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Conserved domains on  [gi|446206951|ref|WP_000284806|]
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AraC family transcriptional regulator [Escherichia coli]

Protein Classification

AraC family transcriptional regulator( domain architecture ID 20041620)

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; similar to Escherichia coli HTH-type transcriptional regulator YdiP

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
196-279 5.79e-26

helix_turn_helix, arabinose operon control protein;


:

Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 98.01  E-value: 5.79e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951   196 KITLEQLSKKFRASVSYICHEFTKEYRISPINYVIQRRMTEAKWLLTNTELSQAEISWRVGYENVDHFGKLFLRHVGCSP 275
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 446206951   276 SDYR 279
Cdd:smart00342  81 SEYR 84
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 30-89 7.20e-11

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: 57.27  E-value: 7.20e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951   30 DPKWESGHHVHDNETELIYVKKGVARFTIDSSLYVAHADDIVVIERGRLHAVASDVNDPA 89
Cdd:pfam07883   6 PPGESSPPHRHPGEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPA 65
cupin_RmlC-like super family cl40423
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 29-158 6.51e-07

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.


The actual alignment was detected with superfamily member pfam02311:

Pssm-ID: 477354 [Multi-domain]  Cd Length: 134  Bit Score: 47.81  E-value: 6.51e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951   29 DDPKWESGHHVHDnETELIYVKKGVARFTIDSSLYVAHADDIVVIERGRLHAVASDVNDPATTCTCALYGFQFQGAEENQ 108
Cdd:pfam02311  10 RYPGHSFPPHVHD-FYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESEDGWRYRWLYFEPELLERILADI 88

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 446206951  109 LLQPHSCPVIAAGQGkevIKTLFNELSVILPQSKNSQTSSLwEAFAYTLA 158
Cdd:pfam02311  89 SILAGGPLPLLRDPE---LAALLRALFRLLEEAGRSDDLLA-EALLYQLL 134
 
Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
196-279 5.79e-26

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 98.01  E-value: 5.79e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951   196 KITLEQLSKKFRASVSYICHEFTKEYRISPINYVIQRRMTEAKWLLTNTELSQAEISWRVGYENVDHFGKLFLRHVGCSP 275
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 446206951   276 SDYR 279
Cdd:smart00342  81 SEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
195-284 9.20e-25

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 100.24  E-value: 9.20e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951 195 EKITLEQLSKKFRASVSYICHEFTKEYRISPINYVIQRRMTEAKWLLTNTELSQAEISWRVGYENVDHFGKLFLRHVGCS 274
Cdd:COG2207  167 LLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVT 246

                         90
                 ....*....|
gi 446206951 275 PSDYRRQFKN 284
Cdd:COG2207  247 PSEYRKRLRA 256
HTH_18 pfam12833
Helix-turn-helix domain;
202-281 4.03e-22

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 88.03  E-value: 4.03e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951  202 LSKKFRASVSYICHEFTKEYRISPINYVIQRRMTEAKWLLT-NTELSQAEISWRVGYENVDHFGKLFLRHVGCSPSDYRR 280
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLeDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 446206951  281 Q 281
Cdd:pfam12833  81 R 81
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
188-281 2.30e-13

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 68.85  E-value: 2.30e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951 188 YLNNNYREKITLEQLSKKFRASVSYICHEFTKEYRISPINYVIQRRMTEAKWLLTNTELSQAEISWRVGYENVDHFGKLF 267
Cdd:PRK10572 191 YISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVF 270

                         90
                 ....*....|....
gi 446206951 268 LRHVGCSPSDYRRQ 281
Cdd:PRK10572 271 KKCTGASPSEFRAR 284
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 30-89 7.20e-11

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: 57.27  E-value: 7.20e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951   30 DPKWESGHHVHDNETELIYVKKGVARFTIDSSLYVAHADDIVVIERGRLHAVASDVNDPA 89
Cdd:pfam07883   6 PPGESSPPHRHPGEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPA 65
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
10-90 4.52e-09

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 52.93  E-value: 4.52e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951  10 SETLFVAGKTPRLSRFAFsdDPKWESGHHVHDNEtELIYVKKGVARFTIDSSLYVAHADDIVVIERGRLHAVASDVNDPA 89
Cdd:COG1917   13 VRVLADGEDELEVVRVTF--EPGARTPWHSHPGE-ELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDEPA 89


                 .
gi 446206951  90 T 90
Cdd:COG1917   90 V 90
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 29-158 6.51e-07

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: 47.81  E-value: 6.51e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951   29 DDPKWESGHHVHDnETELIYVKKGVARFTIDSSLYVAHADDIVVIERGRLHAVASDVNDPATTCTCALYGFQFQGAEENQ 108
Cdd:pfam02311  10 RYPGHSFPPHVHD-FYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESEDGWRYRWLYFEPELLERILADI 88

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 446206951  109 LLQPHSCPVIAAGQGkevIKTLFNELSVILPQSKNSQTSSLwEAFAYTLA 158
Cdd:pfam02311  89 SILAGGPLPLLRDPE---LAALLRALFRLLEEAGRSDDLLA-EALLYQLL 134
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 34-91 4.07e-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: 44.01  E-value: 4.07e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446206951  34 ESGHHVHDNETELIYVKKGVARFTIDSS-LYVAHADDIVVIERGRLHAVASDVNDPATT 91
Cdd:cd02208   11 SSPPHWHPEQDEIFYVLSGEGELTLDDGeTVELKAGDIVLIPPGVPHSFVNTSDEPAVF 69
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
36-279 1.45e-05

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 45.86  E-value: 1.45e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951  36 GHHVHDNeTELIYVKKGVARFTIDSSLYVAHADDIVVIERGRLHAVASdVNDPATT----CTCAL-YGFQFQGAEEN--- 107
Cdd:PRK13500  62 AEHTHDF-CELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYAS-VNDLVLQniiyCPERLkLNLDWQGAIPGfsa 139

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951 108 QLLQPH-SCPVIAAGQGKEVIKTLFNELSVILPqsknsqtsslweaFAYTLAILYYENF-----KNAYRSEQ-GYIKKDV 180
Cdd:PRK13500 140 SAGQPHwRLGSVGMAQARQVIGQLEHESSQHVP-------------FANEMAELLFGQLvmllnRHRYTSDSlPPTSSET 206

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951 181 LIKDILFYLNNNYREKITLEQLSKKFRASVSYICHEFTKEYRISPINYVIQRRMTEAKWLLTNTELSQAEISWRVGYENV 260
Cdd:PRK13500 207 LLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDS 286

                        250
                 ....*....|....*....
gi 446206951 261 DHFGKLFLRHVGCSPSDYR 279
Cdd:PRK13500 287 NYFSVVFTRETGMTPSQWR 305
 
Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
196-279 5.79e-26

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 98.01  E-value: 5.79e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951   196 KITLEQLSKKFRASVSYICHEFTKEYRISPINYVIQRRMTEAKWLLTNTELSQAEISWRVGYENVDHFGKLFLRHVGCSP 275
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 446206951   276 SDYR 279
Cdd:smart00342  81 SEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
195-284 9.20e-25

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 100.24  E-value: 9.20e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951 195 EKITLEQLSKKFRASVSYICHEFTKEYRISPINYVIQRRMTEAKWLLTNTELSQAEISWRVGYENVDHFGKLFLRHVGCS 274
Cdd:COG2207  167 LLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVT 246

                         90
                 ....*....|
gi 446206951 275 PSDYRRQFKN 284
Cdd:COG2207  247 PSEYRKRLRA 256
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 179-282 1.13e-22

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: 1.13e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951 179 DVLIKDILFYLNNNYREKITLEQLSKkfRASVSyichE------FTKEYRISPINYVIQRRMTEAKWLLTNTELSQAEIS 252
Cdd:COG4977  209 DPRLARAQAWMEANLEEPLSVDELAR--RAGMS----PrtlerrFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIA 282

                         90       100       110
                 ....*....|....*....|....*....|
gi 446206951 253 WRVGYENVDHFGKLFLRHVGCSPSDYRRQF 282
Cdd:COG4977  283 AACGFGSASHFRRAFRRRFGVSPSAYRRRF 312
HTH_18 pfam12833
Helix-turn-helix domain;
202-281 4.03e-22

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 88.03  E-value: 4.03e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951  202 LSKKFRASVSYICHEFTKEYRISPINYVIQRRMTEAKWLLT-NTELSQAEISWRVGYENVDHFGKLFLRHVGCSPSDYRR 280
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLeDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 446206951  281 Q 281
Cdd:pfam12833  81 R 81
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
188-281 2.30e-13

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 68.85  E-value: 2.30e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951 188 YLNNNYREKITLEQLSKKFRASVSYICHEFTKEYRISPINYVIQRRMTEAKWLLTNTELSQAEISWRVGYENVDHFGKLF 267
Cdd:PRK10572 191 YISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVF 270

                         90
                 ....*....|....
gi 446206951 268 LRHVGCSPSDYRRQ 281
Cdd:PRK10572 271 KKCTGASPSEFRAR 284
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 181-284 2.37e-13

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: 69.70  E-value: 2.37e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951 181 LIKDILFYLNNNYREKITLEQLSKKFRASVSYICHEFTKEYRISPINYVIQRRMTEAKWLLTnTELSQAEISWRVGYENV 260
Cdd:COG2169   85 LVARACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQ-TGLSVTDAAYAAGFGSL 163

                         90       100
                 ....*....|....*....|....
gi 446206951 261 DHFGKLFLRHVGCSPSDYRRQFKN 284
Cdd:COG2169  164 SRFYEAFKKLLGMTPSAYRRGGAG 187
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 30-89 7.20e-11

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: 57.27  E-value: 7.20e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951   30 DPKWESGHHVHDNETELIYVKKGVARFTIDSSLYVAHADDIVVIERGRLHAVASDVNDPA 89
Cdd:pfam07883   6 PPGESSPPHRHPGEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPA 65
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
10-90 4.52e-09

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 52.93  E-value: 4.52e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951  10 SETLFVAGKTPRLSRFAFsdDPKWESGHHVHDNEtELIYVKKGVARFTIDSSLYVAHADDIVVIERGRLHAVASDVNDPA 89
Cdd:COG1917   13 VRVLADGEDELEVVRVTF--EPGARTPWHSHPGE-ELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDEPA 89


                 .
gi 446206951  90 T 90
Cdd:COG1917   90 V 90
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
122-285 4.98e-09

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 56.07  E-value: 4.98e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951 122 QGKEVIKTLFNElsvilpQSKNSQTS-SLWEAFAYTLAILYYenfKNAYRSEQGYI-----KKDVLIKDILFYLNNNYre 195
Cdd:PRK13501 125 QARPIIQQLAQE------SRKTDSWSiQLTEVLLLQLAIVLK---RHRYRAEQAHLlpdgeQLDLIMSALQQSLGAYF-- 193

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951 196 kiTLEQLSKKFRASVSYICHEFTKEYRISPINYVIQRRMTEAKWLLTNTELSQAEISWRVGYENVDHFGKLFLRHVGCSP 275
Cdd:PRK13501 194 --DMADFCHKNQLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSNYFSAVFTREAGMTP 271

                        170
                 ....*....|
gi 446206951 276 SDYRRQFKNC 285
Cdd:PRK13501 272 RDYRQRFIRS 281
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
179-281 6.05e-09

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 55.84  E-value: 6.05e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951 179 DVLIKDILFYLNNNYREKITLEQLSKKFRASVSYICHEFTKEYRISPINYVIQRRMTEAKWLLTNTELSQAEISWRVGYE 258
Cdd:PRK13503 170 DARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFG 249

                         90       100
                 ....*....|....*....|...
gi 446206951 259 NVDHFGKLFLRHVGCSPSDYRRQ 281
Cdd:PRK13503 250 DSNHFSTLFRREFSWSPRDIRQG 272
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
31-90 4.25e-08

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


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 50.53  E-value: 4.25e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951  31 PKWESGHHVHDNETELIYVKKGVARFTIDSSLYVAHADDIVVIERGRLHAVASDVNDPAT 90
Cdd:COG0662   36 PGAELSLHVHPHRDEFFYVLEGTGEVTIGDEEVELKAGDSVYIPAGVPHRLRNPGDEPLE 95
COG3837 COG3837
Uncharacterized conserved protein, cupin superfamily [Function unknown];
32-90 3.18e-07

Uncharacterized conserved protein, cupin superfamily [Function unknown];


Pssm-ID: 443048 [Multi-domain]  Cd Length: 115  Bit Score: 48.09  E-value: 3.18e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446206951  32 KWESGHHVHDNETELIYVKKGVARFTIDSSLYVAHADDIVVIERGRLHAVASDVNDPAT 90
Cdd:COG3837   39 ASSSPYHAHSAEEEFVYVLEGELTLRIGGEEYVLEPGDSVGFPAGVPHRLRNRGDEPAR 97
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 29-158 6.51e-07

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: 47.81  E-value: 6.51e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951   29 DDPKWESGHHVHDnETELIYVKKGVARFTIDSSLYVAHADDIVVIERGRLHAVASDVNDPATTCTCALYGFQFQGAEENQ 108
Cdd:pfam02311  10 RYPGHSFPPHVHD-FYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESEDGWRYRWLYFEPELLERILADI 88

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 446206951  109 LLQPHSCPVIAAGQGkevIKTLFNELSVILPQSKNSQTSSLwEAFAYTLA 158
Cdd:pfam02311  89 SILAGGPLPLLRDPE---LAALLRALFRLLEEAGRSDDLLA-EALLYQLL 134
ftrA PRK09393
transcriptional activator FtrA; Provisional
 224-282 8.63e-07

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 49.58  E-value: 8.63e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446206951 224 SPINYVIQRRMTEAKWLLTNTELSQAEISWRVGYENVDHFGKLFLRHVGCSPSDYRRQF 282
Cdd:PRK09393 262 TPAEWLLRERLARARDLLESSALSIDQIAERAGFGSEESLRHHFRRRAATSPAAYRKRF 320
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
101-279 1.81e-06

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 48.51  E-value: 1.81e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951 101 FQGAEENqllqPH-SCPVIAAGQGKEVIKTLFNELSVILPQSkNSQTSSLWEAFAYTLAilyyenfKNAYRSEQGYIK-K 178
Cdd:PRK13502 107 FQGAQWH----PHwRLGSMGMNQARQVINQLEHESNGRDPLA-NEMAELLFGQLVMTLK-------RHRYATDDLPATsR 174

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951 179 DVLIKDILFYLNNNYREKITLEQLSKKFRASVSYICHEFTKEYRISPINYVIQRRMTEAKWLLTNTELSQAEISWRVGYE 258
Cdd:PRK13502 175 ETLLDKLITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHSPLMISEISMQCGFE 254

                        170       180
                 ....*....|....*....|.
gi 446206951 259 NVDHFGKLFLRHVGCSPSDYR 279
Cdd:PRK13502 255 DSNYFSVVFTRETGMTPSQWR 275
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 34-91 4.07e-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: 44.01  E-value: 4.07e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446206951  34 ESGHHVHDNETELIYVKKGVARFTIDSS-LYVAHADDIVVIERGRLHAVASDVNDPATT 91
Cdd:cd02208   11 SSPPHWHPEQDEIFYVLSGEGELTLDDGeTVELKAGDIVLIPPGVPHSFVNTSDEPAVF 69
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
36-279 1.45e-05

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 45.86  E-value: 1.45e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951  36 GHHVHDNeTELIYVKKGVARFTIDSSLYVAHADDIVVIERGRLHAVASdVNDPATT----CTCAL-YGFQFQGAEEN--- 107
Cdd:PRK13500  62 AEHTHDF-CELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYAS-VNDLVLQniiyCPERLkLNLDWQGAIPGfsa 139

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951 108 QLLQPH-SCPVIAAGQGKEVIKTLFNELSVILPqsknsqtsslweaFAYTLAILYYENF-----KNAYRSEQ-GYIKKDV 180
Cdd:PRK13500 140 SAGQPHwRLGSVGMAQARQVIGQLEHESSQHVP-------------FANEMAELLFGQLvmllnRHRYTSDSlPPTSSET 206

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951 181 LIKDILFYLNNNYREKITLEQLSKKFRASVSYICHEFTKEYRISPINYVIQRRMTEAKWLLTNTELSQAEISWRVGYENV 260
Cdd:PRK13500 207 LLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDS 286

                        250
                 ....*....|....*....
gi 446206951 261 DHFGKLFLRHVGCSPSDYR 279
Cdd:PRK13500 287 NYFSVVFTRETGMTPSQWR 305
cupin_TM1287-like cd02221
Thermotoga maritima TM1287 decarboxylase, cupin domain; This family includes bacterial ...
 36-88 3.28e-05

Thermotoga maritima TM1287 decarboxylase, cupin domain; This family includes bacterial proteins homologous to TM1287 decarboxylase, a Thermotoga maritima manganese-containing cupin thought to catalyze the conversion of oxalate to formate and carbon dioxide, due to its similarity to oxalate decarboxylase (OXDC) from Bacillus subtilis. TM1287 shows a cupin fold with a conserved "jelly roll-like" beta-barrel fold and forms a homodimer.


Pssm-ID: 380350 [Multi-domain]  Cd Length: 93  Bit Score: 41.69  E-value: 3.28e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446206951  36 GHHVHDNETELIYVKKGVARFTIDSSLYVAHADDIVVIERGRLHAVASDVNDP 88
Cdd:cd02221   33 GYHQHEGEFEIYYILSGEGLYTDNGKEYEVKAGDVTFTRDGESHGIENTGDED 85
cupin_SznF-like_C cd07002
Streptomyces achromogenes SznF and related proteins, C-terminal cupin domain; This family ...
 29-79 3.42e-05

Streptomyces achromogenes SznF and related proteins, C-terminal cupin domain; This family includes bacterial proteins similar to Streptomyces achromogenes SznF, containing an N-terminal helical region that mediates dimerization, a central heme oxygenase domain, and a C-terminal cupin domain. SznF is a metalloenzyme that catalyzes an oxidative rearrangement of the guanidine group of N(omega)-methyl-L-arginine to generate an N-nitrosourea product, during the biosynthesis of streptozotocin, an N-nitrosourea natural product and an approved cancer chemotherapeutic. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold generally capable of homodimerization. However, in SznF, the cupin domain is not involved in dimerization.


Pssm-ID: 380406  Cd Length: 96  Bit Score: 41.90  E-value: 3.42e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446206951  29 DDPKWE-SGHHVHDNEtELIYVKKGVARFTI--DSSLyVAHADDIVVIERGRLH 79
Cdd:cd07002   27 VEPRGElSVTHVHDGD-ELCHVVSGTMRFVSglGSST-ILNAGEGVVIKRNRLH 78
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
179-281 1.99e-04

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 39.91  E-value: 1.99e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951 179 DVLIKDILFYLNNNYREKITLEQLSKKFRASVSYICHEFTKEYRISPINYVIQRRMTEAKWLLTNTELSQAEISWRVGYE 258
Cdd:PRK10219   4 QKIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYV 83

                         90       100
                 ....*....|....*....|...
gi 446206951 259 NVDHFGKLFLRHVGCSPSDYRRQ 281
Cdd:PRK10219  84 SQQTFSRVFRRQFDRTPSDYRHR 106
cupin_OxDC-like cd20306
Oxalate decarboxylase (OxDC)-like cupin domain; This subfamily contains bacterial and ...
 38-79 3.05e-04

Oxalate decarboxylase (OxDC)-like cupin domain; This subfamily contains bacterial and eukaryotic cupin domains of proteins homologous to oxalate decarboxylase (OxDC; EC 4.1.1.2) such as MSMEG_2254, a putative OxDC from Mycobacterium smegmatis. OxDC is a manganese-dependent bicupin that catalyzes the conversion of oxalate to formate and carbon dioxide, utilizing dioxygen as a cofactor. It is evolutionarily related to oxalate oxidase (OxOx or germin; EC 1.2.3.4) which, in contrast, converts oxalate and dioxygen to carbon dioxide and hydrogen peroxide. OxDC is classified as a bicupin because it contains two cupin folds with each domain containing one manganese binding site, with four manganese binding residues (three histidines and one glutamate) conserved as well as a number of hydrophobic residues.


Pssm-ID: 380440 [Multi-domain]  Cd Length: 151  Bit Score: 40.27  E-value: 3.05e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 446206951  38 HVHDNETELIYVKKGVARFTI---DSSL--YVAHADDIVVIERGRLH 79
Cdd:cd20306   50 HWHPNANELGYVISGEARVSIldpTGSLdtFTVKPGQVVFIPQGWLH 96
cupin_MmsR-like_N cd06986
AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This ...
 46-88 1.81e-03

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


Pssm-ID: 380391 [Multi-domain]  Cd Length: 84  Bit Score: 36.69  E-value: 1.81e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 446206951  46 LIYVKKGVARFTIDSSLYVAHADDIVVIERGRLHAVASDVNDP 88
Cdd:cd06986   31 LHYVLSGKGTFSVNGKTYHLKAGQGFLIPPGEPHSYGADEDDP 73
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
180-279 3.21e-03

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 37.00  E-value: 3.21e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951 180 VLIKDILFYLNNNYREKITLEQLSKKFRASVSYICHEFTKEYRISPINYVIQRRMTEAKWLLTNTELSQAEISWRVGYEN 259
Cdd:PRK11511   9 ITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFES 88

                         90       100
                 ....*....|....*....|
gi 446206951 260 VDHFGKLFLRHVGCSPSDYR 279
Cdd:PRK11511  89 QQTLTRTFKNYFDVPPHKYR 108
cupin_DddK cd06988
Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes ...
 31-81 5.52e-03

Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes mostly bacterial proteins homologous to dimethylsulfoniopropionate lyase DddK from marine bacterium Pelagibacter. DddK cleaves dimethylsulfoniopropionate (DMSP), the organic osmolyte and antioxidant produced in marine environments, and yields acrylate and the climate-active gas dimethyl sulfide (DMS). DddK contains a double-stranded beta-helical motif which utilizes various divalent metal ions as cofactors for catalytic activity; however, nickel, an abundant metal ion in marine environments, confers the highest DMSP lyase activity. Also included in this family is Plu4264, a Photorhabdus luminescens manganese-containing cupin shown to have similar metal binding site to TM1287 decarboxylase, but two very different substrate binding pockets. The Plu4264 binding pocket shows a cavity and substrate entry point more than twice as large as and more hydrophobic than TM1287, suggesting that Plu4264 accepts a substrate that is significantly larger than that of TM1287, a putative oxalate decarboxylase. Thus, the function of Plu4264 could be similar to that of TM1287 but with a larger, less charged substrate. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


Pssm-ID: 380393 [Multi-domain]  Cd Length: 76  Bit Score: 35.29  E-value: 5.52e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446206951  31 PKWESGHHVHDnETELIYVKKGVARFTIDSSLYVAHADDIVVIERGRLHAV 81
Cdd:cd06988   11 PGTTSTPHSHH-EYEIFIVISGKGIVVVDGEREPVKAGDVVYIPPGTEHYV 60
PRK15186 PRK15186
AraC family transcriptional regulator; Provisional
 176-284 6.39e-03

AraC family transcriptional regulator; Provisional


Pssm-ID: 185108 [Multi-domain]  Cd Length: 291  Bit Score: 37.74  E-value: 6.39e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446206951 176 IKKDVLIKDILFYLNNNYREKITLEQLSKKFRASVSYICHEFTKEYrISPINYVIQRRMTEAKWLLTNTELSQAEISWRV 255
Cdd:PRK15186 177 LSQNTLAENIYNIIISDISRKWALKDISDSLYMSCSTLKRKLKQEN-TSFSEVYLNARMNKATKLLRNSEYNITRVAYMC 255

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 446206951 256 GYENVDHFGKLFLRHVGCSPSDY-------RRQFKN 284
Cdd:PRK15186 256 GYDSASYFTCVFKKHFKTTPSEFlaflsssRHQYVN 291
cupin_QDO_N_C cd02215
quercetinase, N- and C-terminal cupin domains; This family contains quercetinase (also known ...
 38-80 8.74e-03

quercetinase, N- and C-terminal cupin domains; This family contains quercetinase (also known as quercetin 2,3-dioxygenase, 2,3QD, QDO and YxaG; EC 1.13.11.24), a mononuclear copper-dependent dioxygenase that catalyzes the cleavage of the flavonol quercetin (5,7,3',4'-tetrahydroxyflavonol) heterocyclic ring to produce 2-protocatechuoyl-phloroglucinol carboxylic acid and carbon monoxide. Bacillus subtilis quercetin 2,3-dioxygenase (QDO) is a homodimer that shows oxygenase activity with several divalent metals such as Mn2+, Co2+, Fe2+, and Cu2+, although the preferred one appears to be Mn2+. The dioxygen binds to the metal ion of the Cu-QDO-quercetin complex, yielding a Cu2+-superoxo quercetin radical intermediate, which then forms a Cu2+-alkylperoxo complex which then evolves into endoperoxide intermediate that decomposes to the product. Quercetinase is a bicupin with two tandem cupin beta-barrel domains, both of which are included in this alignment model. The pirins, which also belong to the cupin domain family, have been shown to catalyze a reaction involving quercetin and may have a function similar to that of quercetinase.


Pssm-ID: 380345 [Multi-domain]  Cd Length: 122  Bit Score: 35.59  E-value: 8.74e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 446206951  38 HVHDNETELIYVKKGVARFTIDSSLYVAHADDIVVIERGRLHA 80
Cdd:cd02215   48 HYHKRHHETFYVLEGRLQLWLDGESRLLTPGDFASVPPGTIHA 90
 
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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