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Conserved domains on  [gi|544940211|ref|WP_021348542|]
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MULTISPECIES: AraC family transcriptional regulator [Elizabethkingia]

Protein Classification

AraC family transcriptional regulator( domain architecture ID 15746445)

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_RmlC-like super family cl40423
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 14-99 1.37e-29

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 cd06976:

Pssm-ID: 477354 [Multi-domain]  Cd Length: 83  Bit Score: 107.22  E-value: 1.37e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940211  14 HSFNARKDTMPDVNNKWHYHMVLELIYFRKGTGTQYVGNSIERFKEGDVALIGKNLPHYWLFDAKYFEnpkRNKVEIFVI 93
Cdd:cd06976    1 SSFRVRRHDYPYFPAPWHFHPEYELTLIVKGSGTRFVGDHIGNFEPGDLVLIGPNLPHTWKSDEEYGE---DLRARAIVI 77


                 ....*.
gi 544940211  94 HFGEHF 99
Cdd:cd06976   78 QFSEDF 83
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
150-288 2.82e-24

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


:

Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 98.70  E-value: 2.82e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940211 150 IIRLLEALHSISESAEYEFLTSANFKYHFDEDERHRIMDIYNYTLSNYTQKITLEDVSEIANLSPNSFCKFFKSRTGKTY 229
Cdd:COG2207  118 LLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSP 197

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 544940211 230 TQFVNEIRIGDACQKLIENQMSVKEVCFASGFNNFTSFHECFKNITGKSPLKYQQLYRK 288
Cdd:COG2207  198 KQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLRA 256
 
Name Accession Description Interval E-value
cupin_MtlR-like_N cd06976
AraC/XylS family transcriptional regulators similar to MtlR, N-terminal cupin domain; MtlR is ...
 14-99 1.37e-29

AraC/XylS family transcriptional regulators similar to MtlR, N-terminal cupin domain; MtlR is a Pseudomonas fluorescens protein that acts as a transcriptional regulator of the mannitol utilization genes. It has an N-terminal cupin domain (represented by this alignment) 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.


Pssm-ID: 380381 [Multi-domain]  Cd Length: 83  Bit Score: 107.22  E-value: 1.37e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940211  14 HSFNARKDTMPDVNNKWHYHMVLELIYFRKGTGTQYVGNSIERFKEGDVALIGKNLPHYWLFDAKYFEnpkRNKVEIFVI 93
Cdd:cd06976    1 SSFRVRRHDYPYFPAPWHFHPEYELTLIVKGSGTRFVGDHIGNFEPGDLVLIGPNLPHTWKSDEEYGE---DLRARAIVI 77


                 ....*.
gi 544940211  94 HFGEHF 99
Cdd:cd06976   78 QFSEDF 83
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
150-288 2.82e-24

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 98.70  E-value: 2.82e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940211 150 IIRLLEALHSISESAEYEFLTSANFKYHFDEDERHRIMDIYNYTLSNYTQKITLEDVSEIANLSPNSFCKFFKSRTGKTY 229
Cdd:COG2207  118 LLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSP 197

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 544940211 230 TQFVNEIRIGDACQKLIENQMSVKEVCFASGFNNFTSFHECFKNITGKSPLKYQQLYRK 288
Cdd:COG2207  198 KQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLRA 256
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
200-282 1.22e-19

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 81.06  E-value: 1.22e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940211   200 KITLEDVSEIANLSPNSFCKFFKSRTGKTYTQFVNEIRIGDACQKLIENQMSVKEVCFASGFNNFTSFHECFKNITGKSP 279
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ...
gi 544940211   280 LKY 282
Cdd:smart00342  81 SEY 83
HTH_18 pfam12833
Helix-turn-helix domain;
206-284 1.70e-18

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 78.02  E-value: 1.70e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940211  206 VSEIANLSPNSFCKFFKSRTGKTYTQFVNEIRIGDACQKLIENQ-MSVKEVCFASGFNNFTSFHECFKNITGKSPLKYQQ 284
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEDTgLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
PRK10371 PRK10371
transcriptional regulator MelR;
192-287 1.05e-08

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 55.21  E-value: 1.05e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940211 192 YTLSNYTQKITLEDVSEIANLSPNSFCKFFKSRTGKTYTQFVNEIRIGDACQKLIENQMSVKEVCFASGFNNFTSFHECF 271
Cdd:PRK10371 199 FIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTAGFRSSSRFYSTF 278

                         90
                 ....*....|....*.
gi 544940211 272 KNITGKSPLKYQQLYR 287
Cdd:PRK10371 279 GKYVGMSPQQYRKLSQ 294
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
24-73 3.79e-07

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 47.54  E-value: 3.79e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 544940211  24 PDVNNKWHYHMVLELIYFRKGTGTQYVGNSIERFKEGDVALIGKNLPHYW 73
Cdd:COG1917   32 PGARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAF 81
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 29-94 1.50e-04

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: 39.16  E-value: 1.50e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 544940211   29 KWHYH-MVLELIYFRKGTGTQYVGNSIERFKEGDVALIGKNLPHywlfdakYFENPKRNKVEIFVIH 94
Cdd:pfam07883  12 PPHRHpGEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPH-------RFRNTGDEPARLLDVY 71
 
Name Accession Description Interval E-value
cupin_MtlR-like_N cd06976
AraC/XylS family transcriptional regulators similar to MtlR, N-terminal cupin domain; MtlR is ...
 14-99 1.37e-29

AraC/XylS family transcriptional regulators similar to MtlR, N-terminal cupin domain; MtlR is a Pseudomonas fluorescens protein that acts as a transcriptional regulator of the mannitol utilization genes. It has an N-terminal cupin domain (represented by this alignment) 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.


Pssm-ID: 380381 [Multi-domain]  Cd Length: 83  Bit Score: 107.22  E-value: 1.37e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940211  14 HSFNARKDTMPDVNNKWHYHMVLELIYFRKGTGTQYVGNSIERFKEGDVALIGKNLPHYWLFDAKYFEnpkRNKVEIFVI 93
Cdd:cd06976    1 SSFRVRRHDYPYFPAPWHFHPEYELTLIVKGSGTRFVGDHIGNFEPGDLVLIGPNLPHTWKSDEEYGE---DLRARAIVI 77


                 ....*.
gi 544940211  94 HFGEHF 99
Cdd:cd06976   78 QFSEDF 83
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
150-288 2.82e-24

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 98.70  E-value: 2.82e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940211 150 IIRLLEALHSISESAEYEFLTSANFKYHFDEDERHRIMDIYNYTLSNYTQKITLEDVSEIANLSPNSFCKFFKSRTGKTY 229
Cdd:COG2207  118 LLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSP 197

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 544940211 230 TQFVNEIRIGDACQKLIENQMSVKEVCFASGFNNFTSFHECFKNITGKSPLKYQQLYRK 288
Cdd:COG2207  198 KQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLRA 256
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
200-282 1.22e-19

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 81.06  E-value: 1.22e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940211   200 KITLEDVSEIANLSPNSFCKFFKSRTGKTYTQFVNEIRIGDACQKLIENQMSVKEVCFASGFNNFTSFHECFKNITGKSP 279
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ...
gi 544940211   280 LKY 282
Cdd:smart00342  81 SEY 83
HTH_18 pfam12833
Helix-turn-helix domain;
206-284 1.70e-18

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 78.02  E-value: 1.70e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940211  206 VSEIANLSPNSFCKFFKSRTGKTYTQFVNEIRIGDACQKLIENQ-MSVKEVCFASGFNNFTSFHECFKNITGKSPLKYQQ 284
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEDTgLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 196-287 2.70e-15

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: 74.42  E-value: 2.70e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940211 196 NYTQKITLEDVSEIANLSPNSFCKFFKSRTGKTYTQFVNEIRIGDACQKLIENQMSVKEVCFASGFNNFTSFHECFKNIT 275
Cdd:COG4977  222 NLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHFRRAFRRRF 301

                         90
                 ....*....|..
gi 544940211 276 GKSPLKYQQLYR 287
Cdd:COG4977  302 GVSPSAYRRRFR 313
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 196-284 6.64e-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: 68.16  E-value: 6.64e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940211 196 NYTQKITLEDVSEIANLSPNSFCKFFKSRTGKTYTQFVNEIRIGDACQkLIENQMSVKEVCFASGFNNFTSFHECFKNIT 275
Cdd:COG2169   96 GAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQ-LLQTGLSVTDAAYAAGFGSLSRFYEAFKKLL 174


                 ....*....
gi 544940211 276 GKSPLKYQQ 284
Cdd:COG2169  175 GMTPSAYRR 183
PRK10371 PRK10371
transcriptional regulator MelR;
192-287 1.05e-08

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 55.21  E-value: 1.05e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940211 192 YTLSNYTQKITLEDVSEIANLSPNSFCKFFKSRTGKTYTQFVNEIRIGDACQKLIENQMSVKEVCFASGFNNFTSFHECF 271
Cdd:PRK10371 199 FIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTAGFRSSSRFYSTF 278

                         90
                 ....*....|....*.
gi 544940211 272 KNITGKSPLKYQQLYR 287
Cdd:PRK10371 279 GKYVGMSPQQYRKLSQ 294
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
24-73 3.79e-07

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 47.54  E-value: 3.79e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 544940211  24 PDVNNKWHYHMVLELIYFRKGTGTQYVGNSIERFKEGDVALIGKNLPHYW 73
Cdd:COG1917   32 PGARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAF 81
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
184-287 2.56e-06

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 48.05  E-value: 2.56e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940211 184 HRIMDIYNYTLSNYTQKITLEDVSEIANLSPNSFCKFFKSRTGKTYTQFVNEIRIGDACQKLIENQMSVKEVCFASGFNN 263
Cdd:PRK10572 183 PRVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDD 262

                         90       100
                 ....*....|....*....|....
gi 544940211 264 FTSFHECFKNITGKSPLKYQQLYR 287
Cdd:PRK10572 263 QLYFSRVFKKCTGASPSEFRARCE 286
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 194-234 3.96e-06

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


Pssm-ID: 425497 [Multi-domain]  Cd Length: 42  Bit Score: 42.91  E-value: 3.96e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 544940211  194 LSNYTQKITLEDVSEIANLSPNSFCKFFKSRTGKTYTQFVN 234
Cdd:pfam00165   2 RENLSTNLTIADIADELGFSRSYFSRLFKKYTGVTPSQYRH 42
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
24-99 1.51e-05

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


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 43.21  E-value: 1.51e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 544940211  24 PDVNNKWHYHM-VLELIYFRKGTGTQYVGNSIERFKEGDVALIGKNLPHywlfdakYFENPKRNKVEIFVIHFGEHF 99
Cdd:COG0662   36 PGAELSLHVHPhRDEFFYVLEGTGEVTIGDEEVELKAGDSVYIPAGVPH-------RLRNPGDEPLELLEVQAPAYL 105
cupin_MJ1618 cd02214
Methanocaldococcus jannaschii MJ1618 and related proteins, cupin domain; This family includes ...
 24-72 1.21e-04

Methanocaldococcus jannaschii MJ1618 and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to MJ1618, a Methanocaldococcus jannaschii protein of unknown function with a cupin beta barrel domain. The active site of members of the cupin superfamily is generally located at the center of a conserved barrel and usually includes a metal ion.


Pssm-ID: 380344 [Multi-domain]  Cd Length: 100  Bit Score: 40.19  E-value: 1.21e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 544940211  24 PDVNNKWHYHMVLELIYF-RKGTGTQYVGNSIERFKEGDVALIGKNLPHY 72
Cdd:cd02214   28 PGESTLPHRLKGSEEVYYiLEGEGTMEIDGEPREVGPGDAVLIPPGAVQR 77
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 29-94 1.50e-04

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: 39.16  E-value: 1.50e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 544940211   29 KWHYH-MVLELIYFRKGTGTQYVGNSIERFKEGDVALIGKNLPHywlfdakYFENPKRNKVEIFVIH 94
Cdd:pfam07883  12 PPHRHpGEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPH-------RFRNTGDEPARLLDVY 71
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
196-279 2.42e-04

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 41.97  E-value: 2.42e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940211 196 NYTQKITLEDVSEIANLSPNSFCKFFKSRTGKTYTQFVNEIRIGDACQKLIENQMSVKEVCFASGFNNFTSFHECFKNIT 275
Cdd:PRK13503 183 HFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFGDSNHFSTLFRREF 262


                 ....
gi 544940211 276 GKSP 279
Cdd:PRK13503 263 SWSP 266
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 24-94 3.52e-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: 38.23  E-value: 3.52e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 544940211  24 PDVNNKWHYH-MVLELIYFRKGTGTQYVGNSIER-FKEGDVALIGKNLPHywlfdakYFENPKRNKVEIFVIH 94
Cdd:cd02208    8 PGTSSPPHWHpEQDEIFYVLSGEGELTLDDGETVeLKAGDIVLIPPGVPH-------SFVNTSDEPAVFLVVS 73
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 181-284 5.02e-04

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 40.68  E-value: 5.02e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940211 181 DERHRIMDIYNytlSNYTQKITLEDVSEIANLSPNSFCKFFKSRtGKTYTQFVNEIRIGDACQKLIENQMSVKEVCFASG 260
Cdd:PRK09978 142 NMRTRVCTVIN---NNIAHEWTLARIASELLMSPSLLKKKLREE-ETSYSQLLTECRMQRALQLIVIHGFSIKRVAVSCG 217

                         90       100
                 ....*....|....*....|....
gi 544940211 261 FNNFTSFHECFKNITGKSPLKYQQ 284
Cdd:PRK09978 218 YHSVSYFIYVFRNYYGMTPTEYQE 241
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
186-283 5.74e-04

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 38.93  E-value: 5.74e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940211 186 IMDIYNYTLSNYTQKITLEDVSEIANLSPNSFCKFFKSRTGKTYTQFVNEIRIGDACQKLIENQMSVKEVCFASGFNNFT 265
Cdd:PRK11511  11 IHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQ 90

                         90
                 ....*....|....*...
gi 544940211 266 SFHECFKNITGKSPLKYQ 283
Cdd:PRK11511  91 TLTRTFKNYFDVPPHKYR 108
cupin_DddK cd06988
Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes ...
 31-93 1.54e-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: 36.44  E-value: 1.54e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 544940211  31 HYHMVLELIYFRKGTGTQYVGNSIERFKEGDVALIGKNLPHywlfdakYFENPKRNKVEIFVI 93
Cdd:cd06988   18 HSHHEYEIFIVISGKGIVVVDGEREPVKAGDVVYIPPGTEH-------YVKNDGDEDFEFYSI 73
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
221-285 2.81e-03

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 38.50  E-value: 2.81e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 544940211 221 FKSRTGKTYTQFVNEIRIGDACQKLIENQMSVKEVCFASGFNNFTSFHECFKNITGKSPLKYQQL 285
Cdd:PRK13502 213 FRAQTGMTINQYLRQVRICHAQYLLQHSPLMISEISMQCGFEDSNYFSVVFTRETGMTPSQWRHL 277
 
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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