NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|171701684|ref|NP_418342|]
View 

DNA-binding transcriptional activator RhaR [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

PRK13500 family protein( domain architecture ID 11486656)

PRK13500 family protein

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
1-282 0e+00

HTH-type transcriptional activator RhaR;


:

Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 581.29  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684   1 MAHQLKLLKDDFFASDQQAVAVADRYPQDVFAEHTHDFCELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYASVN 80
Cdd:PRK13500  31 VAHQLKLLKDDFFASDQQAVAVADRYPQDVFAEHTHDFCELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYASVN 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684  81 DLVLQNIIYCPERLKLNLDWQGAIPGFNASAGQPHWRLGSMGMAQARQVIGQLEHESSQHVPFANEMAELLFGQLVMLLN 160
Cdd:PRK13500 111 DLVLQNIIYCPERLKLNLDWQGAIPGFSASAGQPHWRLGSVGMAQARQVIGQLEHESSQHVPFANEMAELLFGQLVMLLN 190

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684 161 RHRYTSDSLPPTSSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHS 240
Cdd:PRK13500 191 RHRYTSDSLPPTSSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHS 270

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 171701684 241 RLLISDISTECGFEDSNYFSVVFTRETGMTPSQWRHLNSQKD 282
Cdd:PRK13500 271 RLLISDISTECGFEDSNYFSVVFTRETGMTPSQWRHLNSQKD 312
 
Name Accession Description Interval E-value
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
1-282 0e+00

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 581.29  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684   1 MAHQLKLLKDDFFASDQQAVAVADRYPQDVFAEHTHDFCELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYASVN 80
Cdd:PRK13500  31 VAHQLKLLKDDFFASDQQAVAVADRYPQDVFAEHTHDFCELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYASVN 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684  81 DLVLQNIIYCPERLKLNLDWQGAIPGFNASAGQPHWRLGSMGMAQARQVIGQLEHESSQHVPFANEMAELLFGQLVMLLN 160
Cdd:PRK13500 111 DLVLQNIIYCPERLKLNLDWQGAIPGFSASAGQPHWRLGSVGMAQARQVIGQLEHESSQHVPFANEMAELLFGQLVMLLN 190

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684 161 RHRYTSDSLPPTSSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHS 240
Cdd:PRK13500 191 RHRYTSDSLPPTSSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHS 270

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 171701684 241 RLLISDISTECGFEDSNYFSVVFTRETGMTPSQWRHLNSQKD 282
Cdd:PRK13500 271 RLLISDISTECGFEDSNYFSVVFTRETGMTPSQWRHLNSQKD 312
cupin_RhaR_RhaS-like_N cd06977
HTH-type transcriptional activator RhaR and RhaS and related proteins, N-terminal cupin domain; ...
 17-163 2.98e-70

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: 213.28  E-value: 2.98e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684  17 QQAVAVADRYPQDVFAEHTHDFCELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYASVNDLVLQNIIYCPERLKL 96
Cdd:cd06977    1 NQPVAVEPRAPQEPFPEHTHDFHEIVIVTKGSGIHVLNGHPYRITAGDVFYIRPDDRHSYESVDDLCLTNILFRPERLFL 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 171701684  97 NLDWQGAIPGFNASAGQPHWRLGSMGMAQARQVIGQLEHESSQHVPFANEMAELLFGQLVMLLNRHR 163
Cdd:cd06977   81 FLDWLDTLPGYLAHQFQSHWRLNSSTLREIRQLIDQLESELEERDAGSELMAEALFLQLLVLLSRHR 147
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
192-275 8.44e-28

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 102.63  E-value: 8.44e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684   192 PFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMTP 271
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 171701684   272 SQWR 275
Cdd:smart00342  81 SEYR 84
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 143-275 8.74e-25

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: 101.00  E-value: 8.74e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684 143 FANEMAEllfgqlVMLLNRHRYTSDS------LPPTSSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQ 216
Cdd:COG4977  177 LANAVAR------RLVVDPRRPGGQAqfspllVPLGHRDPRLARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAA 250

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 171701684 217 TGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMTPSQWR 275
Cdd:COG4977  251 TGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHFRRAFRRRFGVSPSAYR 309
HTH_18 pfam12833
Helix-turn-helix domain;
199-275 1.77e-22

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 88.42  E-value: 1.77e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 171701684  199 CDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHA-QYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMTPSQWR 275
Cdd:pfam12833   2 AAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERArRLLLEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYR 79
 
Name Accession Description Interval E-value
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
1-282 0e+00

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 581.29  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684   1 MAHQLKLLKDDFFASDQQAVAVADRYPQDVFAEHTHDFCELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYASVN 80
Cdd:PRK13500  31 VAHQLKLLKDDFFASDQQAVAVADRYPQDVFAEHTHDFCELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYASVN 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684  81 DLVLQNIIYCPERLKLNLDWQGAIPGFNASAGQPHWRLGSMGMAQARQVIGQLEHESSQHVPFANEMAELLFGQLVMLLN 160
Cdd:PRK13500 111 DLVLQNIIYCPERLKLNLDWQGAIPGFSASAGQPHWRLGSVGMAQARQVIGQLEHESSQHVPFANEMAELLFGQLVMLLN 190

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684 161 RHRYTSDSLPPTSSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHS 240
Cdd:PRK13500 191 RHRYTSDSLPPTSSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHS 270

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 171701684 241 RLLISDISTECGFEDSNYFSVVFTRETGMTPSQWRHLNSQKD 282
Cdd:PRK13500 271 RLLISDISTECGFEDSNYFSVVFTRETGMTPSQWRHLNSQKD 312
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
1-282 0e+00

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 512.68  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684   1 MAHQLKLLKDDFFASDQQAVAVADRYPQDVFAEHTHDFCELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYASVN 80
Cdd:PRK13502   1 MANQLILLKKDFFTDEQQAVTVADRYPQDVFAEHTHEFCELVMVWRGNGLHVLNERPYRITRGDLFYIRAEDKHSYTSVN 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684  81 DLVLQNIIYCPERLKLNLDWQGAIPGFNASAGQPHWRLGSMGMAQARQVIGQLEHESSQHVPFANEMAELLFGQLVMLLN 160
Cdd:PRK13502  81 DLVLQNIIYCPERLKLNVNWQAMIPGFQGAQWHPHWRLGSMGMNQARQVINQLEHESNGRDPLANEMAELLFGQLVMTLK 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684 161 RHRYTSDSLPPTSSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHS 240
Cdd:PRK13502 161 RHRYATDDLPATSRETLLDKLITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHS 240

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 171701684 241 RLLISDISTECGFEDSNYFSVVFTRETGMTPSQWRHLNSQKD 282
Cdd:PRK13502 241 PLMISEISMQCGFEDSNYFSVVFTRETGMTPSQWRHLSNQSD 282
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
1-276 6.39e-124

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 354.98  E-value: 6.39e-124
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684   1 MAHQLKLLKDDFFASDQQAVAVADRYPQDVFAEHTHDFCELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYASVN 80
Cdd:PRK13501   1 MRAPLLLESRDYLLSEQMPVAVTNRYPQETFVEHTHQFCEIVIVWRGNGLHVLNDHPYRITCGDVFYIQAADHHSYESVH 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684  81 DLVLQNIIYCPERLKLNLDWQGAIPGFNASAGQPHWRLGSMGMAQARQVIGQLEHESSQHVPFANEMAELLFGQLVMLLN 160
Cdd:PRK13501  81 DLVLDNIIYCPERLHLNAQWHKLLPPLGPEQNQGYWRLTTQGMAQARPIIQQLAQESRKTDSWSIQLTEVLLLQLAIVLK 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684 161 RHRYTSDSLPPTSSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHS 240
Cdd:PRK13501 161 RHRYRAEQAHLLPDGEQLDLIMSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGS 240

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 171701684 241 RLLISDISTECGFEDSNYFSVVFTRETGMTPSQWRH 276
Cdd:PRK13501 241 EHRISDIAARCGFEDSNYFSAVFTREAGMTPRDYRQ 276
cupin_RhaR_RhaS-like_N cd06977
HTH-type transcriptional activator RhaR and RhaS and related proteins, N-terminal cupin domain; ...
 17-163 2.98e-70

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: 213.28  E-value: 2.98e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684  17 QQAVAVADRYPQDVFAEHTHDFCELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYASVNDLVLQNIIYCPERLKL 96
Cdd:cd06977    1 NQPVAVEPRAPQEPFPEHTHDFHEIVIVTKGSGIHVLNGHPYRITAGDVFYIRPDDRHSYESVDDLCLTNILFRPERLFL 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 171701684  97 NLDWQGAIPGFNASAGQPHWRLGSMGMAQARQVIGQLEHESSQHVPFANEMAELLFGQLVMLLNRHR 163
Cdd:cd06977   81 FLDWLDTLPGYLAHQFQSHWRLNSSTLREIRQLIDQLESELEERDAGSELMAEALFLQLLVLLSRHR 147
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
6-276 9.86e-61

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 193.74  E-value: 9.86e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684   6 KLLKDDFFASDQQAVAVADRYPQDVFAEHTHDFCELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYASVNDLVLQ 85
Cdd:PRK13503   3 VLHSVDFFPSGNAPVAIEPRLPQAAFPEHHHDFHEIVIVEHGTGIHVFNGQPYTLSGGTVCFVRDHDRHLYEHTDNLCLT 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684  86 NIIY-CPERLKLNLDWQGAIPGFNASAGQPHWRLGSMGMAQARQVIGQLEHESSQHVPFANEMAELLFGQLVMLLNRHry 164
Cdd:PRK13503  83 NVLYrSPDAFRFLAGLNQLLPQEQDGQYPSHWRVNQSVLQQVRQLVAQMEQQEESNDLEAIASREILFMQLLVLLRKS-- 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684 165 tSDSLPPTSSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLI 244
Cdd:PRK13503 161 -SLQENGENSDARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASV 239

                        250       260       270
                 ....*....|....*....|....*....|..
gi 171701684 245 SDISTECGFEDSNYFSVVFTRETGMTPSQWRH 276
Cdd:PRK13503 240 TDIAYRCGFGDSNHFSTLFRREFSWSPRDIRQ 271
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
192-275 8.44e-28

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 102.63  E-value: 8.44e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684   192 PFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMTP 271
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 171701684   272 SQWR 275
Cdd:smart00342  81 SEYR 84
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 143-275 8.74e-25

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: 101.00  E-value: 8.74e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684 143 FANEMAEllfgqlVMLLNRHRYTSDS------LPPTSSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQ 216
Cdd:COG4977  177 LANAVAR------RLVVDPRRPGGQAqfspllVPLGHRDPRLARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAA 250

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 171701684 217 TGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMTPSQWR 275
Cdd:COG4977  251 TGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHFRRAFRRRFGVSPSAYR 309
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
48-281 6.76e-24

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 97.54  E-value: 6.76e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684  48 NGLHVLNDRPYRITRGDLFYIHADDKHSYASVNDLVLQNIIYCPERLKLNLDWQGAIPGFNASAGQPHWRLGSMGMAQAR 127
Cdd:COG2207   24 LLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALLALLLLVGLLLLLLLLLL 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684 128 QVIGQLEHESSQHVPFANEMAELLFGQLVMLLNRHRYTSDSLPPTSSETLLDKLITRLAASLKSPFALDKFCDEASCSER 207
Cdd:COG2207  104 LLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARELGLSPR 183

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 171701684 208 VLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMTPSQWRHLNSQK 281
Cdd:COG2207  184 TLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLRAR 257
HTH_18 pfam12833
Helix-turn-helix domain;
199-275 1.77e-22

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 88.42  E-value: 1.77e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 171701684  199 CDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHA-QYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMTPSQWR 275
Cdd:pfam12833   2 AAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERArRLLLEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYR 79
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 20-156 1.19e-21

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: 87.88  E-value: 1.19e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684   20 VAVADRYPQDVFAEHTHDFCELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYASV--NDLVLQNIIYCPERLKLN 97
Cdd:pfam02311   5 EGIEARYPGHSFPPHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPEseDGWRYRWLYFEPELLERI 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 171701684   98 LDWQGAIPGFnasagQPHWRLGSMGMAQARQVIGQLEHESsqhvPFANEMAELLFGQLV 156
Cdd:pfam02311  85 LADISILAGG-----PLPLLRDPELAALLRALFRLLEEAG----RSDDLLAEALLYQLL 134
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 167-275 2.40e-15

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: 75.09  E-value: 2.40e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684 167 DSLPPTS-SETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQhSRLLIS 245
Cdd:COG2169   74 DLAPGSPpRADLVARACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQ-TGLSVT 152

                         90       100       110
                 ....*....|....*....|....*....|
gi 171701684 246 DISTECGFEDSNYFSVVFTRETGMTPSQWR 275
Cdd:COG2169  153 DAAYAAGFGSLSRFYEAFKKLLGMTPSAYR 182
ftrA PRK09393
transcriptional activator FtrA; Provisional
 144-275 1.22e-13

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 69.61  E-value: 1.22e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684 144 ANEMAEllfgQLVMLLNRH----RYTSDSLPPTSSETLlDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGM 219
Cdd:PRK09393 187 ANRVAR----RLVVPPHRDggqaQFVPRPVASRESDRL-GPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGM 261

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 171701684 220 TINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMTPSQWR 275
Cdd:PRK09393 262 TPAEWLLRERLARARDLLESSALSIDQIAERAGFGSEESLRHHFRRRAATSPAAYR 317
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
123-281 1.50e-13

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 69.23  E-value: 1.50e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684 123 MAQARQVIGQLEHESSQHVPFANEMAELLFGQLvmLLNRHRytsdsLPPTSSETLLDKLI----TRLAASLKSPFALDKF 198
Cdd:PRK10572 133 QPEFSDLFGQIEQAGQSEGRYSELLAMNLLERL--LLRCME-----AIPESLHPPMDPRVreacQYISDHLASEFDIESV 205

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684 199 CDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMTPSQWRHLN 278
Cdd:PRK10572 206 AQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFRARC 285


                 ...
gi 171701684 279 SQK 281
Cdd:PRK10572 286 EEK 288
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
12-81 4.73e-10

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 55.63  E-value: 4.73e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684  12 FFASDQQAVAVADRYPQDVFAEHTHDFCELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYASVND 81
Cdd:COG1917   17 ADGEDELEVVRVTFEPGARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGD 86
PRK10371 PRK10371
transcriptional regulator MelR;
213-281 3.69e-09

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 56.37  E-value: 3.69e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 171701684 213 FRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMTPSQWRHLNSQK 281
Cdd:PRK10371 228 FQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTAGFRSSSRFYSTFGKYVGMSPQQYRKLSQQR 296
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
173-276 1.05e-08

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 51.85  E-value: 1.05e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684 173 SSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECG 252
Cdd:PRK10219   2 SHQKIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLG 81

                         90       100
                 ....*....|....*....|....
gi 171701684 253 FEDSNYFSVVFTRETGMTPSQWRH 276
Cdd:PRK10219  82 YVSQQTFSRVFRRQFDRTPSDYRH 105
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 239-276 1.23e-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: 47.15  E-value: 1.23e-07
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 171701684  239 HSRLLISDISTECGFeDSNYFSVVFTRETGMTPSQWRH 276
Cdd:pfam00165   6 STNLTIADIADELGF-SRSYFSRLFKKYTGVTPSQYRH 42
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 185-226 8.77e-06

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: 8.77e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 171701684  185 LAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLR 226
Cdd:pfam00165   1 LRENLSTNLTIADIADELGFSRSYFSRLFKKYTGVTPSQYRH 42
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 27-81 1.38e-05

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: 42.47  E-value: 1.38e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 171701684  27 PQDVFAEHTHDF-CELVIVWRGNGLHVLND-RPYRITRGDLFYIHADDKHSYASVND 81
Cdd:cd02208    8 PGTSSPPHWHPEqDEIFYVLSGEGELTLDDgETVELKAGDIVLIPPGVPHSFVNTSD 64
cupin_TM1459-like cd02222
Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial ...
 34-76 1.88e-05

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: 42.44  E-value: 1.88e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 171701684  34 HTHDFCELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSY 76
Cdd:cd02222   33 HTHPWEHEVYVLRGKGVVVIGGEEYPVKPGDVVYIPPNEPHQF 75
cupin_DddK cd06988
Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes ...
 32-75 2.27e-05

Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes mostly bacterial proteins homologous to dimethylsulfoniopropionate lyase DddK from marine bacterium Pelagibacter. DddK cleaves dimethylsulfoniopropionate (DMSP), the organic osmolyte and antioxidant produced in marine environments, and yields acrylate and the climate-active gas dimethyl sulfide (DMS). DddK contains a double-stranded beta-helical motif which utilizes various divalent metal ions as cofactors for catalytic activity; however, nickel, an abundant metal ion in marine environments, confers the highest DMSP lyase activity. Also included in this family is Plu4264, a Photorhabdus luminescens manganese-containing cupin shown to have similar metal binding site to TM1287 decarboxylase, but two very different substrate binding pockets. The Plu4264 binding pocket shows a cavity and substrate entry point more than twice as large as and more hydrophobic than TM1287, suggesting that Plu4264 accepts a substrate that is significantly larger than that of TM1287, a putative oxalate decarboxylase. Thus, the function of Plu4264 could be similar to that of TM1287 but with a larger, less charged substrate. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


Pssm-ID: 380393 [Multi-domain]  Cd Length: 76  Bit Score: 41.84  E-value: 2.27e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 171701684  32 AEHTHDFCELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHS 75
Cdd:cd06988   16 TPHSHHEYEIFIVISGKGIVVVDGEREPVKAGDVVYIPPGTEHY 59
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
188-278 4.29e-05

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 42.40  E-value: 4.29e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684 188 SLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVFTRET 267
Cdd:PRK11511  21 NLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYF 100

                         90
                 ....*....|.
gi 171701684 268 GMTPSQWRHLN 278
Cdd:PRK11511 101 DVPPHKYRMTN 111
PRK09940 PRK09940
transcriptional regulator YdeO; Provisional
 189-273 4.62e-05

transcriptional regulator YdeO; Provisional


Pssm-ID: 182157 [Multi-domain]  Cd Length: 253  Bit Score: 43.92  E-value: 4.62e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684 189 LKSPFALDKFCDEASCSERVLRQQFRQQTgMTINQYLRQVRVCHAQYLLQhSRLLISDISTECGFEDSNYFSVVFTRETG 268
Cdd:PRK09940 147 LAHPWKLKDICDCLYISESLLKKKLKQEQ-TTFSQILLDARMQHAKNLIR-VEGSVNKIAEQCGYASTSYFIYAFRKHFG 224


                 ....*
gi 171701684 269 MTPSQ 273
Cdd:PRK09940 225 NSPKR 229
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 200-275 1.40e-04

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 42.71  E-value: 1.40e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 171701684 200 DEASCSERVLRQQFRQQtGMTINQYLRQVRV--ChAQYLLQHS-RLLISDISTECGFEDSNYFSVVFTRETGMTPSQWR 275
Cdd:PRK09685 222 GELGISVRSLYRLFAEQ-GLVVAQYIRNRRLdrC-ADDLRPAAdDEKITSIAYKWGFSDSSHFSTAFKQRFGVSPGEYR 298
PRK15186 PRK15186
AraC family transcriptional regulator; Provisional
 173-274 1.82e-04

AraC family transcriptional regulator; Provisional


Pssm-ID: 185108 [Multi-domain]  Cd Length: 291  Bit Score: 42.36  E-value: 1.82e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684 173 SSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLrQVRVCHAQYLLQHSRLLISDISTECG 252
Cdd:PRK15186 178 SQNTLAENIYNIIISDISRKWALKDISDSLYMSCSTLKRKLKQENTSFSEVYL-NARMNKATKLLRNSEYNITRVAYMCG 256

                         90       100
                 ....*....|....*....|..
gi 171701684 253 FEDSNYFSVVFTRETGMTPSQW 274
Cdd:PRK15186 257 YDSASYFTCVFKKHFKTTPSEF 278
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 183-280 1.19e-03

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 39.52  E-value: 1.19e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171701684 183 TRLAASLKSPFA----LDKFCDEASCSERVLRQQFRQQtGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNY 258
Cdd:PRK09978 145 TRVCTVINNNIAhewtLARIASELLMSPSLLKKKLREE-ETSYSQLLTECRMQRALQLIVIHGFSIKRVAVSCGYHSVSY 223

                         90       100
                 ....*....|....*....|..
gi 171701684 259 FSVVFTRETGMTPSQWRHLNSQ 280
Cdd:PRK09978 224 FIYVFRNYYGMTPTEYQERSAQ 245
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 27-77 1.45e-03

Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel).


Pssm-ID: 462300 [Multi-domain]  Cd Length: 71  Bit Score: 36.47  E-value: 1.45e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 171701684   27 PQDVFAEHTHDF-CELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYA 77
Cdd:pfam07883   7 PGESSPPHRHPGeDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFR 58
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH