NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1837859199|gb|QJP65094|]
View 

helix-turn-helix transcriptional regulator [Bordetella parapertussis]

Protein Classification

AraC family transcriptional regulator( domain architecture ID 18598964)

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:0003677|GO:0003700|GO:0006355|GO:0043565
PubMed:  11264412|11282467|33837749|9409145|12270809|19478949|14697267|9573603
SCOP:  3001825

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 39-133 2.07e-34

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: 119.98  E-value: 2.07e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199  39 MAALATDYPAGTVSSLHRHDRGQLLYAMSGVVTVITDLGSWVVAPGQALWIAPGVLHQTRGFESVAIRSLYIDPAHADGL 118
Cdd:cd06124     1 VLARAADYPAGHRTPWHSHPWGQLLYASSGVMTVETEDGRWLVPPQRAVWIPAGVEHSVRMLGAVELRSLYIDPEAAAGL 80

                          90
                  ....*....|....*
gi 1837859199 119 PAACQTIQVSPLLQA 133
Cdd:cd06124    81 PAEPCVLAVSPLLRE 95
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
27-277 2.14e-20

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


:

Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 87.91  E-value: 2.14e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199  27 LLTRQVQSAPGEMAALATDYPAGTVSSLHRHDRGQLLYAMSGVVTVITDLGSWVVAPGQALWIAPGVLHQTRGFESVAIR 106
Cdd:COG2207     7 LLLLLLLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199 107 SLYIDPAHADGLPAACQTIQVSPLLQALILEAVKLPPQDAGSERAGHIRALILDEMRHVCAAPLYVPMPRDARLARICQA 186
Cdd:COG2207    87 ALLLLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199 187 LLRdpanagSLDAWAAYGGLSRRNLTRLFRAQTGASFNAWRQKVLLMEALARLSRGEQ-ITAVALDLGCGSPGAFTAMFR 265
Cdd:COG2207   167 LLL------TLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLsISEIAYELGFSSQSHFSRAFK 240

                         250
                  ....*....|..
gi 1837859199 266 RALGVSPREYFR 277
Cdd:COG2207   241 KRFGVTPSEYRK 252
 
Name Accession Description Interval E-value
cupin_NimR-like_N cd06124
AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This ...
 39-133 2.07e-34

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: 119.98  E-value: 2.07e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199  39 MAALATDYPAGTVSSLHRHDRGQLLYAMSGVVTVITDLGSWVVAPGQALWIAPGVLHQTRGFESVAIRSLYIDPAHADGL 118
Cdd:cd06124     1 VLARAADYPAGHRTPWHSHPWGQLLYASSGVMTVETEDGRWLVPPQRAVWIPAGVEHSVRMLGAVELRSLYIDPEAAAGL 80

                          90
                  ....*....|....*
gi 1837859199 119 PAACQTIQVSPLLQA 133
Cdd:cd06124    81 PAEPCVLAVSPLLRE 95
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
27-277 2.14e-20

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 87.91  E-value: 2.14e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199  27 LLTRQVQSAPGEMAALATDYPAGTVSSLHRHDRGQLLYAMSGVVTVITDLGSWVVAPGQALWIAPGVLHQTRGFESVAIR 106
Cdd:COG2207     7 LLLLLLLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199 107 SLYIDPAHADGLPAACQTIQVSPLLQALILEAVKLPPQDAGSERAGHIRALILDEMRHVCAAPLYVPMPRDARLARICQA 186
Cdd:COG2207    87 ALLLLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199 187 LLRdpanagSLDAWAAYGGLSRRNLTRLFRAQTGASFNAWRQKVLLMEALARLSRGEQ-ITAVALDLGCGSPGAFTAMFR 265
Cdd:COG2207   167 LLL------TLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLsISEIAYELGFSSQSHFSRAFK 240

                         250
                  ....*....|..
gi 1837859199 266 RALGVSPREYFR 277
Cdd:COG2207   241 KRFGVTPSEYRK 252
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
196-275 5.60e-20

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 81.83  E-value: 5.60e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199  196 SLDAWAAYGGLSRRNLTRLFRAQTGASFNAWRQKVLLMEALARLSRGEQ-ITAVALDLGCGSPGAFTAMFRRALGVSPRE 274
Cdd:smart00342   3 TLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLsVTEIALRVGFSSQSYFSRAFKKLFGVTPSE 82


                   .
gi 1837859199  275 Y 275
Cdd:smart00342  83 Y 83
HTH_18 pfam12833
Helix-turn-helix domain;
200-277 1.32e-18

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 78.40  E-value: 1.32e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199 200 WAAYGGLSRRNLTRLFRAQTGASFNAWRQKVLLMEALARLSR--GEQITAVALDLGCGSPGAFTAMFRRALGVSPREYFR 277
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEdtGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
19-112 3.48e-13

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 64.10  E-value: 3.48e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199  19 PRQLSYLDLLTRQVQSAPGEMAALATDYPAGTVSSLHRHDRGQLLYAMSGVVTVITDLGSWVVAPGQALWIAPGVLHQTR 98
Cdd:COG1917     3 LAEIALTGVSVRVLADGEDELEVVRVTFEPGARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFR 82

                          90
                  ....*....|....
gi 1837859199  99 GFESVAIRSLYIDP 112
Cdd:COG1917    83 NLGDEPAVLLVVFS 96
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
162-275 1.18e-10

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 60.76  E-value: 1.18e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199 162 MRHVCAAPLYVPMPRDARLARICQALLRDPANAGSLDAWAAYGGLSRRNLTRLFRAQTGASFNAWRQKVLLMEA-LARLS 240
Cdd:PRK10572  167 LRCMEAIPESLHPPMDPRVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAkLLLQT 246

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1837859199 241 RGEQITAVALDLGCGSPGAFTAMFRRALGVSPREY 275
Cdd:PRK10572  247 TRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEF 281
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 55-132 1.30e-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: 43.96  E-value: 1.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199  55 HRHDRGQLLYAMSGVVTVITDLGSWVVAPGQALWIAPGVLH--QTRGFESVAIRSLYIDPAHADGLPAACQTIQVSPLLQ 132
Cdd:pfam02311  19 HVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHdyEPESEDGWRYRWLYFEPELLERILADISILAGGPLPL 98
 
Name Accession Description Interval E-value
cupin_NimR-like_N cd06124
AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This ...
 39-133 2.07e-34

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: 119.98  E-value: 2.07e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199  39 MAALATDYPAGTVSSLHRHDRGQLLYAMSGVVTVITDLGSWVVAPGQALWIAPGVLHQTRGFESVAIRSLYIDPAHADGL 118
Cdd:cd06124     1 VLARAADYPAGHRTPWHSHPWGQLLYASSGVMTVETEDGRWLVPPQRAVWIPAGVEHSVRMLGAVELRSLYIDPEAAAGL 80

                          90
                  ....*....|....*
gi 1837859199 119 PAACQTIQVSPLLQA 133
Cdd:cd06124    81 PAEPCVLAVSPLLRE 95
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
27-277 2.14e-20

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 87.91  E-value: 2.14e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199  27 LLTRQVQSAPGEMAALATDYPAGTVSSLHRHDRGQLLYAMSGVVTVITDLGSWVVAPGQALWIAPGVLHQTRGFESVAIR 106
Cdd:COG2207     7 LLLLLLLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199 107 SLYIDPAHADGLPAACQTIQVSPLLQALILEAVKLPPQDAGSERAGHIRALILDEMRHVCAAPLYVPMPRDARLARICQA 186
Cdd:COG2207    87 ALLLLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199 187 LLRdpanagSLDAWAAYGGLSRRNLTRLFRAQTGASFNAWRQKVLLMEALARLSRGEQ-ITAVALDLGCGSPGAFTAMFR 265
Cdd:COG2207   167 LLL------TLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLsISEIAYELGFSSQSHFSRAFK 240

                         250
                  ....*....|..
gi 1837859199 266 RALGVSPREYFR 277
Cdd:COG2207   241 KRFGVTPSEYRK 252
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
196-275 5.60e-20

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 81.83  E-value: 5.60e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199  196 SLDAWAAYGGLSRRNLTRLFRAQTGASFNAWRQKVLLMEALARLSRGEQ-ITAVALDLGCGSPGAFTAMFRRALGVSPRE 274
Cdd:smart00342   3 TLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLsVTEIALRVGFSSQSYFSRAFKKLFGVTPSE 82


                   .
gi 1837859199  275 Y 275
Cdd:smart00342  83 Y 83
HTH_18 pfam12833
Helix-turn-helix domain;
200-277 1.32e-18

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 78.40  E-value: 1.32e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199 200 WAAYGGLSRRNLTRLFRAQTGASFNAWRQKVLLMEALARLSR--GEQITAVALDLGCGSPGAFTAMFRRALGVSPREYFR 277
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEdtGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 144-275 5.53e-16

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: 76.35  E-value: 5.53e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199 144 QDAGSERAGHI-RALILDEMR----HVCAAPLYVPMPRDARLARICQALLRDPANAGSLDAWAAYGGLSRRNLTRLFRAQ 218
Cdd:COG4977   171 RDHGAELANAVaRRLVVDPRRpggqAQFSPLLVPLGHRDPRLARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAA 250

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1837859199 219 TGASFNAWRQKVLLMEALARLSRGEQ-ITAVALDLGCGSPGAFTAMFRRALGVSPREY 275
Cdd:COG4977   251 TGTTPARYLQRLRLERARRLLETTDLsIEEIAAACGFGSASHFRRAFRRRFGVSPSAY 308
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 175-275 5.78e-14

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: 71.24  E-value: 5.78e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199 175 PRDARLARICQALLRDPANAGSLDAWAAYGGLSRRNLTRLFRAQTGASFNAWRQKVLLMEALARLSRGEQITAVALDLGC 254
Cdd:COG2169    81 PRADLVARACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQTGLSVTDAAYAAGF 160

                          90       100
                  ....*....|....*....|.
gi 1837859199 255 GSPGAFTAMFRRALGVSPREY 275
Cdd:COG2169   161 GSLSRFYEAFKKLLGMTPSAY 181
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
19-112 3.48e-13

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 64.10  E-value: 3.48e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199  19 PRQLSYLDLLTRQVQSAPGEMAALATDYPAGTVSSLHRHDRGQLLYAMSGVVTVITDLGSWVVAPGQALWIAPGVLHQTR 98
Cdd:COG1917     3 LAEIALTGVSVRVLADGEDELEVVRVTFEPGARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFR 82

                          90
                  ....*....|....
gi 1837859199  99 GFESVAIRSLYIDP 112
Cdd:COG1917    83 NLGDEPAVLLVVFS 96
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
162-275 1.18e-10

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 60.76  E-value: 1.18e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199 162 MRHVCAAPLYVPMPRDARLARICQALLRDPANAGSLDAWAAYGGLSRRNLTRLFRAQTGASFNAWRQKVLLMEA-LARLS 240
Cdd:PRK10572  167 LRCMEAIPESLHPPMDPRVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAkLLLQT 246

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1837859199 241 RGEQITAVALDLGCGSPGAFTAMFRRALGVSPREY 275
Cdd:PRK10572  247 TRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEF 281
ftrA PRK09393
transcriptional activator FtrA; Provisional
 173-275 1.03e-06

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 49.19  E-value: 1.03e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199 173 PMPRD--ARLARICQALLRDPANAGSLDAWAAYGGLSRRNLTRLFRAQTGASFNAWrqkvLLMEALARL-----SRGEQI 245
Cdd:PRK09393  211 PVASResDRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEW----LLRERLARArdlleSSALSI 286

                          90       100       110
                  ....*....|....*....|....*....|
gi 1837859199 246 TAVALDLGCGSPGAFTAMFRRALGVSPREY 275
Cdd:PRK09393  287 DQIAERAGFGSEESLRHHFRRRAATSPAAY 316
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 47-110 2.32e-06

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: 44.40  E-value: 2.32e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1837859199  47 PAGTVSSLHRHDRG-QLLYAMSGVVTVITDLGSWVVA-PGQALWIAPGVLHQTRGFESVAIRSLYI 110
Cdd:cd02208     7 PPGTSSPPHWHPEQdEIFYVLSGEGELTLDDGETVELkAGDIVLIPPGVPHSFVNTSDEPAVFLVV 72
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
46-98 6.33e-06

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


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 44.36  E-value: 6.33e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1837859199  46 YPAGTVSSLHRHDRG-QLLYAMSGVVTVITDLGSWVVAPGQALWIAPGVLHQTR 98
Cdd:COG0662    34 VPPGAELSLHVHPHRdEFFYVLEGTGEVTIGDEEVELKAGDSVYIPAGVPHRLR 87
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 55-132 1.30e-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: 43.96  E-value: 1.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199  55 HRHDRGQLLYAMSGVVTVITDLGSWVVAPGQALWIAPGVLH--QTRGFESVAIRSLYIDPAHADGLPAACQTIQVSPLLQ 132
Cdd:pfam02311  19 HVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHdyEPESEDGWRYRWLYFEPELLERILADISILAGGPLPL 98
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
196-275 2.72e-05

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 42.60  E-value: 2.72e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199 196 SLDAWAAYGGLSRRNLTRLFRAQTGASFNAW-RQKVLLMEALARLSRGEQITAVALDLGCGSPGAFTAMFRRALGVSPRE 274
Cdd:PRK10219   23 NIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYiRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFSRVFRRQFDRTPSD 102


                  .
gi 1837859199 275 Y 275
Cdd:PRK10219  103 Y 103
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
156-275 3.33e-05

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 44.51  E-value: 3.33e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199 156 ALILDemRHVCAAPLYVPMPRDARLARICQALLRDPANAGSLDAWAAYGGLSRRNLTRLFRAQTGASFNAWRQKVLLMEA 235
Cdd:PRK13501  156 AIVLK--RHRYRAEQAHLLPDGEQLDLIMSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMSISHYLRQIRLCHA 233

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1837859199 236 LARLSRGEQ-ITAVALDLGCGSPGAFTAMFRRALGVSPREY 275
Cdd:PRK13501  234 KCLLRGSEHrISDIAARCGFEDSNYFSAVFTREAGMTPRDY 274
PRK15435 PRK15435
bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;
176-277 7.43e-05

bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;


Pssm-ID: 185333 [Multi-domain]  Cd Length: 353  Bit Score: 43.63  E-value: 7.43e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199 176 RDARLARICQALLRDPANAgsLDAWAAYGGLSRRNLTRLFRAQTGASFNAWRQKVLLMEALARLSRGEQITAVALDLGCG 255
Cdd:PRK15435   83 RLDKITHACRLLEQETPVT--LEALADQVAMSPFHLHRLFKATTGMTPKAWQQAWRARRLREALAKGESVTTSILNAGFP 160

                          90       100
                  ....*....|....*....|..
gi 1837859199 256 SPGAFTAMFRRALGVSPREYFR 277
Cdd:PRK15435  161 DSSSYYRKADETLGMTAKQFRH 182
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 46-98 8.93e-05

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: 39.93  E-value: 8.93e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1837859199  46 YPAGTVSSLHRHDR-GQLLYAMSGVVTVITDLGSWVVAPGQALWIAPGVLHQTR 98
Cdd:pfam07883   5 LPPGESSPPHRHPGeDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFR 58
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
206-274 1.38e-04

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 42.36  E-value: 1.38e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199 206 LSRRNLTRLFRAQTGASFNAWRQKVLLMEALARLSRGEQ-ITAVALDLGCGSPGAFTAMFRRALGVSPRE 274
Cdd:PRK13503  199 LSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDAsVTDIAYRCGFGDSNHFSTLFRREFSWSPRD 268
cupin_HpaA-like_N cd06999
AraC/XylS family transcriptional regulators similar to HpaA, N-terminal cupin domain; Members ...
 55-101 2.75e-04

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: 39.41  E-value: 2.75e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1837859199  55 HRHDR-GQLLYAMSGVVTVITDLGSWVVAPGQALWIAPGVLHqtrGFE 101
Cdd:cd06999    38 HRHADlFQVLYIESGGGEVRLDGRTHPLSAPALVVVPPGVVH---GFR 82
cupin_HNL-like cd02233
Granulicella tundricola hydroxynitrile lyase (GtHNL) and related proteins, cupin domain; This ...
 23-95 9.15e-04

Granulicella tundricola hydroxynitrile lyase (GtHNL) and related proteins, cupin domain; This family includes archaeal, eukaryotic, and bacterial proteins homologous to hydroxynitrile lyase from Granulicella tundricola (GtHNL), a novel class of HNLs that does not show any sequence or structural similarity to any other HNL and does not contain conserved motifs typical of HNLs. HNLs comprise a diverse group of enzymes that vary in terms of their substrate specificity, enantioselectivity and the need for a co-factor. In plants, they catalyze the reversible cleavage of cyanohydrins, yielding HCN and aldehydes or ketones. Also included in this family is TM1010 from Thermotoga maritima, a protein of unknown function. Some but not all members of this family have N- or C-terminal carboxymuconolactone decarboxylase domains in addition to the cupin domain. Members of this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380361 [Multi-domain]  Cd Length: 106  Bit Score: 37.92  E-value: 9.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199  23 SYLDLLTRQvqSAPGEMAALATDYPAGTVSSLHRHDRGQLLYAMSGVvtvitdlGsWV---------VAPGQALWIAPGV 93
Cdd:cd02233     5 VWLDPLFPA--DEPSRVSVANVTFEPGARTAWHTHPGGQILIVTSGV-------G-WVqeeggppqeLRPGDVVWIPPGV 74


                  ..
gi 1837859199  94 LH 95
Cdd:cd02233    75 KH 76
cupin_QdtA-like cd20292
sugar 3,4-ketoisomerase QdtA and related proteins, cupin domain; This family includes cupin ...
 44-105 1.56e-03

sugar 3,4-ketoisomerase QdtA and related proteins, cupin domain; This family includes cupin domains of several bacterial proteins homologous to sugar 3,4-ketoisomerases. Thermoanaerobacterium thermosaccharolyticum QdtA catalyzes a key step in the biosynthesis of these sugars, the conversion of thymidine diphosphate (dTDP)-4-keto-6-deoxyglucose to dTDP-3-keto-6-deoxyglucose. In Aneurinibacillus thermoaerophilus, TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase (also known as FdtA) is involved in the biosynthesis of dTDP-Fucp3NAc (3-acetamido-3,6-dideoxy-alpha-d-galactose), which is part of the repeating units of the glycan chain in the S-layer. Shewanella denitrificans bifunctional ketoisomerase/N-acetyltransferase (also known as FdtD) is involved in the third and fifth steps in the production of 3-acetamido-3,6-dideoxy-alpha-d-galactose or Fuc3NAc; the C-terminal cupin domain harbors the active site responsible for the isomerization reaction. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380426  Cd Length: 117  Bit Score: 37.45  E-value: 1.56e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1837859199  44 TDYPAGTVSSLHRHDRG-QLLYAMSGVVTVITDLG--SWVV---APGQALWIAPGVLHQTRGFESVAI 105
Cdd:cd20292    34 YGVPGGAVRGGHAHKKLeQLLICLSGSCEVILDDGkeKEEFvldSPNKGLYIPPGVWHEMYDFSPDAV 101
cupin_TM1459-like cd02222
Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial ...
 49-96 1.99e-03

Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to Thermotoga maritima TM1459, a manganese-containing cupin that has been shown to cleave C=C bonds in the presence of alkylperoxide as oxidant in vitro. Its biological function is still unknown. This family also includes Halorhodospira halophila Hhal_0468. Structures of these proteins show a cupin fold with a conserved "jelly roll-like" beta-barrel fold that form a homodimer.


Pssm-ID: 380351 [Multi-domain]  Cd Length: 91  Bit Score: 36.66  E-value: 1.99e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1837859199  49 GTVSSLHRHDRGQLLYAMSGVVTVITDLGSWVVAPGQALWIAPGVLHQ 96
Cdd:cd02222    27 GGHTPLHTHPWEHEVYVLRGKGVVVIGGEEYPVKPGDVVYIPPNEPHQ 74
cupin_KdgF cd02238
pectin degradation protein KdgF and related proteins, cupin domain; This family includes ...
 45-105 2.44e-03

pectin degradation protein KdgF and related proteins, cupin domain; This family includes bacterial and archaeal pectin degradation protein KdgF that catalyzes the linearization of unsaturated uronates from both pectin and alginate, which are polysaccharides found in the cell walls of plants and brown algae, respectively, and represent an important source of carbon. These polysaccharides, mostly consisting of chains of uronates, can be metabolized by bacteria through a pathway of enzymatic steps to the key metabolite 2-keto-3-deoxygluconate (KDG). Pectin degradation is used by many plant-pathogenic bacteria during infection, and also, pectin and alginate can both represent abundant sources of carbohydrate for the production of biofuels. These proteins belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


Pssm-ID: 380366 [Multi-domain]  Cd Length: 104  Bit Score: 36.68  E-value: 2.44e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1837859199  45 DYPAGTVSSLHRHDRGQLLYAMSGVVTVITDLGSWVVAPGQALWIAPGVLHQTRGFE-SVAI 105
Cdd:cd02238    33 RFEKGAVVPLHSHPHEQIGYVLSGRFEFTIGGETRILKPGDSYYIPPNVPHGAEALEdSVLL 94
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 205-228 2.72e-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: 34.82  E-value: 2.72e-03
                          10        20
                  ....*....|....*....|....
gi 1837859199 205 GLSRRNLTRLFRAQTGASFNAWRQ 228
Cdd:pfam00165  19 GFSRSYFSRLFKKYTGVTPSQYRH 42
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
157-275 3.27e-03

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 38.50  E-value: 3.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1837859199 157 LILDEMRHVCAAPLYVPMPRDARLARICQALLRDPANAGSLDAWAAYGGLSRRNLTRLFRAQTGASFNAWRQKVLLMEAL 236
Cdd:PRK13502  155 LVMTLKRHRYATDDLPATSRETLLDKLITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQ 234

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1837859199 237 ARLSRGE-QITAVALDLGCGSPGAFTAMFRRALGVSPREY 275
Cdd:PRK13502  235 YLLQHSPlMISEISMQCGFEDSNYFSVVFTRETGMTPSQW 274
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH