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MULTISPECIES: LexA family transcriptional regulator [Enterobacteriaceae]

Protein Classification

LexA family protein( domain architecture ID 11449429)

LexA family protein may function as a transcriptional regulator involved in the repression of one or more genes involved in the response to DNA damage (SOS response), including recA and lexA and/or may contain a S24 peptidase domain such as in the translesion error-prone DNA polymerase V autoproteolytic subunit

Gene Ontology:  GO:0003677|GO:0045892
PubMed:  10679470|10908318

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 5-232 2.77e-39

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


:

Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 134.66  E-value: 2.77e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446350463   5 KSLTTEQLEDAKRLKALYesKKKELGITQYSIADELGITQGAVGHYLNgrnALnvevasgfarllqvsiadfsqsiaakv 84
Cdd:COG1974    2 KKLTKRQREILDFIKEYI--RERGYPPSQREIAEALGLSSSAVHRHLK---AL--------------------------- 49

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446350463  85 aEQAESLKSDAN----VRYAGEYRAGKRYPVLSSIQAGSWCEACEpytikDIDVWLESDAHI---QGNAFWLKVEGDSMT 157
Cdd:COG1974   50 -EKKGYLRRDPGksraIELLPASPEVVGLPLLGRVAAGFPIPAEE-----NIEEYLDLPEELvknPGATFALRVKGDSMI 123

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446350463 158 APvglSIPEGTFVLFDTGREAINGSLVIAKLSDsnEATFKKLIIDGGNKYLKGLNPAWPLVPING-NCKIIGVAIE 232
Cdd:COG1974  124 DA---GILDGDLVIVDRQLEAENGDIVVALIDG--EATVKRLYKEGGRVRLQPENPAYPPIIIEGdDVEILGVVVG 194
 
Name Accession Description Interval E-value
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 5-232 2.77e-39

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


Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 134.66  E-value: 2.77e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446350463   5 KSLTTEQLEDAKRLKALYesKKKELGITQYSIADELGITQGAVGHYLNgrnALnvevasgfarllqvsiadfsqsiaakv 84
Cdd:COG1974    2 KKLTKRQREILDFIKEYI--RERGYPPSQREIAEALGLSSSAVHRHLK---AL--------------------------- 49

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446350463  85 aEQAESLKSDAN----VRYAGEYRAGKRYPVLSSIQAGSWCEACEpytikDIDVWLESDAHI---QGNAFWLKVEGDSMT 157
Cdd:COG1974   50 -EKKGYLRRDPGksraIELLPASPEVVGLPLLGRVAAGFPIPAEE-----NIEEYLDLPEELvknPGATFALRVKGDSMI 123

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446350463 158 APvglSIPEGTFVLFDTGREAINGSLVIAKLSDsnEATFKKLIIDGGNKYLKGLNPAWPLVPING-NCKIIGVAIE 232
Cdd:COG1974  124 DA---GILDGDLVIVDRQLEAENGDIVVALIDG--EATVKRLYKEGGRVRLQPENPAYPPIIIEGdDVEILGVVVG 194
Peptidase_S24 pfam00717
Peptidase S24-like;
110-231 8.66e-32

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 112.68  E-value: 8.66e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446350463  110 PVLSSIQAGSWCEACEpyTIKDIDVWLESDAHIQGNAFWLKVEGDSMTApvglSIPEGTFVLFDTGREAINGSLVIAKLS 189
Cdd:pfam00717   1 PLIGRVAAGAPILAEE--EIEGYLPLPESLLSPPGNLFALRVKGDSMEP----GIPDGDLVLVDPSREARNGDIVVARLD 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 446350463  190 DsnEATFKKLIIDGGNKYLKGLNPAWP--LVPINGNCKIIGVAI 231
Cdd:pfam00717  75 G--EATVKRLYRDGGGIRLISLNPEYPpiELPAEDDVEIIGRVV 116
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 147-231 4.51e-17

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: 73.36  E-value: 4.51e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446350463 147 FWLKVEGDSMTaPVglsIPEGTFVLFDTGREAINGSLVIAKLSDsnEATFKKLIIDGGNK-YLKGLNPAWPLVPING-NC 224
Cdd:cd06529    1 FALRVKGDSME-PT---IPDGDLVLVDPSDTPRDGDIVVARLDG--ELTVKRLQRRGGGRlRLISDNPAYPPIEIDEeEL 74


                 ....*..
gi 446350463 225 KIIGVAI 231
Cdd:cd06529   75 EIVGVVG 81
lexA TIGR00498
SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in ...
 5-231 5.36e-09

SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA. [DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 273106 [Multi-domain]  Cd Length: 199  Bit Score: 54.34  E-value: 5.36e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446350463    5 KSLTTEQLEDAKRLKALYESKKKELGITQysIADELGITQ--GAVGHYLNGRNALNVEVASGFARLLQVSiadfsQSIAA 82
Cdd:TIGR00498   2 KPLTARQQEVLDLIRAHIESTGYPPSIRE--IARAVGLRSpsAAEEHLKALERKGYIERDPGKPRAIRIL-----DDEPK 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446350463   83 KVaeqaeslksdanvryageyragkryPVLSSIQAGSWCEACEpyTIKDIDVWLESDAHIQGNAFWLKVEGDSMtapVGL 162
Cdd:TIGR00498  75 GV-------------------------PLIGRVAAGEPILAEQ--HIEEYFPIDFSLLKKPSAVFLLKVMGDSM---VDA 124

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446350463  163 SIPEGTFVLFDTGREAINGSLVIAKLSDsnEATFKKLIIDGGNKYLKGLNPAWPLVPIN-GNCKIIGVAI 231
Cdd:TIGR00498 125 GICDGDLLIVRSQKDARNGEIVAAMIDG--EVTVKRFYKDGTKVELKPENPEFDPIVLNaEDVTILGKVV 192
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
17-76 2.64e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 49.05  E-value: 2.64e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446350463    17 RLKALyeskKKELGITQYSIADELGITQGAVGHYLNGRNALNVEVASGFARLLQVSIADF 76
Cdd:smart00530   1 RLKEL----REEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
 
Name Accession Description Interval E-value
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 5-232 2.77e-39

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


Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 134.66  E-value: 2.77e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446350463   5 KSLTTEQLEDAKRLKALYesKKKELGITQYSIADELGITQGAVGHYLNgrnALnvevasgfarllqvsiadfsqsiaakv 84
Cdd:COG1974    2 KKLTKRQREILDFIKEYI--RERGYPPSQREIAEALGLSSSAVHRHLK---AL--------------------------- 49

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446350463  85 aEQAESLKSDAN----VRYAGEYRAGKRYPVLSSIQAGSWCEACEpytikDIDVWLESDAHI---QGNAFWLKVEGDSMT 157
Cdd:COG1974   50 -EKKGYLRRDPGksraIELLPASPEVVGLPLLGRVAAGFPIPAEE-----NIEEYLDLPEELvknPGATFALRVKGDSMI 123

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446350463 158 APvglSIPEGTFVLFDTGREAINGSLVIAKLSDsnEATFKKLIIDGGNKYLKGLNPAWPLVPING-NCKIIGVAIE 232
Cdd:COG1974  124 DA---GILDGDLVIVDRQLEAENGDIVVALIDG--EATVKRLYKEGGRVRLQPENPAYPPIIIEGdDVEILGVVVG 194
Peptidase_S24 pfam00717
Peptidase S24-like;
110-231 8.66e-32

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 112.68  E-value: 8.66e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446350463  110 PVLSSIQAGSWCEACEpyTIKDIDVWLESDAHIQGNAFWLKVEGDSMTApvglSIPEGTFVLFDTGREAINGSLVIAKLS 189
Cdd:pfam00717   1 PLIGRVAAGAPILAEE--EIEGYLPLPESLLSPPGNLFALRVKGDSMEP----GIPDGDLVLVDPSREARNGDIVVARLD 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 446350463  190 DsnEATFKKLIIDGGNKYLKGLNPAWP--LVPINGNCKIIGVAI 231
Cdd:pfam00717  75 G--EATVKRLYRDGGGIRLISLNPEYPpiELPAEDDVEIIGRVV 116
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 147-231 4.51e-17

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: 73.36  E-value: 4.51e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446350463 147 FWLKVEGDSMTaPVglsIPEGTFVLFDTGREAINGSLVIAKLSDsnEATFKKLIIDGGNK-YLKGLNPAWPLVPING-NC 224
Cdd:cd06529    1 FALRVKGDSME-PT---IPDGDLVLVDPSDTPRDGDIVVARLDG--ELTVKRLQRRGGGRlRLISDNPAYPPIEIDEeEL 74


                 ....*..
gi 446350463 225 KIIGVAI 231
Cdd:cd06529   75 EIVGVVG 81
Peptidase_S24_S26 cd06462
The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal ...
 147-230 3.65e-11

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: 57.66  E-value: 3.65e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446350463 147 FWLKVEGDSMTaPVglsIPEGTFVLFDTG-REAINGSLVIAKlSDSNEATFKKLIIDGGNK--YLKGLNPAWPLVPING- 222
Cdd:cd06462    1 FALRVEGDSME-PT---IPDGDLVLVDKSsYEPKRGDIVVFR-LPGGELTVKRVIGLPGEGhyFLLGDNPNSPDSRIDGp 75


                 ....*....
gi 446350463 223 -NCKIIGVA 230
Cdd:cd06462   76 pELDIVGVV 84
lexA TIGR00498
SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in ...
 5-231 5.36e-09

SOS regulatory protein LexA; LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA. [DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 273106 [Multi-domain]  Cd Length: 199  Bit Score: 54.34  E-value: 5.36e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446350463    5 KSLTTEQLEDAKRLKALYESKKKELGITQysIADELGITQ--GAVGHYLNGRNALNVEVASGFARLLQVSiadfsQSIAA 82
Cdd:TIGR00498   2 KPLTARQQEVLDLIRAHIESTGYPPSIRE--IARAVGLRSpsAAEEHLKALERKGYIERDPGKPRAIRIL-----DDEPK 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446350463   83 KVaeqaeslksdanvryageyragkryPVLSSIQAGSWCEACEpyTIKDIDVWLESDAHIQGNAFWLKVEGDSMtapVGL 162
Cdd:TIGR00498  75 GV-------------------------PLIGRVAAGEPILAEQ--HIEEYFPIDFSLLKKPSAVFLLKVMGDSM---VDA 124

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446350463  163 SIPEGTFVLFDTGREAINGSLVIAKLSDsnEATFKKLIIDGGNKYLKGLNPAWPLVPIN-GNCKIIGVAI 231
Cdd:TIGR00498 125 GICDGDLLIVRSQKDARNGEIVAAMIDG--EVTVKRFYKDGTKVELKPENPEFDPIVLNaEDVTILGKVV 192
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 144-231 6.79e-09

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


Pssm-ID: 442176  Cd Length: 121  Bit Score: 52.27  E-value: 6.79e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446350463 144 GNAFWLKVEGDSMtAPVglsIPEGTFVLFDTGREAI-NGSLVIAKLSDsnEATFKKLIIDGGNKY-LKGLNPAWPLVPIN 221
Cdd:COG2932   33 DNLFAVRVSGDSM-EPT---IRDGDIVLVDPSDTEIrDGGIYVVRTDG--ELLVKRLQRRPDGKLrLISDNPAYPPIEIP 106

                         90
                 ....*....|....
gi 446350463 222 G----NCKIIGVAI 231
Cdd:COG2932  107 PedadEIEIIGRVV 120
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 15-76 1.71e-08

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 49.47  E-value: 1.71e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446350463  15 AKRLKALyeskKKELGITQYSIADELGITQGAVGHYLNGRNALNVEVASGFARLLQVSIADF 76
Cdd:cd00093    1 GERLKEL----RKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
17-76 2.64e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 49.05  E-value: 2.64e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446350463    17 RLKALyeskKKELGITQYSIADELGITQGAVGHYLNGRNALNVEVASGFARLLQVSIADF 76
Cdd:smart00530   1 RLKEL----REEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
15-90 5.38e-08

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 48.84  E-value: 5.38e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446350463  15 AKRLKALyeskKKELGITQYSIADELGITQGAVGHYLNGRNALNVEVASGFARLLQVSIADFSQSIAAKVAEQAES 90
Cdd:COG1396    9 GERLREL----RKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEALLS 80
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 27-76 1.33e-07

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 47.15  E-value: 1.33e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 446350463   27 KELGITQYSIADELGITQGAVGHYLNGRNALNVEVASGFARLLQVSIADF 76
Cdd:pfam01381   6 EELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
15-76 8.45e-07

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 45.22  E-value: 8.45e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446350463  15 AKRLKALyeskKKELGITQYSIADELGITQGAVGHYLNGRNALNVEVASGFARLLQVSIADF 76
Cdd:COG1476    6 GNRLKEL----RKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEEL 63
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 27-76 1.06e-05

Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense mechanisms];


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 42.49  E-value: 1.06e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 446350463  27 KELGITQYSIADELGITQGAVGHYLNGRNALNVEVASGFARLLQVSiADF 76
Cdd:COG3093   19 EPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTS-AEF 67
AF0184 COG2522
Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];
28-54 6.42e-05

Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];


Pssm-ID: 442012 [Multi-domain]  Cd Length: 99  Bit Score: 40.96  E-value: 6.42e-05
                         10        20
                 ....*....|....*....|....*..
gi 446350463  28 ELGITQYSIADELGITQGAVGHYLNGR 54
Cdd:COG2522   26 ERGLSQSEIAKLLGITQAAVSQYLSGK 52
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 27-76 5.13e-03

addiction module antidote protein, HigA family; Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair. [Regulatory functions, DNA interactions, Regulatory functions, Protein interactions, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 274228 [Multi-domain]  Cd Length: 78  Bit Score: 34.90  E-value: 5.13e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 446350463   27 KELGITQYSIADELGITQGAVGHYLNGRNALNVEVASGFARLLQVSiADF 76
Cdd:TIGR02607  15 EPLGLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKALGTS-PEF 63
 
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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