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Conserved domains on  [gi|2055353819|ref|WP_216357926|]
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helix-turn-helix domain-containing protein [Enterobacter quasimori]

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 ...
 14-108 7.17e-36

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: 123.06  E-value: 7.17e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819  14 LVPFAHDYVHGDSEPWHQHDCAQLLHSLTGVVRVDTASGCWVVPPGRGVWLPAGAQHSLRITGNVAARTLFIDPLARADL 93
Cdd:cd06124     1 VLARAADYPAGHRTPWHSHPWGQLLYASSGVMTVETEDGRWLVPPQRAVWIPAGVEHSVRMLGAVELRSLYIDPEAAAGL 80

                          90
                  ....*....|....*
gi 2055353819  94 PATCQIVQISPLLRE 108
Cdd:cd06124    81 PAEPCVLAVSPLLRE 95
HTH_18 pfam12833
Helix-turn-helix domain;
176-253 5.87e-26

Helix-turn-helix domain;


:

Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 96.89  E-value: 5.87e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819 176 ASMMNMSERTLNRHFQQQTGLSYGEWLRRARLLEALVRLAQ--GQPVLRVALDLGYGSHSAFTAMFRRVMGTSPSDYFKN 253
Cdd:pfam12833   2 AAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEdtGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRRR 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 ...
 14-108 7.17e-36

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: 123.06  E-value: 7.17e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819  14 LVPFAHDYVHGDSEPWHQHDCAQLLHSLTGVVRVDTASGCWVVPPGRGVWLPAGAQHSLRITGNVAARTLFIDPLARADL 93
Cdd:cd06124     1 VLARAADYPAGHRTPWHSHPWGQLLYASSGVMTVETEDGRWLVPPQRAVWIPAGVEHSVRMLGAVELRSLYIDPEAAAGL 80

                          90
                  ....*....|....*
gi 2055353819  94 PATCQIVQISPLLRE 108
Cdd:cd06124    81 PAEPCVLAVSPLLRE 95
HTH_18 pfam12833
Helix-turn-helix domain;
176-253 5.87e-26

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 96.89  E-value: 5.87e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819 176 ASMMNMSERTLNRHFQQQTGLSYGEWLRRARLLEALVRLAQ--GQPVLRVALDLGYGSHSAFTAMFRRVMGTSPSDYFKN 253
Cdd:pfam12833   2 AAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEdtGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRRR 81
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
1-253 6.24e-24

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 96.77  E-value: 6.24e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819   1 MTTTATFSFTHRPLVPFAHDYVHGDSEPWHQHDCAQLLHSLTGVVRVDTASGCWVVPPGRGVWLPAGAQHSLRITGNVAA 80
Cdd:COG2207     5 ILLLLLLLLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819  81 RTLFIDPLARADLPATCQIVQISPLLRELILISLTLPESYAPGSRDERVYELILDEIRMMPVLPFHLPEPESEALRRLCL 160
Cdd:COG2207    85 LLALLLLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLL 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819 161 QIRQNpgkswSSAQAASMMNMSERTLNRHFQQQTGLSYGEWLRRARLLEALVRLAQGQ-PVLRVALDLGYGSHSAFTAMF 239
Cdd:COG2207   165 LLLLL-----TLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDlSISEIAYELGFSSQSHFSRAF 239

                         250
                  ....*....|....
gi 2055353819 240 RRVMGTSPSDYFKN 253
Cdd:COG2207   240 KKRFGVTPSEYRKR 253
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 146-250 3.30e-23

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: 95.61  E-value: 3.30e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819 146 HLPEPESEALRRLCLQIRQNPGKSWSSAQAASMMNMSERTLNRHFQQQTGLSYGEWLRRARLLEALVRLAQGQ-PVLRVA 224
Cdd:COG4977   203 VPLGHRDPRLARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDlSIEEIA 282

                          90       100
                  ....*....|....*....|....*.
gi 2055353819 225 LDLGYGSHSAFTAMFRRVMGTSPSDY 250
Cdd:COG4977   283 AACGFGSASHFRRAFRRRFGVSPSAY 308
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
170-250 3.47e-23

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 89.92  E-value: 3.47e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819  170 WSSAQAASMMNMSERTLNRHFQQQTGLSYGEWLRRARLLEALVRLAQGQ-PVLRVALDLGYGSHSAFTAMFRRVMGTSPS 248
Cdd:smart00342   2 LTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDlSVTEIALRVGFSSQSYFSRAFKKLFGVTPS 81


                   ..
gi 2055353819  249 DY 250
Cdd:smart00342  82 EY 83
ftrA PRK09393
transcriptional activator FtrA; Provisional
 147-253 3.72e-18

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 81.93  E-value: 3.72e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819 147 LPEPESEALRRLCLQIRQNPGKSWSSAQAASMMNMSERTLNRHFQQQTGLSYGEWLRRARLLEALVRL-AQGQPVLRVAL 225
Cdd:PRK09393  212 VASRESDRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLeSSALSIDQIAE 291

                          90       100
                  ....*....|....*....|....*...
gi 2055353819 226 DLGYGSHSAFTAMFRRVMGTSPSDYFKN 253
Cdd:PRK09393  292 RAGFGSEESLRHHFRRRAATSPAAYRKR 319
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 23-133 8.93e-05

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: 41.27  E-value: 8.93e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819  23 HGDSEPWHQHDCAQLLHSLTGVVRVDTASGCWVVPPGRGVWLPAGAQHSLRITGN--VAARTLFIDPLARADLPATCQIV 100
Cdd:pfam02311  12 PGHSFPPHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESEdgWRYRWLYFEPELLERILADISIL 91

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2055353819 101 -----------QISPLLRELILIsLTLPESYAPGSRDERVYELI 133
Cdd:pfam02311  92 aggplpllrdpELAALLRALFRL-LEEAGRSDDLLAEALLYQLL 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 ...
 14-108 7.17e-36

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: 123.06  E-value: 7.17e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819  14 LVPFAHDYVHGDSEPWHQHDCAQLLHSLTGVVRVDTASGCWVVPPGRGVWLPAGAQHSLRITGNVAARTLFIDPLARADL 93
Cdd:cd06124     1 VLARAADYPAGHRTPWHSHPWGQLLYASSGVMTVETEDGRWLVPPQRAVWIPAGVEHSVRMLGAVELRSLYIDPEAAAGL 80

                          90
                  ....*....|....*
gi 2055353819  94 PATCQIVQISPLLRE 108
Cdd:cd06124    81 PAEPCVLAVSPLLRE 95
HTH_18 pfam12833
Helix-turn-helix domain;
176-253 5.87e-26

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 96.89  E-value: 5.87e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819 176 ASMMNMSERTLNRHFQQQTGLSYGEWLRRARLLEALVRLAQ--GQPVLRVALDLGYGSHSAFTAMFRRVMGTSPSDYFKN 253
Cdd:pfam12833   2 AAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEdtGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRRR 81
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
1-253 6.24e-24

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 96.77  E-value: 6.24e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819   1 MTTTATFSFTHRPLVPFAHDYVHGDSEPWHQHDCAQLLHSLTGVVRVDTASGCWVVPPGRGVWLPAGAQHSLRITGNVAA 80
Cdd:COG2207     5 ILLLLLLLLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819  81 RTLFIDPLARADLPATCQIVQISPLLRELILISLTLPESYAPGSRDERVYELILDEIRMMPVLPFHLPEPESEALRRLCL 160
Cdd:COG2207    85 LLALLLLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLL 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819 161 QIRQNpgkswSSAQAASMMNMSERTLNRHFQQQTGLSYGEWLRRARLLEALVRLAQGQ-PVLRVALDLGYGSHSAFTAMF 239
Cdd:COG2207   165 LLLLL-----TLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDlSISEIAYELGFSSQSHFSRAF 239

                         250
                  ....*....|....
gi 2055353819 240 RRVMGTSPSDYFKN 253
Cdd:COG2207   240 KKRFGVTPSEYRKR 253
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 146-250 3.30e-23

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: 95.61  E-value: 3.30e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819 146 HLPEPESEALRRLCLQIRQNPGKSWSSAQAASMMNMSERTLNRHFQQQTGLSYGEWLRRARLLEALVRLAQGQ-PVLRVA 224
Cdd:COG4977   203 VPLGHRDPRLARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDlSIEEIA 282

                          90       100
                  ....*....|....*....|....*.
gi 2055353819 225 LDLGYGSHSAFTAMFRRVMGTSPSDY 250
Cdd:COG4977   283 AACGFGSASHFRRAFRRRFGVSPSAY 308
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
170-250 3.47e-23

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 89.92  E-value: 3.47e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819  170 WSSAQAASMMNMSERTLNRHFQQQTGLSYGEWLRRARLLEALVRLAQGQ-PVLRVALDLGYGSHSAFTAMFRRVMGTSPS 248
Cdd:smart00342   2 LTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDlSVTEIALRVGFSSQSYFSRAFKKLFGVTPS 81


                   ..
gi 2055353819  249 DY 250
Cdd:smart00342  82 EY 83
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 149-250 1.41e-20

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: 89.34  E-value: 1.41e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819 149 EPESEALRRLCLQIRQNPGKSWSSAQAASMMNMSERTLNRHFQQQTGLSYGEWLRRARLLEALVRLAQGQPVLRVALDLG 228
Cdd:COG2169    80 PPRADLVARACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQTGLSVTDAAYAAG 159

                          90       100
                  ....*....|....*....|..
gi 2055353819 229 YGSHSAFTAMFRRVMGTSPSDY 250
Cdd:COG2169   160 FGSLSRFYEAFKKLLGMTPSAY 181
ftrA PRK09393
transcriptional activator FtrA; Provisional
 147-253 3.72e-18

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 81.93  E-value: 3.72e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819 147 LPEPESEALRRLCLQIRQNPGKSWSSAQAASMMNMSERTLNRHFQQQTGLSYGEWLRRARLLEALVRL-AQGQPVLRVAL 225
Cdd:PRK09393  212 VASRESDRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLeSSALSIDQIAE 291

                          90       100
                  ....*....|....*....|....*...
gi 2055353819 226 DLGYGSHSAFTAMFRRVMGTSPSDYFKN 253
Cdd:PRK09393  292 RAGFGSEESLRHHFRRRAATSPAAYRKR 319
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
2-87 8.36e-11

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 57.17  E-value: 8.36e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819   2 TTTATFSFTHRPLVPFAHDYVHGDSEPWHQHDCAQLLHSLTGVVRVDTASGCWVVPPGRGVWLPAGAQHSLRITGNVAAR 81
Cdd:COG1917    11 VSVRVLADGEDELEVVRVTFEPGARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDEPAV 90


                  ....*.
gi 2055353819  82 TLFIDP 87
Cdd:COG1917    91 LLVVFS 96
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
162-250 2.97e-10

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 56.09  E-value: 2.97e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819 162 IRQNPGKSWSSAQAASMMNMSERTLNRHFQQQTGLSYGEWLRRARLLEALVRLAQGQ-PVLRVALDLGYGSHSAFTAMFR 240
Cdd:PRK10219   14 IDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTErPIFDIAMDLGYVSQQTFSRVFR 93

                          90
                  ....*....|
gi 2055353819 241 RVMGTSPSDY 250
Cdd:PRK10219   94 RQFDRTPSDY 103
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 132-250 3.54e-09

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 56.09  E-value: 3.54e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819 132 LILDEIRMMPVLpFHLPEPESEAlrRLCLQIRQNPGKSWSSAQAASMMNMSERTLNRHFQQQtGLSYGEWLRRARLLEAL 211
Cdd:PRK09978  124 VFLEDEHFIPLL-LNVLQPNMRT--RVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREE-ETSYSQLLTECRMQRAL 199

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2055353819 212 VRLA-QGQPVLRVALDLGYGSHSAFTAMFRRVMGTSPSDY 250
Cdd:PRK09978  200 QLIViHGFSIKRVAVSCGYHSVSYFIYVFRNYYGMTPTEY 239
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
150-250 1.53e-08

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 54.14  E-value: 1.53e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819 150 PESEALRRLCLQIRQNPGKSWSSAQAASMMNMSERTLNRHFQQQTGLSYGEWLRRARLLEALVRL-AQGQPVLRVALDLG 228
Cdd:PRK13501  173 PDGEQLDLIMSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLrGSEHRISDIAARCG 252

                          90       100
                  ....*....|....*....|..
gi 2055353819 229 YGSHSAFTAMFRRVMGTSPSDY 250
Cdd:PRK13501  253 FEDSNYFSAVFTREAGMTPRDY 274
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
181-249 1.82e-07

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 50.83  E-value: 1.82e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819 181 MSERTLNRHFQQQTGLSYGEWLRRARLLEALVRLAQG-QPVLRVALDLGYGSHSAFTAMFRRVMGTSPSD 249
Cdd:PRK13503  199 LSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSdASVTDIAYRCGFGDSNHFSTLFRREFSWSPRD 268
PRK15185 PRK15185
transcriptional regulator HilD; Provisional
 162-252 7.28e-07

transcriptional regulator HilD; Provisional


Pssm-ID: 185107 [Multi-domain]  Cd Length: 309  Bit Score: 49.22  E-value: 7.28e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819 162 IRQNPGKSWSSAQAASMMNMSERTLNRHFQQQtGLSYGEWLRRARLLEALVRLAQGQ-PVLRVALDLGYGSHSAFTAMFR 240
Cdd:PRK15185  215 ISSSPSRQWKLTDVADHIFMSTSTLKRKLAEE-GTSFSDIYLSARMNQAAKLLRIGNhNVNAVALKCGYDSTSYFIQCFK 293

                          90
                  ....*....|..
gi 2055353819 241 RVMGTSPSDYFK 252
Cdd:PRK15185  294 KYFKTTPSTFIK 305
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
182-250 4.94e-06

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 46.59  E-value: 4.94e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2055353819 182 SERTLNRHFQQQTGLSYGEWLRRARLLEALVrLAQGQPVL--RVALDLGYGSHSAFTAMFRRVMGTSPSDY 250
Cdd:PRK13502  205 SERVLRQQFRAQTGMTINQYLRQVRICHAQY-LLQHSPLMisEISMQCGFEDSNYFSVVFTRETGMTPSQW 274
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
182-250 3.12e-05

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 44.32  E-value: 3.12e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819 182 SERTLNRHFQQQTGLSYGEWLRRARLLEALVRLAQGQPVLR-VALDLGYGSHSAFTAMFRRVMGTSPSDY 250
Cdd:PRK13500  235 SERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISdISTECGFEDSNYFSVVFTRETGMTPSQW 304
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
24-85 5.44e-05

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


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 41.67  E-value: 5.44e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2055353819  24 GDSEPWHQH-DCAQLLHSLTGVVRVDTASGCWVVPPGRGVWLPAGAQHSLRITGNVAARTLFI 85
Cdd:COG0662    37 GAELSLHVHpHRDEFFYVLEGTGEVTIGDEEVELKAGDSVYIPAGVPHRLRNPGDEPLELLEV 99
PRK15186 PRK15186
AraC family transcriptional regulator; Provisional
 149-251 5.63e-05

AraC family transcriptional regulator; Provisional


Pssm-ID: 185108 [Multi-domain]  Cd Length: 291  Bit Score: 43.52  E-value: 5.63e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819 149 EPESEALRRLCLQ----------IRQNPGKSWSSAQAASMMNMSERTLNRHFQQQTgLSYGEWLRRARLLEALVRLAQGQ 218
Cdd:PRK15186  167 EPEAFALFRELSQntlaeniyniIISDISRKWALKDISDSLYMSCSTLKRKLKQEN-TSFSEVYLNARMNKATKLLRNSE 245

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2055353819 219 -PVLRVALDLGYGSHSAFTAMFRRVMGTSPSDYF 251
Cdd:PRK15186  246 yNITRVAYMCGYDSASYFTCVFKKHFKTTPSEFL 279
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 23-133 8.93e-05

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: 41.27  E-value: 8.93e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819  23 HGDSEPWHQHDCAQLLHSLTGVVRVDTASGCWVVPPGRGVWLPAGAQHSLRITGN--VAARTLFIDPLARADLPATCQIV 100
Cdd:pfam02311  12 PGHSFPPHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESEdgWRYRWLYFEPELLERILADISIL 91

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2055353819 101 -----------QISPLLRELILIsLTLPESYAPGSRDERVYELI 133
Cdd:pfam02311  92 aggplpllrdpELAALLRALFRL-LEEAGRSDDLLAEALLYQLL 134
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 162-203 1.04e-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: 38.67  E-value: 1.04e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2055353819 162 IRQNPGKSWSSAQAASMMNMSERTLNRHFQQQTGLSYGEWLR 203
Cdd:pfam00165   1 LRENLSTNLTIADIADELGFSRSYFSRLFKKYTGVTPSQYRH 42
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
132-250 1.68e-04

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 41.88  E-value: 1.68e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055353819 132 LILDEIRMMPVLPFHLPEPEseaLRRLCLQIRQNPGKSWSSAQAASMMNMSERTLNRHFQQQTGLSYGEWLRRARLLEA- 210
Cdd:PRK10572  165 LLLRCMEAIPESLHPPMDPR---VREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAk 241

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2055353819 211 LVRLAQGQPVLRVALDLGYGSHSAFTAMFRRVMGTSPSDY 250
Cdd:PRK10572  242 LLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEF 281
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 24-85 2.09e-04

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


Pssm-ID: 380338 [Multi-domain]  Cd Length: 73  Bit Score: 39.00  E-value: 2.09e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2055353819  24 GDSEPWHQHDCA-QLLHSLTGVVRVDTASGCWV-VPPGRGVWLPAGAQHSLRITGNVAARTLFI 85
Cdd:cd02208     9 GTSSPPHWHPEQdEIFYVLSGEGELTLDDGETVeLKAGDIVLIPPGVPHSFVNTSDEPAVFLVV 72
cupin_YobQ-like_N cd07003
Bacillus subtilis YobQ and related proteins, N-terminal cupin domain; This family includes ...
 30-86 2.40e-03

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


Pssm-ID: 380407 [Multi-domain]  Cd Length: 66  Bit Score: 35.45  E-value: 2.40e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2055353819  30 HQHDCAQLLHSLTGVVRVDTaSGCWV-VPPGRGVWLPAGAQHSLRITGNvaARTLFID 86
Cdd:cd07003    10 HSHEHAQLVLPLSGSLELEV-EGRGSrVKPDIGLYIPPNAEHRFAGSSD--NRCLVLD 64
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 24-85 6.16e-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: 6.16e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2055353819  24 GDSEPWHQH-DCAQLLHSLTGVVRVDTASGCWVVPPGRGVWLPAGAQHSLRITGNVAARTLFI 85
Cdd:pfam07883   8 GESSPPHRHpGEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLDV 70
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 214-252 9.77e-03

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: 33.28  E-value: 9.77e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 2055353819 214 LAQGQPVLRVALDLGYgSHSAFTAMFRRVMGTSPSDYFK 252
Cdd:pfam00165   5 LSTNLTIADIADELGF-SRSYFSRLFKKYTGVTPSQYRH 42
 
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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