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Conserved domains on  [gi|488971963|ref|WP_002882891|]
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MULTISPECIES: HTH-type transcriptional activator RhaR [Gammaproteobacteria]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK13502 super family cl32883
HTH-type transcriptional activator RhaR;
4-277 1.78e-157

HTH-type transcriptional activator RhaR;


The actual alignment was detected with superfamily member PRK13502:

Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 439.87  E-value: 1.78e-157
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963   4 LILRKEEFFPSATQAVAVADRYPQNVFAEHTHEFCELVLVWRGNGLHVLNDRPWRITRGDLFYIRAEDKHSYASVNDLVL 83
Cdd:PRK13502   5 LILLKKDFFTDEQQAVTVADRYPQDVFAEHTHEFCELVMVWRGNGLHVLNERPYRITRGDLFYIRAEDKHSYTSVNDLVL 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963  84 QNIIYCPERLQLNFDWAGAIPGLFGTPWKPHWRMGSTGMAQARQVISQLEHECARRDAQGNAMAELLFAQLALTLQRHRY 163
Cdd:PRK13502  85 QNIIYCPERLKLNVNWQAMIPGFQGAQWHPHWRLGSMGMNQARQVINQLEHESNGRDPLANEMAELLFGQLVMTLKRHRY 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963 164 ATDDPAATQREALLDKLLAALAASLSRPFVLERFCEQEGGSERALRQQFRQQTGMTINHYLRQLRICHAQYLLQHTERLI 243
Cdd:PRK13502 165 ATDDLPATSRETLLDKLITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHSPLMI 244

                        250       260       270
                 ....*....|....*....|....*....|....
gi 488971963 244 GDIAMQCGFEDSNYFSVVFSREIGMSPGQWRQRS 277
Cdd:PRK13502 245 SEISMQCGFEDSNYFSVVFTRETGMTPSQWRHLS 278
 
Name Accession Description Interval E-value
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
4-277 1.78e-157

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 439.87  E-value: 1.78e-157
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963   4 LILRKEEFFPSATQAVAVADRYPQNVFAEHTHEFCELVLVWRGNGLHVLNDRPWRITRGDLFYIRAEDKHSYASVNDLVL 83
Cdd:PRK13502   5 LILLKKDFFTDEQQAVTVADRYPQDVFAEHTHEFCELVMVWRGNGLHVLNERPYRITRGDLFYIRAEDKHSYTSVNDLVL 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963  84 QNIIYCPERLQLNFDWAGAIPGLFGTPWKPHWRMGSTGMAQARQVISQLEHECARRDAQGNAMAELLFAQLALTLQRHRY 163
Cdd:PRK13502  85 QNIIYCPERLKLNVNWQAMIPGFQGAQWHPHWRLGSMGMNQARQVINQLEHESNGRDPLANEMAELLFGQLVMTLKRHRY 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963 164 ATDDPAATQREALLDKLLAALAASLSRPFVLERFCEQEGGSERALRQQFRQQTGMTINHYLRQLRICHAQYLLQHTERLI 243
Cdd:PRK13502 165 ATDDLPATSRETLLDKLITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHSPLMI 244

                        250       260       270
                 ....*....|....*....|....*....|....
gi 488971963 244 GDIAMQCGFEDSNYFSVVFSREIGMSPGQWRQRS 277
Cdd:PRK13502 245 SEISMQCGFEDSNYFSVVFTRETGMTPSQWRHLS 278
cupin_RhaR_RhaS-like_N cd06977
HTH-type transcriptional activator RhaR and RhaS and related proteins, N-terminal cupin domain; ...
 17-162 4.13e-63

HTH-type transcriptional activator RhaR and RhaS and related proteins, N-terminal cupin domain; Members of this family contain an N-terminal cupin domain and a C-terminal AraC/XylS family helix-turn-helix (HTH) DNA-binding domain, including the HTH-type transcription activators RhaS and RhaR. RhaS and RhaR respond to the availability of L-rhamnose and activate transcription of the operons in the Escherichia coli L-rhamnose catabolic regulon. The E. coli RhaR protein activates expression of the rhaSR operon in the presence of its effector, L-rhamnose. The resulting RhaS protein (plus L-rhamnose) activates expression of the L-rhamnose catabolic operon rhaBAD as well as the transport operon rhaT. These proteins bind DNA as dimers, via their HTH motifs. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380382 [Multi-domain]  Cd Length: 147  Bit Score: 195.17  E-value: 4.13e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963  17 QAVAVADRYPQNVFAEHTHEFCELVLVWRGNGLHVLNDRPWRITRGDLFYIRAEDKHSYASVNDLVLQNIIYCPERLQLN 96
Cdd:cd06977    2 QPVAVEPRAPQEPFPEHTHDFHEIVIVTKGSGIHVLNGHPYRITAGDVFYIRPDDRHSYESVDDLCLTNILFRPERLFLF 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488971963  97 FDWAGAIPGLFGTPWKPHWRMGSTGMAQARQVISQLEHECARRDAQGNAMAELLFAQLALTLQRHR 162
Cdd:cd06977   82 LDWLDTLPGYLAHQFQSHWRLNSSTLREIRQLIDQLESELEERDAGSELMAEALFLQLLVLLSRHR 147
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
194-274 2.91e-26

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 98.39  E-value: 2.91e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963   194 LERFCEQEGGSERALRQQFRQQTGMTINHYLRQLRICHAQYLLQHTERLIGDIAMQCGFEDSNYFSVVFSREIGMSPGQW 273
Cdd:smart00342   4 LEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPSEY 83


                   .
gi 488971963   274 R 274
Cdd:smart00342  84 R 84
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 190-281 3.15e-21

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: 90.99  E-value: 3.15e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963 190 RPFVLERFCEQEGGSERALRQQFRQQTGMTINHYLRQLRICHAQYLLQHTERLIGDIAMQCGFEDSNYFSVVFSREIGMS 269
Cdd:COG4977  225 EPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHFRRAFRRRFGVS 304

                         90
                 ....*....|..
gi 488971963 270 PGQWRQRSRAAA 281
Cdd:COG4977  305 PSAYRRRFRARA 316
HTH_18 pfam12833
Helix-turn-helix domain;
204-276 5.30e-20

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 81.87  E-value: 5.30e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488971963  204 SERALRQQFRQQTGMTINHYLRQLRICHA-QYLLQHTERLIGDIAMQCGFEDSNYFSVVFSREIGMSPGQWRQR 276
Cdd:pfam12833   8 SPRTLSRLFKRELGLSPKEYLRRLRLERArRLLLEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRRR 81
 
Name Accession Description Interval E-value
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
4-277 1.78e-157

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 439.87  E-value: 1.78e-157
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963   4 LILRKEEFFPSATQAVAVADRYPQNVFAEHTHEFCELVLVWRGNGLHVLNDRPWRITRGDLFYIRAEDKHSYASVNDLVL 83
Cdd:PRK13502   5 LILLKKDFFTDEQQAVTVADRYPQDVFAEHTHEFCELVMVWRGNGLHVLNERPYRITRGDLFYIRAEDKHSYTSVNDLVL 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963  84 QNIIYCPERLQLNFDWAGAIPGLFGTPWKPHWRMGSTGMAQARQVISQLEHECARRDAQGNAMAELLFAQLALTLQRHRY 163
Cdd:PRK13502  85 QNIIYCPERLKLNVNWQAMIPGFQGAQWHPHWRLGSMGMNQARQVINQLEHESNGRDPLANEMAELLFGQLVMTLKRHRY 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963 164 ATDDPAATQREALLDKLLAALAASLSRPFVLERFCEQEGGSERALRQQFRQQTGMTINHYLRQLRICHAQYLLQHTERLI 243
Cdd:PRK13502 165 ATDDLPATSRETLLDKLITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHSPLMI 244

                        250       260       270
                 ....*....|....*....|....*....|....
gi 488971963 244 GDIAMQCGFEDSNYFSVVFSREIGMSPGQWRQRS 277
Cdd:PRK13502 245 SEISMQCGFEDSNYFSVVFTRETGMTPSQWRHLS 278
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
4-275 7.55e-139

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 393.70  E-value: 7.55e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963   4 LILRKEEFFPSATQAVAVADRYPQNVFAEHTHEFCELVLVWRGNGLHVLNDRPWRITRGDLFYIRAEDKHSYASVNDLVL 83
Cdd:PRK13500  35 LKLLKDDFFASDQQAVAVADRYPQDVFAEHTHDFCELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYASVNDLVL 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963  84 QNIIYCPERLQLNFDWAGAIPGLFGTPWKPHWRMGSTGMAQARQVISQLEHECARRDAQGNAMAELLFAQLALTLQRHRY 163
Cdd:PRK13500 115 QNIIYCPERLKLNLDWQGAIPGFSASAGQPHWRLGSVGMAQARQVIGQLEHESSQHVPFANEMAELLFGQLVMLLNRHRY 194

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963 164 ATDDPAATQREALLDKLLAALAASLSRPFVLERFCEQEGGSERALRQQFRQQTGMTINHYLRQLRICHAQYLLQHTERLI 243
Cdd:PRK13500 195 TSDSLPPTSSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLI 274

                        250       260       270
                 ....*....|....*....|....*....|..
gi 488971963 244 GDIAMQCGFEDSNYFSVVFSREIGMSPGQWRQ 275
Cdd:PRK13500 275 SDISTECGFEDSNYFSVVFTRETGMTPSQWRH 306
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
2-276 1.07e-122

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 351.90  E-value: 1.07e-122
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963   2 AGLILRKEEFFPSATQAVAVADRYPQNVFAEHTHEFCELVLVWRGNGLHVLNDRPWRITRGDLFYIRAEDKHSYASVNDL 81
Cdd:PRK13501   3 APLLLESRDYLLSEQMPVAVTNRYPQETFVEHTHQFCEIVIVWRGNGLHVLNDHPYRITCGDVFYIQAADHHSYESVHDL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963  82 VLQNIIYCPERLQLNFDWAGAIPGLFGTPWKPHWRMGSTGMAQARQVISQLEHECARRDAQGNAMAELLFAQLALTLQRH 161
Cdd:PRK13501  83 VLDNIIYCPERLHLNAQWHKLLPPLGPEQNQGYWRLTTQGMAQARPIIQQLAQESRKTDSWSIQLTEVLLLQLAIVLKRH 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963 162 RYATDDPAATQREALLDKLLAALAASLSRPFVLERFCEQEGGSERALRQQFRQQTGMTINHYLRQLRICHAQYLLQHTER 241
Cdd:PRK13501 163 RYRAEQAHLLPDGEQLDLIMSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEH 242

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 488971963 242 LIGDIAMQCGFEDSNYFSVVFSREIGMSPGQWRQR 276
Cdd:PRK13501 243 RISDIAARCGFEDSNYFSAVFTREAGMTPRDYRQR 277
cupin_RhaR_RhaS-like_N cd06977
HTH-type transcriptional activator RhaR and RhaS and related proteins, N-terminal cupin domain; ...
 17-162 4.13e-63

HTH-type transcriptional activator RhaR and RhaS and related proteins, N-terminal cupin domain; Members of this family contain an N-terminal cupin domain and a C-terminal AraC/XylS family helix-turn-helix (HTH) DNA-binding domain, including the HTH-type transcription activators RhaS and RhaR. RhaS and RhaR respond to the availability of L-rhamnose and activate transcription of the operons in the Escherichia coli L-rhamnose catabolic regulon. The E. coli RhaR protein activates expression of the rhaSR operon in the presence of its effector, L-rhamnose. The resulting RhaS protein (plus L-rhamnose) activates expression of the L-rhamnose catabolic operon rhaBAD as well as the transport operon rhaT. These proteins bind DNA as dimers, via their HTH motifs. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380382 [Multi-domain]  Cd Length: 147  Bit Score: 195.17  E-value: 4.13e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963  17 QAVAVADRYPQNVFAEHTHEFCELVLVWRGNGLHVLNDRPWRITRGDLFYIRAEDKHSYASVNDLVLQNIIYCPERLQLN 96
Cdd:cd06977    2 QPVAVEPRAPQEPFPEHTHDFHEIVIVTKGSGIHVLNGHPYRITAGDVFYIRPDDRHSYESVDDLCLTNILFRPERLFLF 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488971963  97 FDWAGAIPGLFGTPWKPHWRMGSTGMAQARQVISQLEHECARRDAQGNAMAELLFAQLALTLQRHR 162
Cdd:cd06977   82 LDWLDTLPGYLAHQFQSHWRLNSSTLREIRQLIDQLESELEERDAGSELMAEALFLQLLVLLSRHR 147
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
5-275 7.60e-62

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 196.44  E-value: 7.60e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963   5 ILRKEEFFPSATQAVAVADRYPQNVFAEHTHEFCELVLVWRGNGLHVLNDRPWRITRGDLFYIRAEDKHSYASVNDLVLQ 84
Cdd:PRK13503   3 VLHSVDFFPSGNAPVAIEPRLPQAAFPEHHHDFHEIVIVEHGTGIHVFNGQPYTLSGGTVCFVRDHDRHLYEHTDNLCLT 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963  85 NIIY-CPERLQLNFDWAGAIPGLFGTPWKPHWRMGSTGMAQARQVISQLEHECARRDAQGNAMAELLFAQLALTLQRHRY 163
Cdd:PRK13503  83 NVLYrSPDAFRFLAGLNQLLPQEQDGQYPSHWRVNQSVLQQVRQLVAQMEQQEESNDLEAIASREILFMQLLVLLRKSSL 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963 164 ATDDPAATQRealLDKLLAALAASLSRPFVLERFCEQEGGSERALRQQFRQQTGMTINHYLRQLRICHAQYLLQHTERLI 243
Cdd:PRK13503 163 QENGENSDAR---LNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASV 239

                        250       260       270
                 ....*....|....*....|....*....|..
gi 488971963 244 GDIAMQCGFEDSNYFSVVFSREIGMSPGQWRQ 275
Cdd:PRK13503 240 TDIAYRCGFGDSNHFSTLFRREFSWSPRDIRQ 271
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
194-274 2.91e-26

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 98.39  E-value: 2.91e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963   194 LERFCEQEGGSERALRQQFRQQTGMTINHYLRQLRICHAQYLLQHTERLIGDIAMQCGFEDSNYFSVVFSREIGMSPGQW 273
Cdd:smart00342   4 LEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPSEY 83


                   .
gi 488971963   274 R 274
Cdd:smart00342  84 R 84
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 190-281 3.15e-21

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: 90.99  E-value: 3.15e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963 190 RPFVLERFCEQEGGSERALRQQFRQQTGMTINHYLRQLRICHAQYLLQHTERLIGDIAMQCGFEDSNYFSVVFSREIGMS 269
Cdd:COG4977  225 EPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHFRRAFRRRFGVS 304

                         90
                 ....*....|..
gi 488971963 270 PGQWRQRSRAAA 281
Cdd:COG4977  305 PSAYRRRFRARA 316
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
47-281 3.45e-21

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 90.22  E-value: 3.45e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963  47 NGLHVLNDRPWRITRGDLFYIRAEDKHSYASVNDLVLQNIIYCPERLQLNFDWAGAIPGLFGTPWKPHWRMGSTGMAQAR 126
Cdd:COG2207   24 LLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALLALLLLVGLLLLLLLLLL 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963 127 QVISQLEHECARRDAQGNAMAELLFAQLALTLQRHRYATDDPAATQREALLDKLLAALAASLSRPFVLERFCEQEGGSER 206
Cdd:COG2207  104 LLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARELGLSPR 183

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488971963 207 ALRQQFRQQTGMTINHYLRQLRICHAQYLLQHTERLIGDIAMQCGFEDSNYFSVVFSREIGMSPGQWRQRSRAAA 281
Cdd:COG2207  184 TLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLRARA 258
HTH_18 pfam12833
Helix-turn-helix domain;
204-276 5.30e-20

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 81.87  E-value: 5.30e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488971963  204 SERALRQQFRQQTGMTINHYLRQLRICHA-QYLLQHTERLIGDIAMQCGFEDSNYFSVVFSREIGMSPGQWRQR 276
Cdd:pfam12833   8 SPRTLSRLFKRELGLSPKEYLRRLRLERArRLLLEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRRR 81
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 19-155 2.79e-17

AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization domain of the bacterial gene regulatory protein AraC. The domain is found in conjunction with the helix-turn-helix (HTH) DNA-binding motif pfam00165. This domain is distantly related to the Cupin domain pfam00190.


Pssm-ID: 396749 [Multi-domain]  Cd Length: 134  Bit Score: 76.32  E-value: 2.79e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963   19 VAVADRYPQNVFAEHTHEFCELVLVWRGNGLHVLNDRPWRITRGDLFYIRAEDKHSYASV--NDLVLQNIIYCPERLQLN 96
Cdd:pfam02311   5 EGIEARYPGHSFPPHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPEseDGWRYRWLYFEPELLERI 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 488971963   97 FDWAGAIPGLFgtpwkPHWRMGSTGMAQARQVISQLEHEcarrDAQGNAMAELLFAQLA 155
Cdd:pfam02311  85 LADISILAGGP-----LPLLRDPELAALLRALFRLLEEA----GRSDDLLAEALLYQLL 134
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 194-281 2.64e-13

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: 68.93  E-value: 2.64e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963 194 LERFCEQEGGSERALRQQFRQQTGMTINHYLRQLRICHAQYLLQHTERLIgDIAMQCGFEDSNYFSVVFSREIGMSPGQW 273
Cdd:COG2169  103 LEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQTGLSVT-DAAYAAGFGSLSRFYEAFKKLLGMTPSAY 181


                 ....*...
gi 488971963 274 RQRSRAAA 281
Cdd:COG2169  182 RRGGAGAA 189
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
212-278 8.05e-11

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 61.14  E-value: 8.05e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488971963 212 FRQQTGMTINHYLRQLRICHAQYLLQHTERLIGDIAMQCGFEDSNYFSVVFSREIGMSPGQWRQRSR 278
Cdd:PRK10572 220 FRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFRARCE 286
PRK10371 PRK10371
transcriptional regulator MelR;
212-278 9.91e-11

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 60.99  E-value: 9.91e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488971963 212 FRQQTGMTINHYLRQLRICHAQYLLQHTERLIGDIAMQCGFEDSNYFSVVFSREIGMSPGQWRQRSR 278
Cdd:PRK10371 228 FQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTAGFRSSSRFYSTFGKYVGMSPQQYRKLSQ 294
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
190-276 3.71e-10

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 56.09  E-value: 3.71e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963 190 RPFVLERFCEQEGGSERALRQQFRQQTGMTINHYLRQLRICHAQYLLQHTERLIGDIAMQCGFEDSNYFSVVFSREIGMS 269
Cdd:PRK10219  20 QPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFSRVFRRQFDRT 99


                 ....*..
gi 488971963 270 PGQWRQR 276
Cdd:PRK10219 100 PSDYRHR 106
ftrA PRK09393
transcriptional activator FtrA; Provisional
 189-279 1.64e-09

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 57.67  E-value: 1.64e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963 189 SRPFVLERFCEQEGGSERALRQQFRQQTGMTINHYLRQLRICHAQYLLQHTERLIGDIAMQCGFEDSNYFSVVFSREIGM 268
Cdd:PRK09393 232 AEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAERAGFGSEESLRHHFRRRAAT 311

                         90
                 ....*....|.
gi 488971963 269 SPGQWRQRSRA 279
Cdd:PRK09393 312 SPAAYRKRFGR 322
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
26-80 1.37e-08

Cupin domain protein related to quercetin dioxygenase [General function prediction only];


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 51.39  E-value: 1.37e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 488971963  26 PQNVFAEHTHEFCELVLVWRGNGLHVLNDRPWRITRGDLFYIRAEDKHSYASVND 80
Cdd:COG1917   32 PGARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGD 86
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 238-275 2.01e-07

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: 46.38  E-value: 2.01e-07
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 488971963  238 HTERLIGDIAMQCGFeDSNYFSVVFSREIGMSPGQWRQ 275
Cdd:pfam00165   6 STNLTIADIADELGF-SRSYFSRLFKKYTGVTPSQYRH 42
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 204-278 6.71e-07

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 49.64  E-value: 6.71e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488971963 204 SERALRQQFRQQtGMTINHYLRQLRI--CHAQYLLQHTERLIGDIAMQCGFEDSNYFSVVFSREIGMSPGQWRQRSR 278
Cdd:PRK09685 227 SVRSLYRLFAEQ-GLVVAQYIRNRRLdrCADDLRPAADDEKITSIAYKWGFSDSSHFSTAFKQRFGVSPGEYRRKFR 302
PRK09940 PRK09940
transcriptional regulator YdeO; Provisional
 189-278 4.19e-05

transcriptional regulator YdeO; Provisional


Pssm-ID: 182157 [Multi-domain]  Cd Length: 253  Bit Score: 43.92  E-value: 4.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963 189 SRPFVLERFCEQEGGSERALRQQFRQQTgMTINHYLRQLRICHAQYLLQhTERLIGDIAMQCGFEDSNYFSVVFSREIGM 268
Cdd:PRK09940 148 AHPWKLKDICDCLYISESLLKKKLKQEQ-TTFSQILLDARMQHAKNLIR-VEGSVNKIAEQCGYASTSYFIYAFRKHFGN 225

                         90
                 ....*....|
gi 488971963 269 SPGQWRQRSR 278
Cdd:PRK09940 226 SPKRVSKEYR 235
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
191-274 4.93e-05

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 42.01  E-value: 4.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963 191 PFVLERFCEQEGGSERALRQQFRQQTGMTINHYLRQLRICHAQYLLQHTERLIGDIAMQCGFEDSNYFSVVFSREIGMSP 270
Cdd:PRK11511  25 PLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVPP 104


                 ....
gi 488971963 271 GQWR 274
Cdd:PRK11511 105 HKYR 108
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 26-80 3.14e-04

RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP (deoxythymidine diphosphates)-4-dehydrorhamnose 3,5-epimerase)-like cupins. RmlC is a dTDP-sugar isomerase involved in the synthesis of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. Cupins are a functionally diverse superfamily originally discovered based on the highly conserved motif found in germin and germin-like proteins. This conserved motif forms a beta-barrel fold found in all of the cupins, giving rise to the name cupin ('cupa' is the Latin term for small barrel). The active site of members of this superfamily is generally located at the center of a conserved barrel and usually includes a metal ion. The different functional classes in this superfamily include single domain bacterial isomerases and epimerases involved in the modification of cell wall carbohydrates, two domain bicupins such as the desiccation-tolerant seed storage globulins, and multidomain nuclear transcription factors involved in legume root nodulation.


Pssm-ID: 380338 [Multi-domain]  Cd Length: 73  Bit Score: 38.62  E-value: 3.14e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 488971963  26 PQNVFAEHTHEF-CELVLVWRGNGLHVLNDRPWR-ITRGDLFYIRAEDKHSYASVND 80
Cdd:cd02208    8 PGTSSPPHWHPEqDEIFYVLSGEGELTLDDGETVeLKAGDIVLIPPGVPHSFVNTSD 64
cupin_TM1459-like cd02222
Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial ...
 33-75 5.01e-04

Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to Thermotoga maritima TM1459, a manganese-containing cupin that has been shown to cleave C=C bonds in the presence of alkylperoxide as oxidant in vitro. Its biological function is still unknown. This family also includes Halorhodospira halophila Hhal_0468. Structures of these proteins show a cupin fold with a conserved "jelly roll-like" beta-barrel fold that form a homodimer.


Pssm-ID: 380351 [Multi-domain]  Cd Length: 91  Bit Score: 38.20  E-value: 5.01e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 488971963  33 HTHEFCELVLVWRGNGLHVLNDRPWRITRGDLFYIRAEDKHSY 75
Cdd:cd02222   33 HTHPWEHEVYVLRGKGVVVIGGEEYPVKPGDVVYIPPNEPHQF 75
cupin_YobQ-like_N cd07003
Bacillus subtilis YobQ and related proteins, N-terminal cupin domain; This family includes ...
 30-83 2.38e-03

Bacillus subtilis YobQ and related proteins, N-terminal cupin domain; This family includes bacterial proteins homologous to Bacillus subtilis YobQ and Photobacterium leiognathi LumQ, both uncharacterized proteins thought to be DNA-binding proteins that may function as AraC/XylS family transcriptional regulators. YobQ has an N-terminal cupin beta barrel domain (represented by this alignment model) and a C-terminal AraC/XylS family helix-turn-helix (HTH) DNA-binding domain. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380407 [Multi-domain]  Cd Length: 66  Bit Score: 35.83  E-value: 2.38e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 488971963  30 FAEHTHEFCELVLVWRGNGLHVLNDRPWRITRGDLFYIRAEDKHSYASVND---LVL 83
Cdd:cd07003    7 QSSHSHEHAQLVLPLSGSLELEVEGRGSRVKPDIGLYIPPNAEHRFAGSSDnrcLVL 63
PRK15121 PRK15121
MDR efflux pump AcrAB transcriptional activator RobA;
190-277 2.75e-03

MDR efflux pump AcrAB transcriptional activator RobA;


Pssm-ID: 185076 [Multi-domain]  Cd Length: 289  Bit Score: 38.45  E-value: 2.75e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963 190 RPFVLERFCEQEGGSERALRQQFRQQTGMTINHYLRQLRICHAQYLLQHTERLIGDIAMQCGFEDSNYFSVVFSREIGMS 269
Cdd:PRK15121  20 QPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKAAVALRLTSRPILDIALQYRFDSQQTFTRAFKKQFAQT 99


                 ....*...
gi 488971963 270 PGQWRqRS 277
Cdd:PRK15121 100 PALYR-RS 106
PRK15186 PRK15186
AraC family transcriptional regulator; Provisional
 189-273 2.97e-03

AraC family transcriptional regulator; Provisional


Pssm-ID: 185108 [Multi-domain]  Cd Length: 291  Bit Score: 38.51  E-value: 2.97e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488971963 189 SRPFVLERFCEQEGGSERALRQQFRQQTGMTINHYLRQlRICHAQYLLQHTERLIGDIAMQCGFEDSNYFSVVFSREIGM 268
Cdd:PRK15186 195 SRKWALKDISDSLYMSCSTLKRKLKQENTSFSEVYLNA-RMNKATKLLRNSEYNITRVAYMCGYDSASYFTCVFKKHFKT 273


                 ....*
gi 488971963 269 SPGQW 273
Cdd:PRK15186 274 TPSEF 278
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 204-277 5.37e-03

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 37.60  E-value: 5.37e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488971963 204 SERALRQQFRQQtGMTINHYLRQLRICHAQYLLQHTERLIGDIAMQCGFEDSNYFSVVFSREIGMSPGQWRQRS 277
Cdd:PRK09978 171 SPSLLKKKLREE-ETSYSQLLTECRMQRALQLIVIHGFSIKRVAVSCGYHSVSYFIYVFRNYYGMTPTEYQERS 243
PHA01076 PHA01076
putative encapsidation protein
 60-97 6.83e-03

putative encapsidation protein


Pssm-ID: 107017  Cd Length: 378  Bit Score: 37.67  E-value: 6.83e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 488971963  60 TRGDLFYIRAEDKHSYASVN-DLVLQNIIYCPERLQLNF 97
Cdd:PHA01076 240 QNGDFFYIKTDDKYIKVMYNvDTFMTNIIVIPYTKQYEF 278
 
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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