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Conserved domains on  [gi|489188479|ref|WP_003097872|]
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MULTISPECIES: AraC family transcriptional regulator [Pseudomonas]

Protein Classification

AraC family transcriptional regulator( domain architecture ID 13673967)

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
GlxA super family cl34854
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 177-274 4.10e-26

Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH domain [Transcription];


The actual alignment was detected with superfamily member COG4977:

Pssm-ID: 444002 [Multi-domain]  Cd Length: 318  Bit Score: 104.08  E-value: 4.10e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479 177 RLRDWLESRLEYPPNLEELAAFCGLSPWQVLRRFRRHCGLPPHQWLTQLRLERALPLVLRGEQPLSQVAQQFGFYDQAHF 256
Cdd:COG4977  214 RAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHF 293

                         90
                 ....*....|....*...
gi 489188479 257 SRLFRRTYGLPPARLRQR 274
Cdd:COG4977  294 RRAFRRRFGVSPSAYRRR 311
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 12-149 1.27e-23

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: 92.88  E-value: 1.27e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479   12 PGVRLIDAEHNRFSFPRHFHLEYHIGLLLQGRHRYAAGGERRLAGAGDALLMAPESIHDGSSAGEEGYRIRVLALDADWL 91
Cdd:pfam02311   2 PGLEGIEARYPGHSFPPHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESEDGWRYRWLYFEPELL 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 489188479   92 ERASRDFSDGRRGAPrltsSLVRDERLQQRLRQLHLGMlgGAAALENRLALEEHLWQA 149
Cdd:pfam02311  82 ERILADISILAGGPL----PLLRDPELAALLRALFRLL--EEAGRSDDLLAEALLYQL 133
 
Name Accession Description Interval E-value
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 177-274 4.10e-26

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: 104.08  E-value: 4.10e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479 177 RLRDWLESRLEYPPNLEELAAFCGLSPWQVLRRFRRHCGLPPHQWLTQLRLERALPLVLRGEQPLSQVAQQFGFYDQAHF 256
Cdd:COG4977  214 RAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHF 293

                         90
                 ....*....|....*...
gi 489188479 257 SRLFRRTYGLPPARLRQR 274
Cdd:COG4977  294 RRAFRRRFGVSPSAYRRR 311
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
189-272 1.28e-24

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 93.77  E-value: 1.28e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479   189 PPNLEELAAFCGLSPWQVLRRFRRHCGLPPHQWLTQLRLERALPLVLRGEQPLSQVAQQFGFYDQAHFSRLFRRTYGLPP 268
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 489188479   269 ARLR 272
Cdd:smart00342  81 SEYR 84
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 12-149 1.27e-23

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: 92.88  E-value: 1.27e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479   12 PGVRLIDAEHNRFSFPRHFHLEYHIGLLLQGRHRYAAGGERRLAGAGDALLMAPESIHDGSSAGEEGYRIRVLALDADWL 91
Cdd:pfam02311   2 PGLEGIEARYPGHSFPPHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESEDGWRYRWLYFEPELL 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 489188479   92 ERASRDFSDGRRGAPrltsSLVRDERLQQRLRQLHLGMlgGAAALENRLALEEHLWQA 149
Cdd:pfam02311  82 ERILADISILAGGPL----PLLRDPELAALLRALFRLL--EEAGRSDDLLAEALLYQL 133
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
23-274 6.47e-21

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 89.07  E-value: 6.47e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479  23 RFSFPRHFHLEYHIGLLLQGRHRYAAGGERRLAGAGDALLMAPESIHDGSSAGEEGYRIRVLALDADWLERASRDFSDGR 102
Cdd:COG2207    2 RLLILLLLLLLLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479 103 RGAPRLTSSLVRDERLQQRLRQLHLGMLGGAAALENRLALEEHLWQALACLLSLGSSLRLEEGDREGFGQRDWTRLRDWL 182
Cdd:COG2207   82 LLALLALLLLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLL 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479 183 ESRLEYPPNLEELAAFCGLSPWQVLRRFRRHCGLPPHQWLTQLRLERALPLVLRGEQPLSQVAQQFGFYDQAHFSRLFRR 262
Cdd:COG2207  162 LLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKK 241

                        250
                 ....*....|..
gi 489188479 263 TYGLPPARLRQR 274
Cdd:COG2207  242 RFGVTPSEYRKR 253
HTH_18 pfam12833
Helix-turn-helix domain;
195-274 1.02e-20

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 83.79  E-value: 1.02e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479  195 LAAFCGLSPWQVLRRFRRHCGLPPHQWLTQLRLERALPLVLR-GEQPLSQVAQQFGFYDQAHFSRLFRRTYGLPPARLRQ 273
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEdTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 489188479  274 R 274
Cdd:pfam12833  81 R 81
ftrA PRK09393
transcriptional activator FtrA; Provisional
 177-274 3.19e-12

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 65.37  E-value: 3.19e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479 177 RLRDWLESRLEYPPNLEELAAFCGLSPWQVLRRFRRHCGLPPHQWLTQLRLERALPLVLRGEQPLSQVAQQFGFYDQAHF 256
Cdd:PRK09393 222 PLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAERAGFGSEESL 301

                         90
                 ....*....|....*...
gi 489188479 257 SRLFRRTYGLPPARLRQR 274
Cdd:PRK09393 302 RHHFRRRAATSPAAYRKR 319
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 192-268 5.54e-09

YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only one protein with the YSIRK variant form of signal peptide (TIGR01168) were examined for conserved genes near that one tagged protein. This protein is found adjacent to at various classes of repetitive or low-complexity YSIRK proteins (whether unique in genome or not), in a range of species (Enterococcus faecalis X98, Ruminococcus torques, Coprobacillus sp. D7, Lysinibacillus fusiformis ZC1, Streptococcus equi subsp. equi 4047, etc). The affliated YSIRK proteins include Streptococcal protective antigen (see ) and proteins with the Rib/alpha/Esp surface antigen repeat (see TIGR02331). The last quarter of this protein has an AraC family helix-turn-helix (HTH)transcriptional regulator domain.


Pssm-ID: 274977 [Multi-domain]  Cd Length: 383  Bit Score: 56.22  E-value: 5.54e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489188479  192 LEELAAFCGLSPWQVLRRFRRHCGLPPHQWLTQLRLERAlPLVLRGEQPLSQVAQQFGFYDQAHFSRLFRRTYGLPP 268
Cdd:TIGR04094 304 VEEIAKQFFMSESKLRKLFKKEMGISIQEYISKRKIEEA-KYLLRSQIPVSEVSNELGFYDLSHFSRTFKKHTGVSP 379
cupin_YbfI-like_N cd07001
AraC/XylS family transcriptional regulators similar to Bacillus subtilis YbfI, N-terminal ...
 25-69 5.52e-04

AraC/XylS family transcriptional regulators similar to Bacillus subtilis YbfI, 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, including YbfI, an uncharacterized Bacillus subtilis. In Pseudomonas putida, this protein is thought to regulate the expression of phenylserine aldolase. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380405 [Multi-domain]  Cd Length: 76  Bit Score: 37.76  E-value: 5.52e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 489188479  25 SFPRHFHLEYHIGLLLQGRHRYAAGGERRLAGAGDALLMAPESIH 69
Cdd:cd07001   14 SFPNHFHDFYVIGFIESGQRTLFCEGKEYTVEPGDLLLINPRDVH 58
 
Name Accession Description Interval E-value
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 177-274 4.10e-26

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: 104.08  E-value: 4.10e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479 177 RLRDWLESRLEYPPNLEELAAFCGLSPWQVLRRFRRHCGLPPHQWLTQLRLERALPLVLRGEQPLSQVAQQFGFYDQAHF 256
Cdd:COG4977  214 RAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHF 293

                         90
                 ....*....|....*...
gi 489188479 257 SRLFRRTYGLPPARLRQR 274
Cdd:COG4977  294 RRAFRRRFGVSPSAYRRR 311
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
189-272 1.28e-24

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 93.77  E-value: 1.28e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479   189 PPNLEELAAFCGLSPWQVLRRFRRHCGLPPHQWLTQLRLERALPLVLRGEQPLSQVAQQFGFYDQAHFSRLFRRTYGLPP 268
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 489188479   269 ARLR 272
Cdd:smart00342  81 SEYR 84
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 12-149 1.27e-23

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: 92.88  E-value: 1.27e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479   12 PGVRLIDAEHNRFSFPRHFHLEYHIGLLLQGRHRYAAGGERRLAGAGDALLMAPESIHDGSSAGEEGYRIRVLALDADWL 91
Cdd:pfam02311   2 PGLEGIEARYPGHSFPPHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESEDGWRYRWLYFEPELL 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 489188479   92 ERASRDFSDGRRGAPrltsSLVRDERLQQRLRQLHLGMlgGAAALENRLALEEHLWQA 149
Cdd:pfam02311  82 ERILADISILAGGPL----PLLRDPELAALLRALFRLL--EEAGRSDDLLAEALLYQL 133
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
23-274 6.47e-21

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 89.07  E-value: 6.47e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479  23 RFSFPRHFHLEYHIGLLLQGRHRYAAGGERRLAGAGDALLMAPESIHDGSSAGEEGYRIRVLALDADWLERASRDFSDGR 102
Cdd:COG2207    2 RLLILLLLLLLLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479 103 RGAPRLTSSLVRDERLQQRLRQLHLGMLGGAAALENRLALEEHLWQALACLLSLGSSLRLEEGDREGFGQRDWTRLRDWL 182
Cdd:COG2207   82 LLALLALLLLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLL 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479 183 ESRLEYPPNLEELAAFCGLSPWQVLRRFRRHCGLPPHQWLTQLRLERALPLVLRGEQPLSQVAQQFGFYDQAHFSRLFRR 262
Cdd:COG2207  162 LLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKK 241

                        250
                 ....*....|..
gi 489188479 263 TYGLPPARLRQR 274
Cdd:COG2207  242 RFGVTPSEYRKR 253
HTH_18 pfam12833
Helix-turn-helix domain;
195-274 1.02e-20

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 83.79  E-value: 1.02e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479  195 LAAFCGLSPWQVLRRFRRHCGLPPHQWLTQLRLERALPLVLR-GEQPLSQVAQQFGFYDQAHFSRLFRRTYGLPPARLRQ 273
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEdTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 489188479  274 R 274
Cdd:pfam12833  81 R 81
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 176-274 1.15e-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: 70.08  E-value: 1.15e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479 176 TRLRDWLESRLEYPPNLEELAAFCGLSPWQVLRRFRRHCGLPPHQWLTQLRLERALPLvLRGEQPLSQVAQQFGFYDQAH 255
Cdd:COG2169   87 ARACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQL-LQTGLSVTDAAYAAGFGSLSR 165

                         90
                 ....*....|....*....
gi 489188479 256 FSRLFRRTYGLPPARLRQR 274
Cdd:COG2169  166 FYEAFKKLLGMTPSAYRRG 184
ftrA PRK09393
transcriptional activator FtrA; Provisional
 177-274 3.19e-12

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 65.37  E-value: 3.19e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479 177 RLRDWLESRLEYPPNLEELAAFCGLSPWQVLRRFRRHCGLPPHQWLTQLRLERALPLVLRGEQPLSQVAQQFGFYDQAHF 256
Cdd:PRK09393 222 PLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAERAGFGSEESL 301

                         90
                 ....*....|....*...
gi 489188479 257 SRLFRRTYGLPPARLRQR 274
Cdd:PRK09393 302 RHHFRRRAATSPAAYRKR 319
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
180-272 5.23e-11

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 58.96  E-value: 5.23e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479 180 DWLESRLEYPPNLEELAAFCGLSPWQVLRRFRRHCGLPPHQWLTQLRLERALPLVLRGEQPLSQVAQQFGFYDQAHFSRL 259
Cdd:PRK11511  16 DWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRT 95

                         90
                 ....*....|...
gi 489188479 260 FRRTYGLPPARLR 272
Cdd:PRK11511  96 FKNYFDVPPHKYR 108
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
177-273 5.24e-11

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 61.62  E-value: 5.24e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479 177 RLRDWLESRLEYPPNLEELAAFCGLSPWQVLRRFRRHCGLPPHQWLTQLRLERALPLVLRGEQPLSQVAQQFGFYDQAHF 256
Cdd:PRK13503 175 QLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFGDSNHF 254

                         90
                 ....*....|....*..
gi 489188479 257 SRLFRRTYGLPPARLRQ 273
Cdd:PRK13503 255 STLFRREFSWSPRDIRQ 271
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
178-274 6.71e-11

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 58.01  E-value: 6.71e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479 178 LRDWLESRLEYPPNLEELAAFCGLSPWQVLRRFRRHCGLPPHQWLTQLRLERALPLVLRGEQPLSQVAQQFGFYDQAHFS 257
Cdd:PRK10219  10 LIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFS 89

                         90
                 ....*....|....*..
gi 489188479 258 RLFRRTYGLPPARLRQR 274
Cdd:PRK10219  90 RVFRRQFDRTPSDYRHR 106
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 192-268 5.54e-09

YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only one protein with the YSIRK variant form of signal peptide (TIGR01168) were examined for conserved genes near that one tagged protein. This protein is found adjacent to at various classes of repetitive or low-complexity YSIRK proteins (whether unique in genome or not), in a range of species (Enterococcus faecalis X98, Ruminococcus torques, Coprobacillus sp. D7, Lysinibacillus fusiformis ZC1, Streptococcus equi subsp. equi 4047, etc). The affliated YSIRK proteins include Streptococcal protective antigen (see ) and proteins with the Rib/alpha/Esp surface antigen repeat (see TIGR02331). The last quarter of this protein has an AraC family helix-turn-helix (HTH)transcriptional regulator domain.


Pssm-ID: 274977 [Multi-domain]  Cd Length: 383  Bit Score: 56.22  E-value: 5.54e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489188479  192 LEELAAFCGLSPWQVLRRFRRHCGLPPHQWLTQLRLERAlPLVLRGEQPLSQVAQQFGFYDQAHFSRLFRRTYGLPP 268
Cdd:TIGR04094 304 VEEIAKQFFMSESKLRKLFKKEMGISIQEYISKRKIEEA-KYLLRSQIPVSEVSNELGFYDLSHFSRTFKKHTGVSP 379
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
192-274 5.43e-08

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 52.67  E-value: 5.43e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479 192 LEELAAFCGLSPWQVLRRFRRHCGLPPHQWLTQLRLERALPLVLRGEQPLSQVAQQFGFYDQAHFSRLFRRTYGLPPARL 271
Cdd:PRK10572 202 IESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEF 281


                 ...
gi 489188479 272 RQR 274
Cdd:PRK10572 282 RAR 284
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
194-274 1.43e-07

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 51.44  E-value: 1.43e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479 194 ELAAFC---GLSPWQVLRRFRRHCGLPPHQWLTQLRLERALPLVLRGEQPLSQVAQQFGFYDQAHFSRLFRRTYGLPPAR 270
Cdd:PRK13501 194 DMADFChknQLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSNYFSAVFTREAGMTPRD 273


                 ....
gi 489188479 271 LRQR 274
Cdd:PRK13501 274 YRQR 277
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
182-273 2.02e-05

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 45.05  E-value: 2.02e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479 182 LESRLEYPPNLEelaAFCGLSPW--QVLRR-FRRHCGLPPHQWLTQLRLERALPLVLRGEQPLSQVAQQFGFYDQAHFSR 258
Cdd:PRK13502 185 LANSLECPFALD---AFCQQEQCseRVLRQqFRAQTGMTINQYLRQVRICHAQYLLQHSPLMISEISMQCGFEDSNYFSV 261

                         90
                 ....*....|....*
gi 489188479 259 LFRRTYGLPPARLRQ 273
Cdd:PRK13502 262 VFTRETGMTPSQWRH 276
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
24-81 2.59e-05

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 42.14  E-value: 2.59e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489188479  24 FSFPRHFHLEYHIGLLLQGRHRYAAGGERRLAGAGDALLMAPESIHDGSSAGEEGYRI 81
Cdd:COG1917   34 ARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDEPAVL 91
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
182-273 1.36e-04

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 42.78  E-value: 1.36e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479 182 LESRLEYPPNLEELAAFCGLSPWQVLRRFRRHCGLPPHQWLTQLRLERALPLVLRGEQPLSQVAQQFGFYDQAHFSRLFR 261
Cdd:PRK13500 215 LAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVFT 294

                         90
                 ....*....|..
gi 489188479 262 RTYGLPPARLRQ 273
Cdd:PRK13500 295 RETGMTPSQWRH 306
PRK15121 PRK15121
MDR efflux pump AcrAB transcriptional activator RobA;
178-272 1.45e-04

MDR efflux pump AcrAB transcriptional activator RobA;


Pssm-ID: 185076 [Multi-domain]  Cd Length: 289  Bit Score: 42.30  E-value: 1.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479 178 LRD---WLESRLEYPPNLEELAAFCGLSPWQVLRRFRRHCGLPPHQWLTQLRLER---ALPLVLRgeqPLSQVAQQFGFY 251
Cdd:PRK15121   7 IRDlliWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKaavALRLTSR---PILDIALQYRFD 83

                         90       100
                 ....*....|....*....|.
gi 489188479 252 DQAHFSRLFRRTYGLPPARLR 272
Cdd:PRK15121  84 SQQTFTRAFKKQFAQTPALYR 104
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 190-274 2.45e-04

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 41.94  E-value: 2.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489188479 190 PNL--EELAAFCGLSPWQVLRRFRRHcGLPPHQWLTQLRLER---ALPLVLRGEQpLSQVAQQFGFYDQAHFSRLFRRTY 264
Cdd:PRK09685 213 EILrpEWIAGELGISVRSLYRLFAEQ-GLVVAQYIRNRRLDRcadDLRPAADDEK-ITSIAYKWGFSDSSHFSTAFKQRF 290

                         90
                 ....*....|
gi 489188479 265 GLPPARLRQR 274
Cdd:PRK09685 291 GVSPGEYRRK 300
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 241-273 5.32e-04

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


Pssm-ID: 425497 [Multi-domain]  Cd Length: 42  Bit Score: 36.75  E-value: 5.32e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 489188479  241 LSQVAQQFGFyDQAHFSRLFRRTYGLPPARLRQ 273
Cdd:pfam00165  11 IADIADELGF-SRSYFSRLFKKYTGVTPSQYRH 42
cupin_YbfI-like_N cd07001
AraC/XylS family transcriptional regulators similar to Bacillus subtilis YbfI, N-terminal ...
 25-69 5.52e-04

AraC/XylS family transcriptional regulators similar to Bacillus subtilis YbfI, 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, including YbfI, an uncharacterized Bacillus subtilis. In Pseudomonas putida, this protein is thought to regulate the expression of phenylserine aldolase. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380405 [Multi-domain]  Cd Length: 76  Bit Score: 37.76  E-value: 5.52e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 489188479  25 SFPRHFHLEYHIGLLLQGRHRYAAGGERRLAGAGDALLMAPESIH 69
Cdd:cd07001   14 SFPNHFHDFYVIGFIESGQRTLFCEGKEYTVEPGDLLLINPRDVH 58
cupin_KdgF cd02238
pectin degradation protein KdgF and related proteins, cupin domain; This family includes ...
 26-78 5.73e-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: 35.52  E-value: 5.73e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 489188479  26 FPRHFHLEYHIGLLLQGRHRYAAGGERRLAGAGDALLMAPESIHdGSSAGEEG 78
Cdd:cd02238   40 VPLHSHPHEQIGYVLSGRFEFTIGGETRILKPGDSYYIPPNVPH-GAEALEDS 91
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 201-274 5.84e-03

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 37.60  E-value: 5.84e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489188479 201 LSPwQVLRRFRRHCGLPPHQWLTQLRLERALPLVLRGEQPLSQVAQQFGFYDQAHFSRLFRRTYGLPPARLRQR 274
Cdd:PRK09978 170 MSP-SLLKKKLREEETSYSQLLTECRMQRALQLIVIHGFSIKRVAVSCGYHSVSYFIYVFRNYYGMTPTEYQER 242
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 182-223 6.02e-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: 34.05  E-value: 6.02e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 489188479  182 LESRLEYPPNLEELAAFCGLSPWQVLRRFRRHCGLPPHQWLT 223
Cdd:pfam00165   1 LRENLSTNLTIADIADELGFSRSYFSRLFKKYTGVTPSQYRH 42
cupin_BLL4011-like cd02235
Bradyrhizobium diazoefficiens BLL4011 and related proteins, cupin domain; This family includes ...
 27-81 8.03e-03

Bradyrhizobium diazoefficiens BLL4011 and related proteins, cupin domain; This family includes bacterial and fungal proteins homologous to BLL4011, a Bradyrhizobium diazoefficiens protein of unknown function. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380363 [Multi-domain]  Cd Length: 100  Bit Score: 35.25  E-value: 8.03e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 489188479  27 PRHFHLEYHIGLLLQGRHRYAAGGE-RRLAGAGDALLMAPESIHDGSSAGEEGYRI 81
Cdd:cd02235   33 GRHTHPGEESGYVLEGSLELEVDGQpPVTLKAGDSFFIPAGTVHNAKNVGSGPAKL 88
 
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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