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Conserved domains on  [gi|485718788|ref|WP_001350361|]
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MULTISPECIES: arabinose operon transcriptional regulator AraC [Escherichia]

Protein Classification

DNA-binding transcriptional regulator AraC( domain architecture ID 11484804)

DNA-binding transcriptional regulator AraC controls the expression of genes involved in the transport and catabolism of L-arabinose. It regulates initiation of transcription of the araBAD operon and controls its own synthesis

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
1-281 0e+00

arabinose operon transcriptional regulator AraC;


:

Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 572.30  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788   1 MAEAQNDPLLPGYSFNAHLVAGLTPIEANGYLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIH 80
Cdd:PRK10572   6 MAEAQNNPLLPGYSFNAHLVAGLTPIEAGGYLDFFIDRPLGMKGYILNLTIRGQGVIFNGGRAFVCRPGDLLLFPPGEIH 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788  81 HYGRHPEAHEWYHQWVYFRPRAYWHEWLNWPSIFANTGFFR-PDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQL 159
Cdd:PRK10572  86 HYGRHPDSDEWYHQWVYFRPRAYWADWLNWPSIFAGVGRLRiPDEALQPEFSDLFGQIEQAGQSEGRYSELLAMNLLERL 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788 160 LLRRMEAINESLHPPMDNRVREACQYISDHLAdSNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLL 239
Cdd:PRK10572 166 LLRCMEAIPESLHPPMDPRVREACQYISDHLA-SEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLL 244

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 485718788 240 STTRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFRAGCE 281
Cdd:PRK10572 245 QTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFRARCE 286
 
Name Accession Description Interval E-value
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
1-281 0e+00

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 572.30  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788   1 MAEAQNDPLLPGYSFNAHLVAGLTPIEANGYLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIH 80
Cdd:PRK10572   6 MAEAQNNPLLPGYSFNAHLVAGLTPIEAGGYLDFFIDRPLGMKGYILNLTIRGQGVIFNGGRAFVCRPGDLLLFPPGEIH 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788  81 HYGRHPEAHEWYHQWVYFRPRAYWHEWLNWPSIFANTGFFR-PDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQL 159
Cdd:PRK10572  86 HYGRHPDSDEWYHQWVYFRPRAYWADWLNWPSIFAGVGRLRiPDEALQPEFSDLFGQIEQAGQSEGRYSELLAMNLLERL 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788 160 LLRRMEAINESLHPPMDNRVREACQYISDHLAdSNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLL 239
Cdd:PRK10572 166 LLRCMEAIPESLHPPMDPRVREACQYISDHLA-SEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLL 244

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 485718788 240 STTRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFRAGCE 281
Cdd:PRK10572 245 QTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFRARCE 286
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
194-277 6.08e-29

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 105.33  E-value: 6.08e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788   194 NFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASP 273
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 485718788   274 SEFR 277
Cdd:smart00342  81 SEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
34-279 4.38e-26

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 103.32  E-value: 4.38e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788  34 FFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEAHEWYHQWVYFRPRAYWHEWLNWPSI 113
Cdd:COG2207   11 LLLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALLALLL 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788 114 FANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLLLRRMEAINESLHPPMDNRVREACQYISDHLADS 193
Cdd:COG2207   91 LVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLT 170

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788 194 nfdIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASP 273
Cdd:COG2207  171 ---LEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTP 247


                 ....*.
gi 485718788 274 SEFRAG 279
Cdd:COG2207  248 SEYRKR 253
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 21-156 6.13e-25

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: 96.74  E-value: 6.13e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788   21 AGLTPIEANGYLDFFIDRPLGmkGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEaHEWYHQWVYFRP 100
Cdd:pfam02311   2 PGLEGIEARYPGHSFPPHVHD--FYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESE-DGWRYRWLYFEP 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 485718788  101 RAYWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLL 156
Cdd:pfam02311  79 ELLERILADISILAGGPLPLLRDPELAALLRALFRLLEEAGRSDDLLAEALLYQLL 134
cupin_MmsR-like_N cd06986
AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This ...
 26-101 1.63e-17

AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This family contains bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included is MmsR, a bacterial transcriptional regulator thought to positively regulate the expression of the mmsAB operon. The mmsAB operon contains two structural genes involved in valine metabolism: mmsA which encodes methylmalonate-semialdehyde dehydrogenase, and mmsB which encodes 3-hydroxyisobutyrate dehydrogenase. The cupin domain of members of this subfamily does not contain a metal binding site.


Pssm-ID: 380391 [Multi-domain]  Cd Length: 84  Bit Score: 75.21  E-value: 1.63e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 485718788  26 IEANGYLDF---FIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEaHEWYHQWVYFRPR 101
Cdd:cd06986    7 LTDCGYEPCepgHSYGPAVRDYYILHYVLSGKGTFSVNGKTYHLKAGQGFLIPPGEPHSYGADED-DPWTYYWIGFSGS 84
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 151-277 3.67e-15

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: 74.71  E-value: 3.67e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788  151 LAINLLEQLLLRR------MEAINESLHPPMDNRVREACQYISDHLADsNFDIASVAQHVCLSPSRLSHLFRQQLGISVL 224
Cdd:TIGR04094 253 EQTSLMDVLKLRDsaiiyfTELLHEISINHHSPLIRAVIQYINLNLYD-PLKVEEIAKQFFMSESKLRKLFKKEMGISIQ 331

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 485718788  225 SWREDQRISQAKLLLSTtRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFR 277
Cdd:TIGR04094 332 EYISKRKIEEAKYLLRS-QIPVSEVSNELGFYDLSHFSRTFKKHTGVSPKQYQ 383
 
Name Accession Description Interval E-value
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
1-281 0e+00

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 572.30  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788   1 MAEAQNDPLLPGYSFNAHLVAGLTPIEANGYLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIH 80
Cdd:PRK10572   6 MAEAQNNPLLPGYSFNAHLVAGLTPIEAGGYLDFFIDRPLGMKGYILNLTIRGQGVIFNGGRAFVCRPGDLLLFPPGEIH 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788  81 HYGRHPEAHEWYHQWVYFRPRAYWHEWLNWPSIFANTGFFR-PDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQL 159
Cdd:PRK10572  86 HYGRHPDSDEWYHQWVYFRPRAYWADWLNWPSIFAGVGRLRiPDEALQPEFSDLFGQIEQAGQSEGRYSELLAMNLLERL 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788 160 LLRRMEAINESLHPPMDNRVREACQYISDHLAdSNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLL 239
Cdd:PRK10572 166 LLRCMEAIPESLHPPMDPRVREACQYISDHLA-SEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLL 244

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 485718788 240 STTRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFRAGCE 281
Cdd:PRK10572 245 QTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFRARCE 286
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
194-277 6.08e-29

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 105.33  E-value: 6.08e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788   194 NFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASP 273
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 485718788   274 SEFR 277
Cdd:smart00342  81 SEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
34-279 4.38e-26

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 103.32  E-value: 4.38e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788  34 FFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEAHEWYHQWVYFRPRAYWHEWLNWPSI 113
Cdd:COG2207   11 LLLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALLALLL 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788 114 FANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLLLRRMEAINESLHPPMDNRVREACQYISDHLADS 193
Cdd:COG2207   91 LVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLT 170

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788 194 nfdIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASP 273
Cdd:COG2207  171 ---LEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTP 247


                 ....*.
gi 485718788 274 SEFRAG 279
Cdd:COG2207  248 SEYRKR 253
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 21-156 6.13e-25

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: 96.74  E-value: 6.13e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788   21 AGLTPIEANGYLDFFIDRPLGmkGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEaHEWYHQWVYFRP 100
Cdd:pfam02311   2 PGLEGIEARYPGHSFPPHVHD--FYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESE-DGWRYRWLYFEP 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 485718788  101 RAYWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLL 156
Cdd:pfam02311  79 ELLERILADISILAGGPLPLLRDPELAALLRALFRLLEEAGRSDDLLAEALLYQLL 134
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 172-278 8.82e-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: 100.62  E-value: 8.82e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788 172 HPPMDNRVREACQYISDHLADsNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGR 251
Cdd:COG4977  205 LGHRDPRLARAQAWMEANLEE-PLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAA 283

                         90       100
                 ....*....|....*....|....*..
gi 485718788 252 NVGFDDQLYFSRVFKKCTGASPSEFRA 278
Cdd:COG4977  284 ACGFGSASHFRRAFRRRFGVSPSAYRR 310
HTH_18 pfam12833
Helix-turn-helix domain;
200-278 2.15e-22

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 88.03  E-value: 2.15e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788  200 VAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAK-LLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFRA 278
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARrLLLEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
cupin_MmsR-like_N cd06986
AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This ...
 26-101 1.63e-17

AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This family contains bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included is MmsR, a bacterial transcriptional regulator thought to positively regulate the expression of the mmsAB operon. The mmsAB operon contains two structural genes involved in valine metabolism: mmsA which encodes methylmalonate-semialdehyde dehydrogenase, and mmsB which encodes 3-hydroxyisobutyrate dehydrogenase. The cupin domain of members of this subfamily does not contain a metal binding site.


Pssm-ID: 380391 [Multi-domain]  Cd Length: 84  Bit Score: 75.21  E-value: 1.63e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 485718788  26 IEANGYLDF---FIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEaHEWYHQWVYFRPR 101
Cdd:cd06986    7 LTDCGYEPCepgHSYGPAVRDYYILHYVLSGKGTFSVNGKTYHLKAGQGFLIPPGEPHSYGADED-DPWTYYWIGFSGS 84
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 170-279 6.72e-16

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: 76.63  E-value: 6.72e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788 170 SLHPPMDNRVREACQYISDHlADSNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTrMPIATV 249
Cdd:COG2169   77 PGSPPRADLVARACRLIEAG-AEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQTG-LSVTDA 154

                         90       100       110
                 ....*....|....*....|....*....|
gi 485718788 250 GRNVGFDDQLYFSRVFKKCTGASPSEFRAG 279
Cdd:COG2169  155 AYAAGFGSLSRFYEAFKKLLGMTPSAYRRG 184
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 151-277 3.67e-15

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: 74.71  E-value: 3.67e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788  151 LAINLLEQLLLRR------MEAINESLHPPMDNRVREACQYISDHLADsNFDIASVAQHVCLSPSRLSHLFRQQLGISVL 224
Cdd:TIGR04094 253 EQTSLMDVLKLRDsaiiyfTELLHEISINHHSPLIRAVIQYINLNLYD-PLKVEEIAKQFFMSESKLRKLFKKEMGISIQ 331

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 485718788  225 SWREDQRISQAKLLLSTtRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFR 277
Cdd:TIGR04094 332 EYISKRKIEEAKYLLRS-QIPVSEVSNELGFYDLSHFSRTFKKHTGVSPKQYQ 383
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
137-277 4.43e-14

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 70.70  E-value: 4.43e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788 137 IINAGQGEGRYSELLAINLLEQLLL-------RRMEAINESLHPPMDNRVREACQYISDHLAdSNFDIASVAQHVCLSPS 209
Cdd:PRK13501 129 IIQQLAQESRKTDSWSIQLTEVLLLqlaivlkRHRYRAEQAHLLPDGEQLDLIMSALQQSLG-AYFDMADFCHKNQLVER 207

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 485718788 210 RLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFR 277
Cdd:PRK13501 208 SLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSNYFSAVFTREAGMTPRDYR 275
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
133-277 4.35e-10

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 58.91  E-value: 4.35e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788 133 LFGQIINAGQGEGRYSELLAINLLEQLLLRRMEAINESLHPPmdnrvreacqyisdhladsnFDIASVAQHVCLSPSRLS 212
Cdd:PRK13502 151 LFGQLVMTLKRHRYATDDLPATSRETLLDKLITALANSLECP--------------------FALDAFCQQEQCSERVLR 210

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 485718788 213 HLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFR 277
Cdd:PRK13502 211 QQFRAQTGMTINQYLRQVRICHAQYLLQHSPLMISEISMQCGFEDSNYFSVVFTRETGMTPSQWR 275
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
125-277 2.54e-09

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 57.03  E-value: 2.54e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788 125 AHQPHFS----------DLFGQIINAGQGEGRYSELLAINLLEQL--LLRRMEAINESLhPPMDNRV-------REACQY 185
Cdd:PRK13500 141 AGQPHWRlgsvgmaqarQVIGQLEHESSQHVPFANEMAELLFGQLvmLLNRHRYTSDSL-PPTSSETlldklitRLAASL 219

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788 186 ISDHLADSNFDIASVAQHVclspsrLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVF 265
Cdd:PRK13500 220 KSPFALDKFCDEASCSERV------LRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVF 293

                        170
                 ....*....|..
gi 485718788 266 KKCTGASPSEFR 277
Cdd:PRK13500 294 TRETGMTPSQWR 305
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
184-277 3.74e-07

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 47.61  E-value: 3.74e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788 184 QYISDHLaDSNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSR 263
Cdd:PRK10219  12 AWIDEHI-DQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFSR 90

                         90
                 ....*....|....
gi 485718788 264 VFKKCTGASPSEFR 277
Cdd:PRK10219  91 VFRRQFDRTPSDYR 104
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 180-280 6.18e-07

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 49.64  E-value: 6.18e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788 180 REACQYISDHLADSNFDIASVAQHVCLSPSRLSHLFRQQlGISVLswredQRISQAKLLLSTTRM-------PIATVGRN 252
Cdd:PRK09685 200 QKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQ-GLVVA-----QYIRNRRLDRCADDLrpaaddeKITSIAYK 273

                         90       100
                 ....*....|....*....|....*...
gi 485718788 253 VGFDDQLYFSRVFKKCTGASPSEFRAGC 280
Cdd:PRK09685 274 WGFSDSSHFSTAFKQRFGVSPGEYRRKF 301
PRK10371 PRK10371
transcriptional regulator MelR;
179-277 7.76e-07

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 49.43  E-value: 7.76e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788 179 VREACQYISDHLaDSNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQ 258
Cdd:PRK10371 193 VSQMLGFIAENY-DQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTAGFRSS 271

                         90
                 ....*....|....*....
gi 485718788 259 LYFSRVFKKCTGASPSEFR 277
Cdd:PRK10371 272 SRFYSTFGKYVGMSPQQYR 290
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 186-227 1.03e-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: 44.45  E-value: 1.03e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 485718788  186 ISDHLAdSNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWR 227
Cdd:pfam00165   1 LRENLS-TNLTIADIADELGFSRSYFSRLFKKYTGVTPSQYR 41
ftrA PRK09393
transcriptional activator FtrA; Provisional
 184-278 1.85e-06

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 48.42  E-value: 1.85e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788 184 QYISDHLADsNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSR 263
Cdd:PRK09393 225 DWMRAHLAE-PHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAERAGFGSEESLRH 303

                         90
                 ....*....|....*
gi 485718788 264 VFKKCTGASPSEFRA 278
Cdd:PRK09393 304 HFRRRAATSPAAYRK 318
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 241-277 1.72e-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: 40.99  E-value: 1.72e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 485718788  241 TTRMPIATVGRNVGFDdQLYFSRVFKKCTGASPSEFR 277
Cdd:pfam00165   6 STNLTIADIADELGFS-RSYFSRLFKKYTGVTPSQYR 41
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 171-277 2.49e-04

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 41.83  E-value: 2.49e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788 171 LHPPMDNRVreaCQYISDHLADsNFDIASVAQHVCLSPSRLSHLFRQQlGISVLSWREDQRISQAKLLLSTTRMPIATVG 250
Cdd:PRK09978 139 LQPNMRTRV---CTVINNNIAH-EWTLARIASELLMSPSLLKKKLREE-ETSYSQLLTECRMQRALQLIVIHGFSIKRVA 213

                         90       100
                 ....*....|....*....|....*..
gi 485718788 251 RNVGFDDQLYFSRVFKKCTGASPSEFR 277
Cdd:PRK09978 214 VSCGYHSVSYFIYVFRNYYGMTPTEYQ 240
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
148-279 1.14e-03

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 39.66  E-value: 1.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788 148 SELLAINLLeqLLLRRmEAINESLHPPmDNRVREACQYISDHLADSnFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWR 227
Cdd:PRK13503 146 REILFMQLL--VLLRK-SSLQENGENS-DARLNQLLAWLEDHFAEE-VNWEALADQFSLSLRTLHRQLKQQTGLTPQRYL 220

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 485718788 228 EDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFRAG 279
Cdd:PRK13503 221 NRLRLLKARHLLRHSDASVTDIAYRCGFGDSNHFSTLFRREFSWSPRDIRQG 272
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
185-277 1.36e-03

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 38.16  E-value: 1.36e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485718788 185 YISDHLaDSNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRV 264
Cdd:PRK11511  17 WIEDNL-ESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRT 95

                         90
                 ....*....|...
gi 485718788 265 FKKCTGASPSEFR 277
Cdd:PRK11511  96 FKNYFDVPPHKYR 108
cupin_TM1459-like cd02222
Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial ...
 51-82 1.65e-03

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: 36.66  E-value: 1.65e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 485718788  51 IRGQGVVKNQGREFVCRPGDILLFPPGEIHHY 82
Cdd:cd02222   44 LRGKGVVVIGGEEYPVKPGDVVYIPPNEPHQF 75
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
51-88 2.63e-03

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 36.37  E-value: 2.63e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 485718788  51 IRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEA 88
Cdd:COG1917   50 LEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDE 87
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 44-82 6.17e-03

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: 34.77  E-value: 6.17e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 485718788  44 GYILNLTIRGQGVVK-NQGREFVCRPGDILLFPPGEIHHY 82
Cdd:cd02208   20 QDEIFYVLSGEGELTlDDGETVELKAGDIVLIPPGVPHSF 59
cupin_YbfI-like_N cd07001
AraC/XylS family transcriptional regulators similar to Bacillus subtilis YbfI, N-terminal ...
 45-80 8.39e-03

AraC/XylS family transcriptional regulators similar to Bacillus subtilis YbfI, N-terminal cupin domain; This family contains bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators, including YbfI, an uncharacterized Bacillus subtilis. In Pseudomonas putida, this protein is thought to regulate the expression of phenylserine aldolase. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380405 [Multi-domain]  Cd Length: 76  Bit Score: 34.67  E-value: 8.39e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 485718788  45 YILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIH 80
Cdd:cd07001   23 YVIGFIESGQRTLFCEGKEYTVEPGDLLLINPRDVH 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.
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