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Conserved domains on  [gi|504344073|ref|WP_014531175|]
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helix-turn-helix domain-containing protein [Sinorhizobium meliloti]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 1000956)

helix-turn-helix domain-containing protein binds DNA and may function as a transcriptional regulator

Gene Ontology:  GO:0003677
PubMed:  15808743

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
GlxA super family cl34854
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 209-333 8.74e-39

Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH domain [Transcription];


The actual alignment was detected with superfamily member COG4977:

Pssm-ID: 444002 [Multi-domain]  Cd Length: 318  Bit Score: 139.52  E-value: 8.74e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 209 LAVHLIRNY----AANEAAD-------------------DRQNALTGfKLRRAVAHLEEHLAEPFNLAQLAETVGMSEFH 265
Cdd:COG4977  164 LALHLVERDhgaeLANAVARrlvvdprrpggqaqfspllVPLGHRDP-RLARAQAWMEANLEEPLSVDELARRAGMSPRT 242

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504344073 266 FSRLFKKATGLSPSRYFIRQRVARAQLLLQETDTSIIEIGMSVGYSSPSHFAQVFRRETGLPPSHYRR 333
Cdd:COG4977  243 LERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHFRRAFRRRFGVSPSAYRR 310
 
Name Accession Description Interval E-value
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 209-333 8.74e-39

Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH domain [Transcription];


Pssm-ID: 444002 [Multi-domain]  Cd Length: 318  Bit Score: 139.52  E-value: 8.74e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 209 LAVHLIRNY----AANEAAD-------------------DRQNALTGfKLRRAVAHLEEHLAEPFNLAQLAETVGMSEFH 265
Cdd:COG4977  164 LALHLVERDhgaeLANAVARrlvvdprrpggqaqfspllVPLGHRDP-RLARAQAWMEANLEEPLSVDELARRAGMSPRT 242

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504344073 266 FSRLFKKATGLSPSRYFIRQRVARAQLLLQETDTSIIEIGMSVGYSSPSHFAQVFRRETGLPPSHYRR 333
Cdd:COG4977  243 LERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHFRRAFRRRFGVSPSAYRR 310
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
249-332 5.81e-32

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 114.57  E-value: 5.81e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073   249 PFNLAQLAETVGMSEFHFSRLFKKATGLSPSRYFIRQRVARAQLLLQETDTSIIEIGMSVGYSSPSHFAQVFRRETGLPP 328
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 504344073   329 SHYR 332
Cdd:smart00342  81 SEYR 84
HTH_18 pfam12833
Helix-turn-helix domain;
255-333 2.42e-27

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 102.28  E-value: 2.42e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073  255 LAETVGMSEFHFSRLFKKATGLSPSRYFIRQRVARA-QLLLQETDTSIIEIGMSVGYSSPSHFAQVFRRETGLPPSHYRR 333
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERArRLLLEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
242-334 7.14e-21

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 90.80  E-value: 7.14e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 242 LEEHLAEPFNLAQLAETVGMSEFHFSRLFKKATGLSPSRYFIRQRVARAQLLLQETDTSIIEIGMSVGYSSPSHFAQVFR 321
Cdd:PRK10572 192 ISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFK 271

                         90
                 ....*....|...
gi 504344073 322 RETGLPPSHYRRG 334
Cdd:PRK10572 272 KCTGASPSEFRAR 284
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 235-332 8.77e-13

YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only one protein with the YSIRK variant form of signal peptide (TIGR01168) were examined for conserved genes near that one tagged protein. This protein is found adjacent to at various classes of repetitive or low-complexity YSIRK proteins (whether unique in genome or not), in a range of species (Enterococcus faecalis X98, Ruminococcus torques, Coprobacillus sp. D7, Lysinibacillus fusiformis ZC1, Streptococcus equi subsp. equi 4047, etc). The affliated YSIRK proteins include Streptococcal protective antigen (see ) and proteins with the Rib/alpha/Esp surface antigen repeat (see TIGR02331). The last quarter of this protein has an AraC family helix-turn-helix (HTH)transcriptional regulator domain.


Pssm-ID: 274977 [Multi-domain]  Cd Length: 383  Bit Score: 68.55  E-value: 8.77e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073  235 LRRAVAHLEEHLAEPFNLAQLAETVGMSEFHFSRLFKKATGLSPSRYFIRQRVARAQLLLQEtDTSIIEIGMSVGYSSPS 314
Cdd:TIGR04094 287 IRAVIQYINLNLYDPLKVEEIAKQFFMSESKLRKLFKKEMGISIQEYISKRKIEEAKYLLRS-QIPVSEVSNELGFYDLS 365

                          90
                  ....*....|....*...
gi 504344073  315 HFAQVFRRETGLPPSHYR 332
Cdd:TIGR04094 366 HFSRTFKKHTGVSPKQYQ 383
 
Name Accession Description Interval E-value
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 209-333 8.74e-39

Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH domain [Transcription];


Pssm-ID: 444002 [Multi-domain]  Cd Length: 318  Bit Score: 139.52  E-value: 8.74e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 209 LAVHLIRNY----AANEAAD-------------------DRQNALTGfKLRRAVAHLEEHLAEPFNLAQLAETVGMSEFH 265
Cdd:COG4977  164 LALHLVERDhgaeLANAVARrlvvdprrpggqaqfspllVPLGHRDP-RLARAQAWMEANLEEPLSVDELARRAGMSPRT 242

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504344073 266 FSRLFKKATGLSPSRYFIRQRVARAQLLLQETDTSIIEIGMSVGYSSPSHFAQVFRRETGLPPSHYRR 333
Cdd:COG4977  243 LERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHFRRAFRRRFGVSPSAYRR 310
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
249-332 5.81e-32

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 114.57  E-value: 5.81e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073   249 PFNLAQLAETVGMSEFHFSRLFKKATGLSPSRYFIRQRVARAQLLLQETDTSIIEIGMSVGYSSPSHFAQVFRRETGLPP 328
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 504344073   329 SHYR 332
Cdd:smart00342  81 SEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
90-334 1.30e-30

AraC-type DNA-binding domain and AraC-containing proteins [Transcription];


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 116.80  E-value: 1.30e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073  90 LIVWVMSGEAVVEERDLDGDWVANTVTVGDFFLTRSPTPYEMRWRSVDAAPFQVMHLYLSVPLFERVAYDVLGCAAPPAL 169
Cdd:COG2207   10 LLLLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALLALL 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 170 RDISGGRDTQLSHLLALVHQELTAEGKGSQLFIQGLAQSLAVHLIRNYAANEAADDRQNALTGFKLRRAVAhLEEHLAEP 249
Cdd:COG2207   90 LLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLL-LLLLLLLL 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 250 FNLAQLAETVGMSEFHFSRLFKKATGLSPSRYFIRQRVARAQLLLQETDTSIIEIGMSVGYSSPSHFAQVFRRETGLPPS 329
Cdd:COG2207  169 LTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPS 248


                 ....*
gi 504344073 330 HYRRG 334
Cdd:COG2207  249 EYRKR 253
HTH_18 pfam12833
Helix-turn-helix domain;
255-333 2.42e-27

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 102.28  E-value: 2.42e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073  255 LAETVGMSEFHFSRLFKKATGLSPSRYFIRQRVARA-QLLLQETDTSIIEIGMSVGYSSPSHFAQVFRRETGLPPSHYRR 333
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERArRLLLEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 236-334 4.36e-26

Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), contains Zn-binding and two AraC-type DNA-binding domains [Replication, recombination and repair];


Pssm-ID: 441772 [Multi-domain]  Cd Length: 358  Bit Score: 106.29  E-value: 4.36e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 236 RRAVAHLEEHLAEPFNLAQLAETVGMSEFHFSRLFKKATGLSPSRYFIRQRVARAQLLLQeTDTSIIEIGMSVGYSSPSH 315
Cdd:COG2169   87 ARACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQ-TGLSVTDAAYAAGFGSLSR 165

                         90
                 ....*....|....*....
gi 504344073 316 FAQVFRRETGLPPSHYRRG 334
Cdd:COG2169  166 FYEAFKKLLGMTPSAYRRG 184
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
242-334 7.14e-21

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 90.80  E-value: 7.14e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 242 LEEHLAEPFNLAQLAETVGMSEFHFSRLFKKATGLSPSRYFIRQRVARAQLLLQETDTSIIEIGMSVGYSSPSHFAQVFR 321
Cdd:PRK10572 192 ISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFK 271

                         90
                 ....*....|...
gi 504344073 322 RETGLPPSHYRRG 334
Cdd:PRK10572 272 KCTGASPSEFRAR 284
ftrA PRK09393
transcriptional activator FtrA; Provisional
 241-333 4.34e-19

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 86.17  E-value: 4.34e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 241 HLEEHLAEPFNLAQLAETVGMSEFHFSRLFKKATGLSPSRYFIRQRVARAQLLLQETDTSIIEIGMSVGYSSPSHFAQVF 320
Cdd:PRK09393 226 WMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAERAGFGSEESLRHHF 305

                         90
                 ....*....|...
gi 504344073 321 RRETGLPPSHYRR 333
Cdd:PRK09393 306 RRRAATSPAAYRK 318
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
179-334 6.66e-17

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 79.34  E-value: 6.66e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 179 QLSHLLALVHQ-----ELTAEGKGSQLFIQGLAqslavhLIRNYAANEAADDRQNaltgfKLRRAVAHLEEHLAEPFNLA 253
Cdd:PRK13503 123 QVRQLVAQMEQqeesnDLEAIASREILFMQLLV------LLRKSSLQENGENSDA-----RLNQLLAWLEDHFAEEVNWE 191

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 254 QLAETVGMSEFHFSRLFKKATGLSPSRYFIRQRVARAQLLLQETDTSIIEIGMSVGYSSPSHFAQVFRRETGLPPSHYRR 333
Cdd:PRK13503 192 ALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFGDSNHFSTLFRREFSWSPRDIRQ 271


                 .
gi 504344073 334 G 334
Cdd:PRK13503 272 G 272
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
87-333 5.39e-16

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 76.87  E-value: 5.39e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073  87 AEPLIVWVMSGEAVVEERDldgdWVantVTVGDFFLTRSPtpyemrwrsvDAAPFQVMH-LYLSVPLF--ERVAYDV-LG 162
Cdd:PRK13501  39 CEIVIVWRGNGLHVLNDHP----YR---ITCGDVFYIQAA----------DHHSYESVHdLVLDNIIYcpERLHLNAqWH 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 163 CAAPPALRDISGGRDTQLSHLLAL---VHQELTAEG-KGSQLFIQgLAQSLAVHLIRNYAANEAADDRQNAL-TGFKLRR 237
Cdd:PRK13501 102 KLLPPLGPEQNQGYWRLTTQGMAQarpIIQQLAQESrKTDSWSIQ-LTEVLLLQLAIVLKRHRYRAEQAHLLpDGEQLDL 180

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 238 AVAHLEEHLAEPFNLAQLAETVGMSEFHFSRLFKKATGLSPSRYFIRQRVARAQLLLQETDTSIIEIGMSVGYSSPSHFA 317
Cdd:PRK13501 181 IMSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSNYFS 260

                        250
                 ....*....|....*.
gi 504344073 318 QVFRRETGLPPSHYRR 333
Cdd:PRK13501 261 AVFTREAGMTPRDYRQ 276
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
242-332 2.20e-13

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 65.72  E-value: 2.20e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 242 LEEHLAEPFNLAQLAETVGMSEFHFSRLFKKATGLSPSRYFIRQRVARAQLLLQETDTSIIEIGMSVGYSSPSHFAQVFR 321
Cdd:PRK10219  14 IDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFSRVFR 93

                         90
                 ....*....|.
gi 504344073 322 RETGLPPSHYR 332
Cdd:PRK10219  94 RQFDRTPSDYR 104
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 235-332 8.77e-13

YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only one protein with the YSIRK variant form of signal peptide (TIGR01168) were examined for conserved genes near that one tagged protein. This protein is found adjacent to at various classes of repetitive or low-complexity YSIRK proteins (whether unique in genome or not), in a range of species (Enterococcus faecalis X98, Ruminococcus torques, Coprobacillus sp. D7, Lysinibacillus fusiformis ZC1, Streptococcus equi subsp. equi 4047, etc). The affliated YSIRK proteins include Streptococcal protective antigen (see ) and proteins with the Rib/alpha/Esp surface antigen repeat (see TIGR02331). The last quarter of this protein has an AraC family helix-turn-helix (HTH)transcriptional regulator domain.


Pssm-ID: 274977 [Multi-domain]  Cd Length: 383  Bit Score: 68.55  E-value: 8.77e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073  235 LRRAVAHLEEHLAEPFNLAQLAETVGMSEFHFSRLFKKATGLSPSRYFIRQRVARAQLLLQEtDTSIIEIGMSVGYSSPS 314
Cdd:TIGR04094 287 IRAVIQYINLNLYDPLKVEEIAKQFFMSESKLRKLFKKEMGISIQEYISKRKIEEAKYLLRS-QIPVSEVSNELGFYDLS 365

                          90
                  ....*....|....*...
gi 504344073  315 HFAQVFRRETGLPPSHYR 332
Cdd:TIGR04094 366 HFSRTFKKHTGVSPKQYQ 383
PRK10371 PRK10371
transcriptional regulator MelR;
233-333 2.40e-12

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 66.38  E-value: 2.40e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 233 FKLRRAVAHLEEHLAEPFNLAQLAETVGMSEFHFSRLFKKATGLSPSRYFIRQRVARAQLLLQETDTSIIEIGMSVGYSS 312
Cdd:PRK10371 191 FYVSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTAGFRS 270

                         90       100
                 ....*....|....*....|.
gi 504344073 313 PSHFAQVFRRETGLPPSHYRR 333
Cdd:PRK10371 271 SSRFYSTFGKYVGMSPQQYRK 291
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 242-281 6.06e-12

Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added.


Pssm-ID: 425497 [Multi-domain]  Cd Length: 42  Bit Score: 59.47  E-value: 6.06e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 504344073  242 LEEHLAEPFNLAQLAETVGMSEFHFSRLFKKATGLSPSRY 281
Cdd:pfam00165   1 LRENLSTNLTIADIADELGFSRSYFSRLFKKYTGVTPSQY 40
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
235-332 8.73e-12

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 64.69  E-value: 8.73e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 235 LRRAVAHLEEHLAEPFNLAQLAETVGMSEFHFSRLFKKATGLSPSRYFIRQRVARAQLLLQETDTSIIEIGMSVGYSSPS 314
Cdd:PRK13502 178 LDKLITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHSPLMISEISMQCGFEDSN 257

                         90
                 ....*....|....*...
gi 504344073 315 HFAQVFRRETGLPPSHYR 332
Cdd:PRK13502 258 YFSVVFTRETGMTPSQWR 275
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
242-332 2.76e-11

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 60.12  E-value: 2.76e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 242 LEEHLAEPFNLAQLAETVGMSEFHFSRLFKKATGLSPSRYFIRQRVARAQLLLQETDTSIIEIGMSVGYSSPSHFAQVFR 321
Cdd:PRK11511  18 IEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFK 97

                         90
                 ....*....|.
gi 504344073 322 RETGLPPSHYR 332
Cdd:PRK11511  98 NYFDVPPHKYR 108
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
235-332 3.40e-11

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 63.20  E-value: 3.40e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 235 LRRAVAHLEEHLAEPFNLAQLAETVGMSEFHFSRLFKKATGLSPSRYFIRQRVARAQLLLQETDTSIIEIGMSVGYSSPS 314
Cdd:PRK13500 208 LDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSN 287

                         90
                 ....*....|....*...
gi 504344073 315 HFAQVFRRETGLPPSHYR 332
Cdd:PRK13500 288 YFSVVFTRETGMTPSQWR 305
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 179-334 1.94e-10

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 60.82  E-value: 1.94e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 179 QLSHLLAlvhQELTAEGKGSQLFIQGLAQSLAVhLIRnyaanEAADDRQNALTGF--KLRRAVAHLEEHLAEPfNL--AQ 254
Cdd:PRK09685 150 QLSHRLL---QQSMNGPALSETESEALLEALIA-LLR-----PALHQRESVQPRRerQFQKVVALIDQSIQEE-ILrpEW 219

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 255 LAETVGMSEFHFSRLFKKaTGLSPSRYFIRQRVARAQLLLQE--TDTSIIEIGMSVGYSSPSHFAQVFRRETGLPPSHYR 332
Cdd:PRK09685 220 IAGELGISVRSLYRLFAE-QGLVVAQYIRNRRLDRCADDLRPaaDDEKITSIAYKWGFSDSSHFSTAFKQRFGVSPGEYR 298


                 ..
gi 504344073 333 RG 334
Cdd:PRK09685 299 RK 300
PRK15435 PRK15435
bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;
234-334 2.91e-09

bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;


Pssm-ID: 185333 [Multi-domain]  Cd Length: 353  Bit Score: 57.50  E-value: 2.91e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 234 KLRRAVAHLEEHlaEPFNLAQLAETVGMSEFHFSRLFKKATGLSPSRYfirQRVARAQLLlqetdTSIIEIGMSV----- 308
Cdd:PRK15435  86 KITHACRLLEQE--TPVTLEALADQVAMSPFHLHRLFKATTGMTPKAW---QQAWRARRL-----REALAKGESVttsil 155

                         90       100
                 ....*....|....*....|....*...
gi 504344073 309 --GYSSPSHFAQVFRRETGLPPSHYRRG 334
Cdd:PRK15435 156 naGFPDSSSYYRKADETLGMTAKQFRHG 183
PRK15340 PRK15340
AraC family transcriptional regulator InvF;
252-328 6.47e-07

AraC family transcriptional regulator InvF;


Pssm-ID: 185240  Cd Length: 216  Bit Score: 49.59  E-value: 6.47e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 504344073 252 LAQLAETVGMSEFHFSRLFKKATGLSPSRYFIRQRVARAQLLLQETDTSIIEIGMSVGYSSPSHFAQVFRRETGLPP 328
Cdd:PRK15340 128 MRMLGEDYGVSYTHFRRLCSRALGGKAKSELRNWRMAQSLLNSVEGHENITQLAVNHGYSSPSHFSSEIKELIGVSP 204
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 297-333 1.09e-05

Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added.


Pssm-ID: 425497 [Multi-domain]  Cd Length: 42  Bit Score: 41.76  E-value: 1.09e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 504344073  297 TDTSIIEIGMSVGYSsPSHFAQVFRRETGLPPSHYRR 333
Cdd:pfam00165   7 TNLTIADIADELGFS-RSYFSRLFKKYTGVTPSQYRH 42
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 237-332 1.85e-05

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 45.69  E-value: 1.85e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504344073 237 RAVAHLEEHLAEPFNLAQLAETVGMSEfhfSRLFKK--ATGLSPSRYFIRQRVARAQLLLQETDTSIIEIGMSVGYSSPS 314
Cdd:PRK09978 146 RVCTVINNNIAHEWTLARIASELLMSP---SLLKKKlrEEETSYSQLLTECRMQRALQLIVIHGFSIKRVAVSCGYHSVS 222

                         90
                 ....*....|....*...
gi 504344073 315 HFAQVFRRETGLPPSHYR 332
Cdd:PRK09978 223 YFIYVFRNYYGMTPTEYQ 240
PRK10296 PRK10296
DNA-binding transcriptional regulator ChbR; Provisional
 283-333 1.28e-04

DNA-binding transcriptional regulator ChbR; Provisional


Pssm-ID: 182362 [Multi-domain]  Cd Length: 278  Bit Score: 42.82  E-value: 1.28e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 504344073 283 IRQRVARAQLllQETDTSIIEIGMSVGYSSPSHFAQVFRRETGLPPSHYRR 333
Cdd:PRK10296 224 IRINFAKKQL--EMTNYSVTDIAFEAGYSSPSLFIKTFKKLTSFTPGSYRK 272
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
234-286 2.89e-04

AraC-type DNA-binding domain and AraC-containing proteins [Transcription];


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 41.69  E-value: 2.89e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 504344073 234 KLRRAVAHLEEHlaePFNLAQLAETVGM-SEFHFSRLFKKATGLSPSRYFIRQR 286
Cdd:COG2207  205 RLERAKRLLAET---DLSISEIAYELGFsSQSHFSRAFKKRFGVTPSEYRKRLR 255
 
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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