGRVVW 121
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 133-214 2.21e-25

Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the protein. In the presence of single-stranded DNA, the LexA, UmuD and MucA proteins interact with RecA, activating self cleavage, thus either derepressing transcription in the case of LexA or activating the lesion-bypass polymerase in the case of UmuD and MucA. The LexA proteins are serine proteases that carry out catalysis using a serine/lysine dyad instead of the prototypical serine/histidine/aspartic acid triad found in most serine proteases. LexA sequence homologs are found in almost all of the bacterial genomes sequenced to date, covering a large number of phyla, suggesting both, an ancient origin and a widespread distribution of lexA and the SOS response.


Pssm-ID: 119397 [Multi-domain]  Cd Length: 81  Bit Score: 94.55  E-value: 2.21e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550395606 133 YALEVQGDSMLPLYRDGDVLIVDPSAQVRRNDRVVVKTrGGEVMAKVLARQTPRGIELVSLNPDHPNRNFEMNDVEWIAR 212
Cdd:cd06529     1 FALRVKGDSMEPTIPDGDLVLVDPSDTPRDGDIVVARL-DGELTVKRLQRRGGGRLRLISDNPAYPPIEIDEEELEIVGV 79


                  ..
gi 1550395606 213 II 214
Cdd:cd06529    80 VG 81
Peptidase_S24 pfam00717
Peptidase S24-like;
127-214 2.34e-25

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 95.35  E-value: 2.34e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550395606 127 RRQGGTYALEVQGDSMLPLYRDGDVLIVDPSAQVRRNDRVVVKTrGGEVMAKVLARQtPRGIELVSLNPDHPNRNFEMND 206
Cdd:pfam00717  30 SPPGNLFALRVKGDSMEPGIPDGDLVLVDPSREARNGDIVVARL-DGEATVKRLYRD-GGGIRLISLNPEYPPIELPAED 107


                  ....*....
gi 1550395606 207 -VEWIARII 214
Cdd:pfam00717 108 dVEIIGRVV 116
Peptidase_S24_S26 cd06462
The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal ...
 133-214 8.24e-17

The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the transport of proteins across membranes in all living organisms. All members in this superfamily are unique serine proteases that carry out catalysis using a serine/lysine dyad instead of the prototypical serine/histidine/aspartic acid triad found in most serine proteases.


Pssm-ID: 119396 [Multi-domain]  Cd Length: 84  Bit Score: 72.30  E-value: 8.24e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550395606 133 YALEVQGDSMLPLYRDGDVLIVDPSA-QVRRNDRVVVKTRGGEVMAK-VLARQTPRGIELVSLNPDHPNRNFEMNDVEWI 210
Cdd:cd06462     1 FALRVEGDSMEPTIPDGDLVLVDKSSyEPKRGDIVVFRLPGGELTVKrVIGLPGEGHYFLLGDNPNSPDSRIDGPPELDI 80


                  ....
gi 1550395606 211 ARII 214
Cdd:cd06462    81 VGVV 84
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 118-208 1.93e-16

SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, Signal transduction mechanisms];


Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 74.18  E-value: 1.93e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550395606 118 DTIE--FPTPE---RRQGGTYALEVQGDSML-PLYRDGDVLIVDPSAQVRRNDRVVVKTrGGEVMAKVLaRQTPRGIELV 191
Cdd:COG1974    93 ENIEeyLDLPEelvKNPGATFALRVKGDSMIdAGILDGDLVIVDRQLEAENGDIVVALI-DGEATVKRL-YKEGGRVRLQ 170

                          90
                  ....*....|....*..
gi 1550395606 192 SLNPDHPNRNFEMNDVE 208
Cdd:COG1974   171 PENPAYPPIIIEGDDVE 187
PRK10276 PRK10276
translesion error-prone DNA polymerase V autoproteolytic subunit;
130-197 4.96e-05

translesion error-prone DNA polymerase V autoproteolytic subunit;


Pssm-ID: 182350  Cd Length: 139  Bit Score: 41.71  E-value: 4.96e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1550395606 130 GGTYALEVQGDSMLPL-YRDGDVLIVDPSAQVRRNDrVVVKTRGGEVMAKVLaRQTPRgIELVSLNPDH 197
Cdd:PRK10276   49 SATYFVKASGDSMIDAgISDGDLLIVDSAITASHGD-IVIAAVDGEFTVKKL-QLRPT-VQLIPMNSAY 114
S26_SPase_I cd06530
The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4. ...
 137-174 6.34e-03

The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa) belong to this family and they process many proteins that enter the ER for retention or for export to the Golgi apparatus, secretory vesicles, plasma membranes or vacuole. An atypical member of the S26 SPase type I family is the TraF peptidase which has the remarkable activity of producing a cyclic protein of the Pseudomonas pilin system. The type I signal peptidases are unique serine proteases that utilize a serine/lysine catalytic dyad mechanism in place of the classical serine/histidine/aspartic acid catalytic triad mechanism.


Pssm-ID: 119398 [Multi-domain]  Cd Length: 85  Bit Score: 34.87  E-value: 6.34e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1550395606 137 VQGDSMLPLYRDGDVLIVDP----SAQVRRNDRVVVKTRGGE 174
Cdd:cd06530     5 VPGGSMEPTLQPGDLVLVNKlsygFREPKRGDVVVFKSPGDP 46
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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