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Conserved domains on  [gi|694096084|ref|WP_032440572|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Enterobacterales]

Protein Classification

HTH_XRE and REC domain-containing protein( domain architecture ID 10428508)

HTH_XRE and REC domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
OmpR super family cl34028
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ...
 156-249 8.11e-09

DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain [Signal transduction mechanisms, Transcription];


The actual alignment was detected with superfamily member COG0745:

Pssm-ID: 440508 [Multi-domain]  Cd Length: 204  Bit Score: 54.19  E-value: 8.11e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694096084 156 KHRIAVLDDDKNIVQSLSSLLEGDRYTIKEFYSIDELDDAIEQTPFDAYILDWIVDNKTVFNTIKKIRSSGnKHAMVMVL 235
Cdd:COG0745    1 MPRILVVEDDPDIRELLADALEREGYEVDTAADGEEALELLEEERPDLILLDLMLPGMDGLEVCRRLRARP-SDIPIIML 79

                         90
                 ....*....|....
gi 694096084 236 TgqlsgAVDSEISR 249
Cdd:COG0745   80 T-----ARDDEEDR 88
HTH_XRE super family cl22854
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 8-149 1.23e-08

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


The actual alignment was detected with superfamily member pfam08667:

Pssm-ID: 473980  Cd Length: 148  Bit Score: 52.92  E-value: 1.23e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694096084    8 VGDLVAKVLTSGGVPEKKHSMHVGHVLEMSSTAATKKLAGGSEWRVQQLLEVVHSVGMRLDDFFRLYYQEQSN---KDVE 84
Cdd:pfam08667   6 FAVRVRQLLDRTGIAERQQTTWLRDILGLSFSQANRKLKGSIPWNLAQLAKVAKYFGCPAAYLLGLTENSGCNpgiQTTL 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 694096084   85 VHEAVWSDGELNEPCKIYISENPSE--PTNYSALKINDVWHVVKtssiRDDVLFESKMNIDLIEIIP 149
Cdd:pfam08667  86 LCDALLAQEAMAVAARAWISCLADAqaAPQFVAWKEHGGWWVGG----RTEAPEQRVYAVLRLEIRP 148
 
Name Accession Description Interval E-value
OmpR COG0745
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ...
 156-249 8.11e-09

DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain [Signal transduction mechanisms, Transcription];


Pssm-ID: 440508 [Multi-domain]  Cd Length: 204  Bit Score: 54.19  E-value: 8.11e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694096084 156 KHRIAVLDDDKNIVQSLSSLLEGDRYTIKEFYSIDELDDAIEQTPFDAYILDWIVDNKTVFNTIKKIRSSGnKHAMVMVL 235
Cdd:COG0745    1 MPRILVVEDDPDIRELLADALEREGYEVDTAADGEEALELLEEERPDLILLDLMLPGMDGLEVCRRLRARP-SDIPIIML 79

                         90
                 ....*....|....
gi 694096084 236 TgqlsgAVDSEISR 249
Cdd:COG0745   80 T-----ARDDEEDR 88
BetR pfam08667
BetR domain; This family includes an N-terminal helix-turn-helix domain.
 8-149 1.23e-08

BetR domain; This family includes an N-terminal helix-turn-helix domain.


Pssm-ID: 400827  Cd Length: 148  Bit Score: 52.92  E-value: 1.23e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694096084    8 VGDLVAKVLTSGGVPEKKHSMHVGHVLEMSSTAATKKLAGGSEWRVQQLLEVVHSVGMRLDDFFRLYYQEQSN---KDVE 84
Cdd:pfam08667   6 FAVRVRQLLDRTGIAERQQTTWLRDILGLSFSQANRKLKGSIPWNLAQLAKVAKYFGCPAAYLLGLTENSGCNpgiQTTL 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 694096084   85 VHEAVWSDGELNEPCKIYISENPSE--PTNYSALKINDVWHVVKtssiRDDVLFESKMNIDLIEIIP 149
Cdd:pfam08667  86 LCDALLAQEAMAVAARAWISCLADAqaAPQFVAWKEHGGWWVGG----RTEAPEQRVYAVLRLEIRP 148
REC cd00156
phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response ...
 161-263 1.40e-07

phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response regulators (PRRs); Two-component systems (TCSs) involving a sensor and a response regulator are used by bacteria to adapt to changing environments. Processes regulated by two-component systems in bacteria include sporulation, pathogenicity, virulence, chemotaxis, and membrane transport. Response regulators (RRs) share the common phosphoacceptor REC domain and different effector/output domains such as DNA, RNA, ligand-binding, protein-binding, or enzymatic domains. Response regulators regulate transcription, post-transcription or post-translation, or have functions such as methylesterases, adenylate or diguanylate cyclase, c-di-GMP-specific phosphodiesterases, histidine kinases, serine/threonine protein kinases, and protein phosphatases, depending on their output domains. The function of some output domains are still unknown. TCSs are found in all three domains of life - bacteria, archaea, and eukaryotes, however, the presence and abundance of particular RRs vary between the lineages. Archaea encode very few RRs with DNA-binding output domains; most are stand-alone REC domains. Among eukaryotes, TCSs are found primarily in protozoa, fungi, algae, and green plants. REC domains function as phosphorylation-mediated switches within RRs, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381085 [Multi-domain]  Cd Length: 99  Bit Score: 48.76  E-value: 1.40e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694096084 161 VLDDDKNIVQSLSSLLEGDRYTIKEFYSIDELDDAIEQTPFDAYILDWIVDNKTVFNTIKKIRSSgNKHAMVMVLTgqls 240
Cdd:cd00156    2 IVDDDPAIRELLKSLLEREGYEVDTAADGEEALELLREERPDLVLLDLMMPGMDGLELLRKLREL-PPDIPVIVLT---- 76

                         90       100
                 ....*....|....*....|...
gi 694096084 241 GAVDSEISRAINELDIIGPYEKP 263
Cdd:cd00156   77 AKADEEDAVRALELGADDYLVKP 99
 
Name Accession Description Interval E-value
OmpR COG0745
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ...
 156-249 8.11e-09

DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain [Signal transduction mechanisms, Transcription];


Pssm-ID: 440508 [Multi-domain]  Cd Length: 204  Bit Score: 54.19  E-value: 8.11e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694096084 156 KHRIAVLDDDKNIVQSLSSLLEGDRYTIKEFYSIDELDDAIEQTPFDAYILDWIVDNKTVFNTIKKIRSSGnKHAMVMVL 235
Cdd:COG0745    1 MPRILVVEDDPDIRELLADALEREGYEVDTAADGEEALELLEEERPDLILLDLMLPGMDGLEVCRRLRARP-SDIPIIML 79

                         90
                 ....*....|....
gi 694096084 236 TgqlsgAVDSEISR 249
Cdd:COG0745   80 T-----ARDDEEDR 88
BetR pfam08667
BetR domain; This family includes an N-terminal helix-turn-helix domain.
 8-149 1.23e-08

BetR domain; This family includes an N-terminal helix-turn-helix domain.


Pssm-ID: 400827  Cd Length: 148  Bit Score: 52.92  E-value: 1.23e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694096084    8 VGDLVAKVLTSGGVPEKKHSMHVGHVLEMSSTAATKKLAGGSEWRVQQLLEVVHSVGMRLDDFFRLYYQEQSN---KDVE 84
Cdd:pfam08667   6 FAVRVRQLLDRTGIAERQQTTWLRDILGLSFSQANRKLKGSIPWNLAQLAKVAKYFGCPAAYLLGLTENSGCNpgiQTTL 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 694096084   85 VHEAVWSDGELNEPCKIYISENPSE--PTNYSALKINDVWHVVKtssiRDDVLFESKMNIDLIEIIP 149
Cdd:pfam08667  86 LCDALLAQEAMAVAARAWISCLADAqaAPQFVAWKEHGGWWVGG----RTEAPEQRVYAVLRLEIRP 148
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 155-264 6.10e-08

DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, and a Fis-type DNA-binding domains [Signal transduction mechanisms];


Pssm-ID: 441806 [Multi-domain]  Cd Length: 418  Bit Score: 53.04  E-value: 6.10e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694096084 155 EKHRIAVLDDDKNIVQSLSSLLEGDRYTIKEFYSIDELDDAIEQTPFDAYILDWIVDNKTVFNTIKKIRSSgNKHAMVMV 234
Cdd:COG2204    1 SMARILVVDDDPDIRRLLKELLERAGYEVETAASGEEALALLREEPPDLVLLDLRMPGMDGLELLRELRAL-DPDLPVIL 79

                         90       100       110
                 ....*....|....*....|....*....|..
gi 694096084 235 LTGQlsGAVDSEIsRAINE--LDIIgpyEKPI 264
Cdd:COG2204   80 LTGY--GDVETAV-EAIKAgaFDYL---TKPF 105
REC cd00156
phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response ...
 161-263 1.40e-07

phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response regulators (PRRs); Two-component systems (TCSs) involving a sensor and a response regulator are used by bacteria to adapt to changing environments. Processes regulated by two-component systems in bacteria include sporulation, pathogenicity, virulence, chemotaxis, and membrane transport. Response regulators (RRs) share the common phosphoacceptor REC domain and different effector/output domains such as DNA, RNA, ligand-binding, protein-binding, or enzymatic domains. Response regulators regulate transcription, post-transcription or post-translation, or have functions such as methylesterases, adenylate or diguanylate cyclase, c-di-GMP-specific phosphodiesterases, histidine kinases, serine/threonine protein kinases, and protein phosphatases, depending on their output domains. The function of some output domains are still unknown. TCSs are found in all three domains of life - bacteria, archaea, and eukaryotes, however, the presence and abundance of particular RRs vary between the lineages. Archaea encode very few RRs with DNA-binding output domains; most are stand-alone REC domains. Among eukaryotes, TCSs are found primarily in protozoa, fungi, algae, and green plants. REC domains function as phosphorylation-mediated switches within RRs, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381085 [Multi-domain]  Cd Length: 99  Bit Score: 48.76  E-value: 1.40e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694096084 161 VLDDDKNIVQSLSSLLEGDRYTIKEFYSIDELDDAIEQTPFDAYILDWIVDNKTVFNTIKKIRSSgNKHAMVMVLTgqls 240
Cdd:cd00156    2 IVDDDPAIRELLKSLLEREGYEVDTAADGEEALELLREERPDLVLLDLMMPGMDGLELLRKLREL-PPDIPVIVLT---- 76

                         90       100
                 ....*....|....*....|...
gi 694096084 241 GAVDSEISRAINELDIIGPYEKP 263
Cdd:cd00156   77 AKADEEDAVRALELGADDYLVKP 99
REC_OmpR cd17574
phosphoacceptor receiver (REC) domain of OmpR family response regulators; OmpR-like proteins ...
 161-249 8.94e-07

phosphoacceptor receiver (REC) domain of OmpR family response regulators; OmpR-like proteins are one of the most widespread transcriptional regulators. OmpR family members contain REC and winged helix-turn-helix (wHTH) DNA-binding output effector domain. They are involved in the control of environmental stress tolerance (such as the oxidative, osmotic and acid stress response), motility, virulence, outer membrane biogenesis and other processes. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381116 [Multi-domain]  Cd Length: 99  Bit Score: 46.25  E-value: 8.94e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694096084 161 VLDDDKNIVQSLSSLLEGDRYTIKEFYSIDELDDAIEQTPFDAYILDWIVDNKTVFNTIKKIRSSGnKHAMVMVLTgqls 240
Cdd:cd17574    2 VVEDDEEIAELLSDYLEKEGYEVDTAADGEEALELAREEQPDLIILDVMLPGMDGFEVCRRLREKG-SDIPIIMLT---- 76


                 ....*....
gi 694096084 241 gAVDSEISR 249
Cdd:cd17574   77 -AKDEEEDK 84
RpfG COG3437
Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains ...
 153-280 9.49e-07

Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains [Signal transduction mechanisms];


Pssm-ID: 442663 [Multi-domain]  Cd Length: 224  Bit Score: 48.62  E-value: 9.49e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694096084 153 DKEKHRIAVLDDDKNIVQSLSSLLEGDRYTIKEFYSIDELDDAIEQTPFDAYILDWIVDNKTVFNTIKKIRS-SGNKHAM 231
Cdd:COG3437    3 TGQAPTVLIVDDDPENLELLRQLLRTLGYDVVTAESGEEALELLLEAPPDLILLDVRMPGMDGFELLRLLRAdPSTRDIP 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 694096084 232 VMVLTGQLSgavDSEISRAINE--LDIIgpyEKPIKSFVIKSNVDKFFPNK 280
Cdd:COG3437   83 VIFLTALAD---PEDRERALEAgaDDYL---TKPFDPEELLARVRNALELR 127
CheY COG0784
CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator ...
 153-237 1.53e-05

CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator Spo0F [Signal transduction mechanisms];


Pssm-ID: 440547 [Multi-domain]  Cd Length: 128  Bit Score: 43.69  E-value: 1.53e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694096084 153 DKEKHRIAVLDDDKNIVQSLSSLLEGDRYTIKEFYSIDELDDAIEQTPFDAYILDWIVDNKTVFNTIKKIRS-SGNKHAM 231
Cdd:COG0784    2 PLGGKRILVVDDNPDNRELLRRLLERLGYEVTTAEDGAEALELLRAGPPDLILLDINMPGMDGLELLRRIRAlPRLPDIP 81


                 ....*.
gi 694096084 232 VMVLTG 237
Cdd:COG0784   82 IIALTA 87
REC_OmpR_PmrA-like cd17624
phosphoacceptor receiver (REC) domain of PmrA-like OmpR family response regulators; This ...
 159-255 8.47e-04

phosphoacceptor receiver (REC) domain of PmrA-like OmpR family response regulators; This subfamily contains various OmpR family response regulators including PmrA, BasR, QseB, tctD, and RssB, which are components of two-component regulatory systems (TCSs). The PmrA/PmrB TCS controls transcription of genes that are involved in lipopolysaccharide modification in the outer membrane of bacteria, increasing bacterial resistance to host-derived antimicrobial peptides. The BasS/BasR TCS functions as an iron- and zinc-sensing transcription regulator. The QseB/QseC TCS activates the flagella regulon by activating transcription of FlhDC. The RssA/RssB TCS regulates swarming behavior in Serratia marcescens. OmpR family DNA-binding response regulators contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381139 [Multi-domain]  Cd Length: 115  Bit Score: 38.23  E-value: 8.47e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694096084 159 IAVLDDDKNIVQSLSSLLEGDRYTIKEFYSIDELDDAIEQTPFDAYILDWIVDNKTVFNTIKKIRSSGNKHAmVMVLTgq 238
Cdd:cd17624    1 ILLVEDDALLGDGLKTGLRKAGYAVDWVRTGAEAEAALASGPYDLVILDLGLPDGDGLDLLRRWRRQGQSLP-VLILT-- 77

                         90
                 ....*....|....*..
gi 694096084 239 lsgAVDSEISRaINELD 255
Cdd:cd17624   78 ---ARDGVDDR-VAGLD 90
REC_NtrX-like cd17550
phosphoacceptor receiver (REC) domain of nitrogen assimilation regulatory protein NtrX and ...
 159-222 1.21e-03

phosphoacceptor receiver (REC) domain of nitrogen assimilation regulatory protein NtrX and similar proteins; NtrX is part of the two-component regulatory system NtrY/NtrX that is involved in the activation of nitrogen assimilatory genes such as Gln. It is phosphorylated by the histidine kinase NtrY and interacts with sigma-54. NtrX is a member of the NtrC family, characterized by a domain architecture containing an N-terminal REC domain, followed by a central sigma-54 interaction/ATPase domain, and a C-terminal DNA binding domain. NtrC family response regulators are sigma54-dependent transcriptional activators. Also included in this subfamily is Aquifex aeolicus NtrC4. The ability of the central domain to hydrolyze ATP and thus to interact effectively with a complex of RNA polymerase, sigma54, and promoter, is controlled by the phosphorylation status of the REC domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381102 [Multi-domain]  Cd Length: 115  Bit Score: 37.86  E-value: 1.21e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 694096084 159 IAVLDDDKNIVQSLSSLLEGDRYTIKEFYSIDELDDAIEQTPFDAYILD-WI--VDNKTVFNTIKKI 222
Cdd:cd17550    1 ILIVDDEEDIRESLSGILEDEGYEVDTAADGEEALKLIKERRPDLVLLDiWLpdMDGLELLKEIKEK 67
 
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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