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Conserved domains on  [gi|769928712|ref|WP_045062908|]
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helix-turn-helix domain-containing protein [Photobacterium leiognathi]

Protein Classification

AraC family transcriptional regulator( domain architecture ID 14398448)

AraC family transcriptional regulator containing a cupin domain as its effector domain and an AraC family helix-turn-helix (HTH) DNA binding domain, controls the expression of genes with diverse biological functions including metabolism, stress response, and virulence

CATH:  2.60.120.10
Gene Ontology:  GO:0003700|GO:0006355|GO:0043565
PubMed:  11282467|33837749|9409145|12270809|19478949|14697267|9573603
SCOP:  3001825

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
cupin_NimR-like_N cd06124
AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This ...
 19-113 7.71e-29

AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This family contains mostly 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 in this family is Escherichia coli HTH-type transcriptional regulator NimR (also called YeaM) that negatively regulates expression of the nimT operon and its own expression. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


:

Pssm-ID: 380379 [Multi-domain]  Cd Length: 95  Bit Score: 104.96  E-value: 7.71e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928712  19 VVAMSLSGADiDEEIPFHHHHKGQLVLPLNGYVRCKIADAIWMVPANCAVWIPSQVPHSLSISEDADLCNLFVDQDVV-G 97
Cdd:cd06124    1 VLARAADYPA-GHRTPWHSHPWGQLLYASSGVMTVETEDGRWLVPPQRAVWIPAGVEHSVRMLGAVELRSLYIDPEAAaG 79

                         90
                 ....*....|....*.
gi 769928712  98 MPLKACTLSVSPLLRE 113
Cdd:cd06124   80 LPAEPCVLAVSPLLRE 95
HTH_18 pfam12833
Helix-turn-helix domain;
185-258 3.36e-19

Helix-turn-helix domain;


:

Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 79.56  E-value: 3.36e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 769928712  185 AMSERTLARLVKQELGLTFGNWRGQLHIVLALQKL--SSGEAVQRVSEDLGYESVSAFITFFKKTLGRPPKQYIKQ 258
Cdd:pfam12833   6 GMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLleDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRRR 81
 
Name Accession Description Interval E-value
cupin_NimR-like_N cd06124
AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This ...
 19-113 7.71e-29

AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This family contains mostly 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 in this family is Escherichia coli HTH-type transcriptional regulator NimR (also called YeaM) that negatively regulates expression of the nimT operon and its own expression. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380379 [Multi-domain]  Cd Length: 95  Bit Score: 104.96  E-value: 7.71e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928712  19 VVAMSLSGADiDEEIPFHHHHKGQLVLPLNGYVRCKIADAIWMVPANCAVWIPSQVPHSLSISEDADLCNLFVDQDVV-G 97
Cdd:cd06124    1 VLARAADYPA-GHRTPWHSHPWGQLLYASSGVMTVETEDGRWLVPPQRAVWIPAGVEHSVRMLGAVELRSLYIDPEAAaG 79

                         90
                 ....*....|....*.
gi 769928712  98 MPLKACTLSVSPLLRE 113
Cdd:cd06124   80 LPAEPCVLAVSPLLRE 95
HTH_18 pfam12833
Helix-turn-helix domain;
185-258 3.36e-19

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 79.56  E-value: 3.36e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 769928712  185 AMSERTLARLVKQELGLTFGNWRGQLHIVLALQKL--SSGEAVQRVSEDLGYESVSAFITFFKKTLGRPPKQYIKQ 258
Cdd:pfam12833   6 GMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLleDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRRR 81
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
132-259 3.26e-18

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 81.36  E-value: 3.26e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928712 132 ARLVEVLIDELTTMPSEHFDFPIPEEPRLHKIALALIENPSDRSTVGEWGSKYAMSERTLARLVKQELGLTFGNWRGQLH 211
Cdd:COG2207  126 LLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELR 205

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 769928712 212 IVLALQKLSSGEA-VQRVSEDLGYESVSAFITFFKKTLGRPPKQYIKQR 259
Cdd:COG2207  206 LERAKRLLAETDLsISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRL 254
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
176-255 1.01e-17

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 75.67  E-value: 1.01e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928712   176 TVGEWGSKYAMSERTLARLVKQELGLTFGNWRGQLHIVLALQKLSSGE-AVQRVSEDLGYESVSAFITFFKKTLGRPPKQ 254
Cdd:smart00342   3 TLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDlSVTEIALRVGFSSQSYFSRAFKKLFGVTPSE 82


                   .
gi 769928712   255 Y 255
Cdd:smart00342  83 Y 83
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 170-255 3.71e-09

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: 56.61  E-value: 3.71e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928712  170 NPSDRSTVGEWGSKYAMSERTLARLVKQELGLTFGNWRGQLHIVLALQKLSSGEAVQRVSEDLGYESVSAFITFFKKTLG 249
Cdd:TIGR04094 297 NLYDPLKVEEIAKQFFMSESKLRKLFKKEMGISIQEYISKRKIEEAKYLLRSQIPVSEVSNELGFYDLSHFSRTFKKHTG 376


                  ....*.
gi 769928712  250 RPPKQY 255
Cdd:TIGR04094 377 VSPKQY 382
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
31-93 3.33e-07

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 47.54  E-value: 3.33e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 769928712  31 EEIPFHHHHKGQLVLPLNGYVRCKIADAIWMVPANCAVWIPSQVPHSLSISEDADLCNLFVDQ 93
Cdd:COG1917   34 ARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDEPAVLLVVFS 96
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
110-259 1.16e-04

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 42.58  E-value: 1.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928712 110 LLRELIVRLTEldQSYKSEGSTARLVEVLIDELTTMPSEH-----FDFPIPEEPRLHKIALALIENPSDRSTVGEWGSKY 184
Cdd:PRK13501 125 QARPIIQQLAQ--ESRKTDSWSIQLTEVLLLQLAIVLKRHryraeQAHLLPDGEQLDLIMSALQQSLGAYFDMADFCHKN 202

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 769928712 185 AMSERTLARLVKQELGLTFGNWRGQLHIVLALQKLSSGEA-VQRVSEDLGYESVSAFITFFKKTLGRPPKQYiKQR 259
Cdd:PRK13501 203 QLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHrISDIAARCGFEDSNYFSAVFTREAGMTPRDY-RQR 277
ftrA PRK09393
transcriptional activator FtrA; Provisional
 153-258 2.71e-04

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 41.49  E-value: 2.71e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928712 153 PIPEEP--RLHKIALALIENPSDRSTVGEWGSKYAMSERTLARLVKQELGLTFGNW--RGQLHIVLALQKlSSGEAVQRV 228
Cdd:PRK09393 211 PVASREsdRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWllRERLARARDLLE-SSALSIDQI 289

                         90       100       110
                 ....*....|....*....|....*....|
gi 769928712 229 SEDLGYESVSAFITFFKKTLGRPPKQYIKQ 258
Cdd:PRK09393 290 AERAGFGSEESLRHHFRRRAATSPAAYRKR 319
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 34-138 8.49e-03

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: 35.49  E-value: 8.49e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928712   34 PFHHHHKGQLVLPLNGYVRCKIADAIWMVPANCAVWIPSQVPHSLSISEDADL--CNLFVDQDVVGMPLKACTLS----- 106
Cdd:pfam02311  17 PPHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESEDGWryRWLYFEPELLERILADISILaggpl 96

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 769928712  107 -------VSPLLRELIVRLTELDQSYkSEGSTARLVEVL 138
Cdd:pfam02311  97 pllrdpeLAALLRALFRLLEEAGRSD-DLLAEALLYQLL 134
 
Name Accession Description Interval E-value
cupin_NimR-like_N cd06124
AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This ...
 19-113 7.71e-29

AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This family contains mostly 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 in this family is Escherichia coli HTH-type transcriptional regulator NimR (also called YeaM) that negatively regulates expression of the nimT operon and its own expression. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380379 [Multi-domain]  Cd Length: 95  Bit Score: 104.96  E-value: 7.71e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928712  19 VVAMSLSGADiDEEIPFHHHHKGQLVLPLNGYVRCKIADAIWMVPANCAVWIPSQVPHSLSISEDADLCNLFVDQDVV-G 97
Cdd:cd06124    1 VLARAADYPA-GHRTPWHSHPWGQLLYASSGVMTVETEDGRWLVPPQRAVWIPAGVEHSVRMLGAVELRSLYIDPEAAaG 79

                         90
                 ....*....|....*.
gi 769928712  98 MPLKACTLSVSPLLRE 113
Cdd:cd06124   80 LPAEPCVLAVSPLLRE 95
HTH_18 pfam12833
Helix-turn-helix domain;
185-258 3.36e-19

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 79.56  E-value: 3.36e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 769928712  185 AMSERTLARLVKQELGLTFGNWRGQLHIVLALQKL--SSGEAVQRVSEDLGYESVSAFITFFKKTLGRPPKQYIKQ 258
Cdd:pfam12833   6 GMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLleDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRRR 81
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
132-259 3.26e-18

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 81.36  E-value: 3.26e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928712 132 ARLVEVLIDELTTMPSEHFDFPIPEEPRLHKIALALIENPSDRSTVGEWGSKYAMSERTLARLVKQELGLTFGNWRGQLH 211
Cdd:COG2207  126 LLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELR 205

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 769928712 212 IVLALQKLSSGEA-VQRVSEDLGYESVSAFITFFKKTLGRPPKQYIKQR 259
Cdd:COG2207  206 LERAKRLLAETDLsISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRL 254
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
176-255 1.01e-17

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 75.67  E-value: 1.01e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928712   176 TVGEWGSKYAMSERTLARLVKQELGLTFGNWRGQLHIVLALQKLSSGE-AVQRVSEDLGYESVSAFITFFKKTLGRPPKQ 254
Cdd:smart00342   3 TLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDlSVTEIALRVGFSSQSYFSRAFKKLFGVTPSE 82


                   .
gi 769928712   255 Y 255
Cdd:smart00342  83 Y 83
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 164-255 2.28e-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: 74.70  E-value: 2.28e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928712 164 ALALIE-NPSDRSTVGEWGSKYAMSERTLARLVKQELGLTFGNWRGQLHIVLALQKLSSGEAVQRVSEDLGYESVSAFIT 242
Cdd:COG2169   89 ACRLIEaGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQTGLSVTDAAYAAGFGSLSRFYE 168

                         90
                 ....*....|...
gi 769928712 243 FFKKTLGRPPKQY 255
Cdd:COG2169  169 AFKKLLGMTPSAY 181
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 155-255 7.24e-13

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: 67.10  E-value: 7.24e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928712 155 PEEPRLHKIALALIENPSDRSTVGEWGSKYAMSERTLARLVKQELGLTFGNWRGQLHIVLALQKL-SSGEAVQRVSEDLG 233
Cdd:COG4977  207 HRDPRLARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLeTTDLSIEEIAAACG 286

                         90       100
                 ....*....|....*....|..
gi 769928712 234 YESVSAFITFFKKTLGRPPKQY 255
Cdd:COG4977  287 FGSASHFRRAFRRRFGVSPSAY 308
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 170-255 3.71e-09

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: 56.61  E-value: 3.71e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928712  170 NPSDRSTVGEWGSKYAMSERTLARLVKQELGLTFGNWRGQLHIVLALQKLSSGEAVQRVSEDLGYESVSAFITFFKKTLG 249
Cdd:TIGR04094 297 NLYDPLKVEEIAKQFFMSESKLRKLFKKEMGISIQEYISKRKIEEAKYLLRSQIPVSEVSNELGFYDLSHFSRTFKKHTG 376


                  ....*.
gi 769928712  250 RPPKQY 255
Cdd:TIGR04094 377 VSPKQY 382
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
31-93 3.33e-07

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 47.54  E-value: 3.33e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 769928712  31 EEIPFHHHHKGQLVLPLNGYVRCKIADAIWMVPANCAVWIPSQVPHSLSISEDADLCNLFVDQ 93
Cdd:COG1917   34 ARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDEPAVLLVVFS 96
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
110-259 1.16e-04

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 42.58  E-value: 1.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928712 110 LLRELIVRLTEldQSYKSEGSTARLVEVLIDELTTMPSEH-----FDFPIPEEPRLHKIALALIENPSDRSTVGEWGSKY 184
Cdd:PRK13501 125 QARPIIQQLAQ--ESRKTDSWSIQLTEVLLLQLAIVLKRHryraeQAHLLPDGEQLDLIMSALQQSLGAYFDMADFCHKN 202

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 769928712 185 AMSERTLARLVKQELGLTFGNWRGQLHIVLALQKLSSGEA-VQRVSEDLGYESVSAFITFFKKTLGRPPKQYiKQR 259
Cdd:PRK13501 203 QLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHrISDIAARCGFEDSNYFSAVFTREAGMTPRDY-RQR 277
ftrA PRK09393
transcriptional activator FtrA; Provisional
 153-258 2.71e-04

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 41.49  E-value: 2.71e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928712 153 PIPEEP--RLHKIALALIENPSDRSTVGEWGSKYAMSERTLARLVKQELGLTFGNW--RGQLHIVLALQKlSSGEAVQRV 228
Cdd:PRK09393 211 PVASREsdRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWllRERLARARDLLE-SSALSIDQI 289

                         90       100       110
                 ....*....|....*....|....*....|
gi 769928712 229 SEDLGYESVSAFITFFKKTLGRPPKQYIKQ 258
Cdd:PRK09393 290 AERAGFGSEESLRHHFRRRAATSPAAYRKR 319
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 216-257 8.32e-04

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: 36.36  E-value: 8.32e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 769928712  216 LQKLSSGEAVQRVSEDLGYeSVSAFITFFKKTLGRPPKQYIK 257
Cdd:pfam00165   2 RENLSTNLTIADIADELGF-SRSYFSRLFKKYTGVTPSQYRH 42
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
168-261 1.19e-03

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 38.16  E-value: 1.19e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928712 168 IENPSDRSTVGEWgskyamserTLARLVKQELGLTFGNW-RGQLHIVLALQKLSSGEAVQRVSEDLGYESVSAFITFFKK 246
Cdd:PRK11511  28 LEKVSERSGYSKW---------HLQRMFKKETGHSLGQYiRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKN 98

                         90
                 ....*....|....*
gi 769928712 247 TLGRPPKQYIKQRIH 261
Cdd:PRK11511  99 YFDVPPHKYRMTNMQ 113
cupin_HpaA-like_N cd06999
AraC/XylS family transcriptional regulators similar to HpaA, N-terminal cupin domain; Members ...
 32-85 1.40e-03

AraC/XylS family transcriptional regulators similar to HpaA, 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, similar to Escherichia coli 4-hydroxyphenylacetate catabolism regulatory protein HpaA (also known as 4HPA). HpaA is encoded by the hpaA gene which is located upstream of hpaBC. It is activated by 4-HPA, 3-HPA and phenylacetate, and represents a member of the AraC/XylS family of regulators that recognizes aromatic effectors. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380403 [Multi-domain]  Cd Length: 98  Bit Score: 37.09  E-value: 1.40e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 769928712  32 EIPFH-HHHKGQLVLPLNGYVRCKIADAIWMVPANCAVWIPSQVPHSLSISEDAD 85
Cdd:cd06999   34 EIAPHrHADLFQVLYIESGGGEVRLDGRTHPLSAPALVVVPPGVVHGFRFSPDTD 88
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
183-259 2.10e-03

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 38.89  E-value: 2.10e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 769928712 183 KYAMSERTLARLVKQELGLTFGNWRGQLHIVLALQKLS-SGEAVQRVSEDLGYESVSAFITFFKKTLGRPPKQYIKQR 259
Cdd:PRK13503 196 QFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRhSDASVTDIAYRCGFGDSNHFSTLFRREFSWSPRDIRQGR 273
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 179-261 3.07e-03

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 38.37  E-value: 3.07e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928712 179 EW-----GSKYAMSERTLARLVKQElGLTFGNWRGQLHIVLALQKLS-SGEAVQRVSEDLGYESVSAFITFFKKTLGRPP 252
Cdd:PRK09978 158 EWtlariASELLMSPSLLKKKLREE-ETSYSQLLTECRMQRALQLIViHGFSIKRVAVSCGYHSVSYFIYVFRNYYGMTP 236


                 ....*....
gi 769928712 253 KQYIKQRIH 261
Cdd:PRK09978 237 TEYQERSAQ 245
PRK15185 PRK15185
transcriptional regulator HilD; Provisional
 186-261 4.02e-03

transcriptional regulator HilD; Provisional


Pssm-ID: 185107 [Multi-domain]  Cd Length: 309  Bit Score: 38.05  E-value: 4.02e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 769928712 186 MSERTLARLVKQElGLTFGNWRGQLHIVLALQKLSSGE-AVQRVSEDLGYESVSAFITFFKKTLGRPPKQYIKQRIH 261
Cdd:PRK15185 234 MSTSTLKRKLAEE-GTSFSDIYLSARMNQAAKLLRIGNhNVNAVALKCGYDSTSYFIQCFKKYFKTTPSTFIKMANH 309
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
186-259 6.13e-03

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 37.26  E-value: 6.13e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 769928712 186 MSERTLARLVKQELGLTFGNWRGQLHIVLALQKLS-SGEAVQRVSEDLGYESVSAFITFFKKTLGRPPKQYIKQR 259
Cdd:PRK10572 211 LSPSRLAHLFRQQLGISVLRWREDQRISRAKLLLQtTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFRARC 285
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
31-91 8.44e-03

Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 35.12  E-value: 8.44e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 769928712  31 EEIPFHHHHKG-QLVLPLNGYVRCKIADAIWMVPANCAVWIPSQVPHSLSISEDADLCNLFV 91
Cdd:COG0662   38 AELSLHVHPHRdEFFYVLEGTGEVTIGDEEVELKAGDSVYIPAGVPHRLRNPGDEPLELLEV 99
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 34-138 8.49e-03

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: 35.49  E-value: 8.49e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928712   34 PFHHHHKGQLVLPLNGYVRCKIADAIWMVPANCAVWIPSQVPHSLSISEDADL--CNLFVDQDVVGMPLKACTLS----- 106
Cdd:pfam02311  17 PPHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESEDGWryRWLYFEPELLERILADISILaggpl 96

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 769928712  107 -------VSPLLRELIVRLTELDQSYkSEGSTARLVEVL 138
Cdd:pfam02311  97 pllrdpeLAALLRALFRLLEEAGRSD-DLLAEALLYQLL 134
 
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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