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Conserved domains on  [gi|1335032047|gb|AUT31214|]
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arabinose operon regulatory protein [cloning vector pBAD-kan-BlaP-VEB-4]

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;
14-302 0e+00

arabinose operon transcriptional regulator AraC;


:

Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 585.40  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047  14 SMKSMAEAQNDPLLPGYSFNAHLVAGLTPIEANGYLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPP 93
Cdd:PRK10572    2 YHRMMAEAQNNPLLPGYSFNAHLVAGLTPIEAGGYLDFFIDRPLGMKGYILNLTIRGQGVIFNGGRAFVCRPGDLLLFPP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047  94 GEIHHYGRHPEAREWYHQWVYFRPRAYWHEWLNWPSIFANTGFFR-PDEAHQPHFSDLFGQIINAGQGEGRYSELLAINL 172
Cdd:PRK10572   82 GEIHHYGRHPDSDEWYHQWVYFRPRAYWADWLNWPSIFAGVGRLRiPDEALQPEFSDLFGQIEQAGQSEGRYSELLAMNL 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 173 LEQLLLRRMEAINESLHPPMDNRVREACQYISDHLAdSNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQA 252
Cdd:PRK10572  162 LERLLLRCMEAIPESLHPPMDPRVREACQYISDHLA-SEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRA 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1335032047 253 KLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFRAGCEEKVN 302
Cdd:PRK10572  241 KLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFRARCEEKNN 290
 
Name Accession Description Interval E-value
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
14-302 0e+00

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 585.40  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047  14 SMKSMAEAQNDPLLPGYSFNAHLVAGLTPIEANGYLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPP 93
Cdd:PRK10572    2 YHRMMAEAQNNPLLPGYSFNAHLVAGLTPIEAGGYLDFFIDRPLGMKGYILNLTIRGQGVIFNGGRAFVCRPGDLLLFPP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047  94 GEIHHYGRHPEAREWYHQWVYFRPRAYWHEWLNWPSIFANTGFFR-PDEAHQPHFSDLFGQIINAGQGEGRYSELLAINL 172
Cdd:PRK10572   82 GEIHHYGRHPDSDEWYHQWVYFRPRAYWADWLNWPSIFAGVGRLRiPDEALQPEFSDLFGQIEQAGQSEGRYSELLAMNL 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 173 LEQLLLRRMEAINESLHPPMDNRVREACQYISDHLAdSNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQA 252
Cdd:PRK10572  162 LERLLLRCMEAIPESLHPPMDPRVREACQYISDHLA-SEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRA 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1335032047 253 KLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFRAGCEEKVN 302
Cdd:PRK10572  241 KLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFRARCEEKNN 290
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
211-294 7.93e-29

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 105.71  E-value: 7.93e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047  211 NFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASP 290
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 1335032047  291 SEFR 294
Cdd:smart00342  81 SEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
51-296 9.22e-27

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 105.63  E-value: 9.22e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047  51 FFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEAREWYHQWVYFRPRAYWHEWLNWPSI 130
Cdd:COG2207    11 LLLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALLALLL 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 131 FANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLLLRRMEAINESLHPPMDNRVREACQYISDHLADS 210
Cdd:COG2207    91 LVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLT 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 211 nfdIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASP 290
Cdd:COG2207   171 ---LEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTP 247


                  ....*.
gi 1335032047 291 SEFRAG 296
Cdd:COG2207   248 SEYRKR 253
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 38-173 7.41e-26

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: 99.82  E-value: 7.41e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047  38 AGLTPIEANGYLDFFIDRPLGmkGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEArEWYHQWVYFRP 117
Cdd:pfam02311   2 PGLEGIEARYPGHSFPPHVHD--FYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESED-GWRYRWLYFEP 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1335032047 118 RAYWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLL 173
Cdd:pfam02311  79 ELLERILADISILAGGPLPLLRDPELAALLRALFRLLEEAGRSDDLLAEALLYQLL 134
cupin_MmsR-like_N cd06986
AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This ...
 43-118 1.51e-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: 75.98  E-value: 1.51e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1335032047  43 IEANGYLDF---FIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEaREWYHQWVYFRPR 118
Cdd:cd06986     7 LTDCGYEPCepgHSYGPAVRDYYILHYVLSGKGTFSVNGKTYHLKAGQGFLIPPGEPHSYGADED-DPWTYYWIGFSGS 84
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 168-294 5.36e-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: 5.36e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 168 LAINLLEQLLLRR------MEAINESLHPPMDNRVREACQYISDHLADsNFDIASVAQHVCLSPSRLSHLFRQQLGISVL 241
Cdd:TIGR04094 253 EQTSLMDVLKLRDsaiiyfTELLHEISINHHSPLIRAVIQYINLNLYD-PLKVEEIAKQFFMSESKLRKLFKKEMGISIQ 331

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1335032047 242 SWREDQRISQAKLLLSTtRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFR 294
Cdd:TIGR04094 332 EYISKRKIEEAKYLLRS-QIPVSEVSNELGFYDLSHFSRTFKKHTGVSPKQYQ 383
 
Name Accession Description Interval E-value
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
14-302 0e+00

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 585.40  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047  14 SMKSMAEAQNDPLLPGYSFNAHLVAGLTPIEANGYLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPP 93
Cdd:PRK10572    2 YHRMMAEAQNNPLLPGYSFNAHLVAGLTPIEAGGYLDFFIDRPLGMKGYILNLTIRGQGVIFNGGRAFVCRPGDLLLFPP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047  94 GEIHHYGRHPEAREWYHQWVYFRPRAYWHEWLNWPSIFANTGFFR-PDEAHQPHFSDLFGQIINAGQGEGRYSELLAINL 172
Cdd:PRK10572   82 GEIHHYGRHPDSDEWYHQWVYFRPRAYWADWLNWPSIFAGVGRLRiPDEALQPEFSDLFGQIEQAGQSEGRYSELLAMNL 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 173 LEQLLLRRMEAINESLHPPMDNRVREACQYISDHLAdSNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQA 252
Cdd:PRK10572  162 LERLLLRCMEAIPESLHPPMDPRVREACQYISDHLA-SEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRA 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1335032047 253 KLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFRAGCEEKVN 302
Cdd:PRK10572  241 KLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFRARCEEKNN 290
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
211-294 7.93e-29

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 105.71  E-value: 7.93e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047  211 NFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASP 290
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 1335032047  291 SEFR 294
Cdd:smart00342  81 SEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
51-296 9.22e-27

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 105.63  E-value: 9.22e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047  51 FFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEAREWYHQWVYFRPRAYWHEWLNWPSI 130
Cdd:COG2207    11 LLLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALLALLL 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 131 FANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLLLRRMEAINESLHPPMDNRVREACQYISDHLADS 210
Cdd:COG2207    91 LVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLT 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 211 nfdIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASP 290
Cdd:COG2207   171 ---LEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTP 247


                  ....*.
gi 1335032047 291 SEFRAG 296
Cdd:COG2207   248 SEYRKR 253
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 38-173 7.41e-26

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: 99.82  E-value: 7.41e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047  38 AGLTPIEANGYLDFFIDRPLGmkGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEArEWYHQWVYFRP 117
Cdd:pfam02311   2 PGLEGIEARYPGHSFPPHVHD--FYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESED-GWRYRWLYFEP 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1335032047 118 RAYWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLL 173
Cdd:pfam02311  79 ELLERILADISILAGGPLPLLRDPELAALLRALFRLLEEAGRSDDLLAEALLYQLL 134
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 189-295 5.68e-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: 102.16  E-value: 5.68e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 189 HPPMDNRVREACQYISDHLADsNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGR 268
Cdd:COG4977   205 LGHRDPRLARAQAWMEANLEE-PLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAA 283

                          90       100
                  ....*....|....*....|....*..
gi 1335032047 269 NVGFDDQLYFSRVFKKCTGASPSEFRA 295
Cdd:COG4977   284 ACGFGSASHFRRAFRRRFGVSPSAYRR 310
HTH_18 pfam12833
Helix-turn-helix domain;
217-295 1.72e-22

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 89.19  E-value: 1.72e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 217 VAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAK-LLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFRA 295
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARrLLLEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
cupin_MmsR-like_N cd06986
AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This ...
 43-118 1.51e-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: 75.98  E-value: 1.51e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1335032047  43 IEANGYLDF---FIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEaREWYHQWVYFRPR 118
Cdd:cd06986     7 LTDCGYEPCepgHSYGPAVRDYYILHYVLSGKGTFSVNGKTYHLKAGQGFLIPPGEPHSYGADED-DPWTYYWIGFSGS 84
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 187-296 3.57e-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: 77.79  E-value: 3.57e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 187 SLHPPMDNRVREACQYISDHlADSNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTrMPIATV 266
Cdd:COG2169    77 PGSPPRADLVARACRLIEAG-AEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQTG-LSVTDA 154

                          90       100       110
                  ....*....|....*....|....*....|
gi 1335032047 267 GRNVGFDDQLYFSRVFKKCTGASPSEFRAG 296
Cdd:COG2169   155 AYAAGFGSLSRFYEAFKKLLGMTPSAYRRG 184
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 168-294 5.36e-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: 5.36e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 168 LAINLLEQLLLRR------MEAINESLHPPMDNRVREACQYISDHLADsNFDIASVAQHVCLSPSRLSHLFRQQLGISVL 241
Cdd:TIGR04094 253 EQTSLMDVLKLRDsaiiyfTELLHEISINHHSPLIRAVIQYINLNLYD-PLKVEEIAKQFFMSESKLRKLFKKEMGISIQ 331

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1335032047 242 SWREDQRISQAKLLLSTtRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFR 294
Cdd:TIGR04094 332 EYISKRKIEEAKYLLRS-QIPVSEVSNELGFYDLSHFSRTFKKHTGVSPKQYQ 383
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
154-294 3.73e-14

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 71.47  E-value: 3.73e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 154 IINAGQGEGRYSELLAINLLEQLLL-------RRMEAINESLHPPMDNRVREACQYISDHLAdSNFDIASVAQHVCLSPS 226
Cdd:PRK13501  129 IIQQLAQESRKTDSWSIQLTEVLLLqlaivlkRHRYRAEQAHLLPDGEQLDLIMSALQQSLG-AYFDMADFCHKNQLVER 207

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1335032047 227 RLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFR 294
Cdd:PRK13501  208 SLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSNYFSAVFTREAGMTPRDYR 275
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
150-301 3.96e-10

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 59.68  E-value: 3.96e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 150 LFGQIINAGQGEGRYSELLAINLLEQLLLRRMEAINESLHPPmdnrvreacqyisdhladsnFDIASVAQHVCLSPSRLS 229
Cdd:PRK13502  151 LFGQLVMTLKRHRYATDDLPATSRETLLDKLITALANSLECP--------------------FALDAFCQQEQCSERVLR 210

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1335032047 230 HLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFRAGCEEKV 301
Cdd:PRK13502  211 QQFRAQTGMTINQYLRQVRICHAQYLLQHSPLMISEISMQCGFEDSNYFSVVFTRETGMTPSQWRHLSNQSD 282
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
142-294 2.47e-09

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 57.42  E-value: 2.47e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 142 AHQPHFS----------DLFGQIINAGQGEGRYSELLAINLLEQL--LLRRMEAINESLhPPMDNRV-------REACQY 202
Cdd:PRK13500  141 AGQPHWRlgsvgmaqarQVIGQLEHESSQHVPFANEMAELLFGQLvmLLNRHRYTSDSL-PPTSSETlldklitRLAASL 219

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 203 ISDHLADSNFDIASVAQHVclspsrLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVF 282
Cdd:PRK13500  220 KSPFALDKFCDEASCSERV------LRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVF 293

                         170
                  ....*....|..
gi 1335032047 283 KKCTGASPSEFR 294
Cdd:PRK13500  294 TRETGMTPSQWR 305
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
201-294 3.49e-07

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 48.00  E-value: 3.49e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 201 QYISDHLaDSNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSR 280
Cdd:PRK10219   12 AWIDEHI-DQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFSR 90

                          90
                  ....*....|....
gi 1335032047 281 VFKKCTGASPSEFR 294
Cdd:PRK10219   91 VFRRQFDRTPSDYR 104
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 197-297 6.38e-07

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 50.03  E-value: 6.38e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 197 REACQYISDHLADSNFDIASVAQHVCLSPSRLSHLFRQQlGISVLswredQRISQAKLLLSTTRM-------PIATVGRN 269
Cdd:PRK09685  200 QKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQ-GLVVA-----QYIRNRRLDRCADDLrpaaddeKITSIAYK 273

                          90       100
                  ....*....|....*....|....*...
gi 1335032047 270 VGFDDQLYFSRVFKKCTGASPSEFRAGC 297
Cdd:PRK09685  274 WGFSDSSHFSTAFKQRFGVSPGEYRRKF 301
PRK10371 PRK10371
transcriptional regulator MelR;
196-294 7.56e-07

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 49.82  E-value: 7.56e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 196 VREACQYISDHLaDSNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQ 275
Cdd:PRK10371  193 VSQMLGFIAENY-DQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTAGFRSS 271

                          90
                  ....*....|....*....
gi 1335032047 276 LYFSRVFKKCTGASPSEFR 294
Cdd:PRK10371  272 SRFYSTFGKYVGMSPQQYR 290
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 203-244 1.04e-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: 44.84  E-value: 1.04e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1335032047 203 ISDHLAdSNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWR 244
Cdd:pfam00165   1 LRENLS-TNLTIADIADELGFSRSYFSRLFKKYTGVTPSQYR 41
ftrA PRK09393
transcriptional activator FtrA; Provisional
 201-295 1.59e-06

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 48.81  E-value: 1.59e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 201 QYISDHLADsNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSR 280
Cdd:PRK09393  225 DWMRAHLAE-PHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAERAGFGSEESLRH 303

                          90
                  ....*....|....*
gi 1335032047 281 VFKKCTGASPSEFRA 295
Cdd:PRK09393  304 HFRRRAATSPAAYRK 318
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 258-294 1.71e-05

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


Pssm-ID: 425497 [Multi-domain]  Cd Length: 42  Bit Score: 41.37  E-value: 1.71e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1335032047 258 TTRMPIATVGRNVGFDdQLYFSRVFKKCTGASPSEFR 294
Cdd:pfam00165   6 STNLTIADIADELGFS-RSYFSRLFKKYTGVTPSQYR 41
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 188-294 3.02e-04

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 41.83  E-value: 3.02e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 188 LHPPMDNRVreaCQYISDHLADsNFDIASVAQHVCLSPSRLSHLFRQQlGISVLSWREDQRISQAKLLLSTTRMPIATVG 267
Cdd:PRK09978  139 LQPNMRTRV---CTVINNNIAH-EWTLARIASELLMSPSLLKKKLREE-ETSYSQLLTECRMQRALQLIVIHGFSIKRVA 213

                          90       100
                  ....*....|....*....|....*..
gi 1335032047 268 RNVGFDDQLYFSRVFKKCTGASPSEFR 294
Cdd:PRK09978  214 VSCGYHSVSYFIYVFRNYYGMTPTEYQ 240
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
165-296 8.41e-04

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 40.43  E-value: 8.41e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 165 SELLAINLLeqLLLRRmEAINESLHPPmDNRVREACQYISDHLADSnFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWR 244
Cdd:PRK13503  146 REILFMQLL--VLLRK-SSLQENGENS-DARLNQLLAWLEDHFAEE-VNWEALADQFSLSLRTLHRQLKQQTGLTPQRYL 220

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1335032047 245 EDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFRAG 296
Cdd:PRK13503  221 NRLRLLKARHLLRHSDASVTDIAYRCGFGDSNHFSTLFRREFSWSPRDIRQG 272
cupin_TM1459-like cd02222
Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial ...
 62-99 1.20e-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: 37.43  E-value: 1.20e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1335032047  62 YILnltiRGQGVVKNQGREFVCRPGDILLFPPGEIHHY 99
Cdd:cd02222    42 YVL----RGKGVVVIGGEEYPVKPGDVVYIPPNEPHQF 75
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
202-294 1.45e-03

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 38.16  E-value: 1.45e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 202 YISDHLaDSNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRV 281
Cdd:PRK11511   17 WIEDNL-ESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRT 95

                          90
                  ....*....|...
gi 1335032047 282 FKKCTGASPSEFR 294
Cdd:PRK11511   96 FKNYFDVPPHKYR 108
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
68-105 1.79e-03

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 37.14  E-value: 1.79e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1335032047  68 IRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEA 105
Cdd:COG1917    50 LEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDE 87
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 61-99 3.03e-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: 35.92  E-value: 3.03e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1335032047  61 GYILNLTIRGQGVVK-NQGREFVCRPGDILLFPPGEIHHY 99
Cdd:cd02208    20 QDEIFYVLSGEGELTlDDGETVELKAGDIVLIPPGVPHSF 59
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
15-248 4.86e-03

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 37.84  E-value: 4.86e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047  15 MKSMAEAQNDPLLPGYSFNAHLVAGLTPIEANGYLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPG 94
Cdd:COG2207     7 LLLLLLLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047  95 EIHHYGRHPEAREWYHQWVYFRPRAYWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLe 174
Cdd:COG2207    87 ALLLLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLL- 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1335032047 175 qLLLRRMEAINESLH----------------PPMD----NRVREACQYisdhLADSNFDIASVAQHV-CLSPSRLSHLFR 233
Cdd:COG2207   166 -LLLLTLEELARELGlsprtlsrlfkeetgtSPKQylreLRLERAKRL----LAETDLSISEIAYELgFSSQSHFSRAFK 240

                         250
                  ....*....|....*
gi 1335032047 234 QQLGISVLSWREDQR 248
Cdd:COG2207   241 KRFGVTPSEYRKRLR 255
cupin_YbfI-like_N cd07001
AraC/XylS family transcriptional regulators similar to Bacillus subtilis YbfI, N-terminal ...
 62-97 5.70e-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: 35.06  E-value: 5.70e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1335032047  62 YILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIH 97
Cdd:cd07001    23 YVIGFIESGQRTLFCEGKEYTVEPGDLLLINPRDVH 58
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 68-99 7.96e-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: 34.54  E-value: 7.96e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1335032047  68 IRGQGVVKNQGREFVCRPGDILLFPPGEIHHY 99
Cdd:pfam07883  26 LEGEGELTVDGEEVVLKAGDSVYFPAGVPHRF 57
 
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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