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Conserved domains on  [gi|496047562|ref|WP_008772069|]
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MULTISPECIES: GyrI-like domain-containing protein [Parabacteroides]

Protein Classification

GyrI-like domain-containing protein( domain architecture ID 10007405)

GyrI-like domain-containing protein adopts a beta-barrel fold similar to the effector-binding region of AraC/XylS transcription activators and may bind a small molecule; similar to Escherichia coli probable transcriptional regulator YgiV

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SbmC COG3449
DNA gyrase inhibitor GyrI/SbmC [Replication, recombination and repair];
1-280 1.51e-45

DNA gyrase inhibitor GyrI/SbmC [Replication, recombination and repair];


:

Pssm-ID: 442672 [Multi-domain]  Cd Length: 286  Bit Score: 155.02  E-value: 1.51e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562   1 MKPDTENIYQRKINQVIDYINANLHLPLRLDIIAGQVNVSERQLLRIMKGALNESLYAYVARQRVERAVLYMHTEDMSLA 80
Cdd:COG3449    3 KLRTREADQRRRILLVLIALHDDLDLLLLALLLAFAFHFFFFHRRRRFRALIGRRARLLLRRRLLAALALLLLSSSAIIA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562  81 DLASRVGYDNPQSFSKAFKKQFSVSPKAYMDKLRARLREET-EKWSNPHDLEVEVCEVDDLDLVYIRIFGKYGEaepYEE 159
Cdd:COG3449   83 AAAAASGYSSSASFRRFFRAFGGSSRSRRRRAKAKLLALPPlDPPRLEPMMDVEIKELPPRRVAYLRHRGPYEE---IGE 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562 160 AWNLLIGFLKENQALSEDTRFIGLSFDDPNVTHPDQCRFYACASVGKEIIPSGMFGTIRLQKGKYAVYTLKGSYAGLQEL 239
Cdd:COG3449  160 AFERLIAWAKARGLLPPDSRTIGIYYDDPDITPPEKLRYDACVTVPEDVALPGGVEVKTIPGGRYAVLRHKGPYEDLGAA 239

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 496047562 240 YNTINIDF----NYTKRHGMAFEEYVSYSEEDDDTQ-VTKIYIPIK 280
Cdd:COG3449  240 WDWLYGEWlpasGYELRDRPCFEIYLNDPRETPEGElITDIYLPLK 285
 
Name Accession Description Interval E-value
SbmC COG3449
DNA gyrase inhibitor GyrI/SbmC [Replication, recombination and repair];
1-280 1.51e-45

DNA gyrase inhibitor GyrI/SbmC [Replication, recombination and repair];


Pssm-ID: 442672 [Multi-domain]  Cd Length: 286  Bit Score: 155.02  E-value: 1.51e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562   1 MKPDTENIYQRKINQVIDYINANLHLPLRLDIIAGQVNVSERQLLRIMKGALNESLYAYVARQRVERAVLYMHTEDMSLA 80
Cdd:COG3449    3 KLRTREADQRRRILLVLIALHDDLDLLLLALLLAFAFHFFFFHRRRRFRALIGRRARLLLRRRLLAALALLLLSSSAIIA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562  81 DLASRVGYDNPQSFSKAFKKQFSVSPKAYMDKLRARLREET-EKWSNPHDLEVEVCEVDDLDLVYIRIFGKYGEaepYEE 159
Cdd:COG3449   83 AAAAASGYSSSASFRRFFRAFGGSSRSRRRRAKAKLLALPPlDPPRLEPMMDVEIKELPPRRVAYLRHRGPYEE---IGE 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562 160 AWNLLIGFLKENQALSEDTRFIGLSFDDPNVTHPDQCRFYACASVGKEIIPSGMFGTIRLQKGKYAVYTLKGSYAGLQEL 239
Cdd:COG3449  160 AFERLIAWAKARGLLPPDSRTIGIYYDDPDITPPEKLRYDACVTVPEDVALPGGVEVKTIPGGRYAVLRHKGPYEDLGAA 239

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 496047562 240 YNTINIDF----NYTKRHGMAFEEYVSYSEEDDDTQ-VTKIYIPIK 280
Cdd:COG3449  240 WDWLYGEWlpasGYELRDRPCFEIYLNDPRETPEGElITDIYLPLK 285
GyrI-like pfam06445
GyrI-like small molecule binding domain; This family contains the small molecule binding ...
 131-279 4.22e-24

GyrI-like small molecule binding domain; This family contains the small molecule binding domain of a number of different bacterial transcription activators. This family also contains DNA gyrase inhibitors. The GyrI superfamily contains a diad of the SHS2 module, adapted for small-molecule binding. The GyrI superfamily includes a family of secreted forms that is found only in animals and the bacterial pathogen Leptospira.


Pssm-ID: 428947  Cd Length: 153  Bit Score: 94.78  E-value: 4.22e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562  131 EVEVCEVDDLDLVYIRIFGKYGEaEPYEEAWNLLIGFLKENQALSEDTRFIGLSFDDPNVTHPDQCRFYACASVGKEIIP 210
Cdd:pfam06445   1 EVEIVELPAFRVAGLRHRGPYNE-EGIGALWEELCAWASENGLSPAPSPLIGVSYDDPEVTEDEELRYDAGVAVPIPVEG 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 496047562  211 SGMFGTIRLQKGKYAVYTLKGSYAGLQELYNTINIDF----NYTKRHGMAFEEYVS-YSEEDDDTQVTKIYIPI 279
Cdd:pfam06445  80 PEGVEELELPGGEYAVFRHKGPYDDLQETYAKIYGEWlpesGYERRDGPSFEIYLNdPREVPEEELKTEIYIPV 153
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
27-110 1.49e-22

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 88.76  E-value: 1.49e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562    27 PLRLDIIAGQVNVSERQLLRIMKGALNESLYAYVARQRVERAVLYMHTEDMSLADLASRVGYDNPQSFSKAFKKQFSVSP 106
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 496047562   107 KAYM 110
Cdd:smart00342  81 SEYR 84
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
12-119 2.79e-15

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 74.24  E-value: 2.79e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562  12 KINQVIDYINANLHLPLRLDIIAGQVNVSERQLLRIMKGALNESLYAYVARQRVERAVLYMHTEDMSLADLASRVGYDNP 91
Cdd:PRK10572 184 RVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQ 263

                         90       100
                 ....*....|....*....|....*...
gi 496047562  92 QSFSKAFKKQFSVSPKAYmdklRARLRE 119
Cdd:PRK10572 264 LYFSRVFKKCTGASPSEF----RARCEE 287
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 13-109 2.39e-13

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: 69.32  E-value: 2.39e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562   13 INQVIDYINANLHLPLRLDIIAGQVNVSERQLLRIMKGALNESLYAYVARQRVERAVlYMHTEDMSLADLASRVGYDNPQ 92
Cdd:TIGR04094 287 IRAVIQYINLNLYDPLKVEEIAKQFFMSESKLRKLFKKEMGISIQEYISKRKIEEAK-YLLRSQIPVSEVSNELGFYDLS 365

                          90
                  ....*....|....*..
gi 496047562   93 SFSKAFKKQFSVSPKAY 109
Cdd:TIGR04094 366 HFSRTFKKHTGVSPKQY 382
 
Name Accession Description Interval E-value
SbmC COG3449
DNA gyrase inhibitor GyrI/SbmC [Replication, recombination and repair];
1-280 1.51e-45

DNA gyrase inhibitor GyrI/SbmC [Replication, recombination and repair];


Pssm-ID: 442672 [Multi-domain]  Cd Length: 286  Bit Score: 155.02  E-value: 1.51e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562   1 MKPDTENIYQRKINQVIDYINANLHLPLRLDIIAGQVNVSERQLLRIMKGALNESLYAYVARQRVERAVLYMHTEDMSLA 80
Cdd:COG3449    3 KLRTREADQRRRILLVLIALHDDLDLLLLALLLAFAFHFFFFHRRRRFRALIGRRARLLLRRRLLAALALLLLSSSAIIA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562  81 DLASRVGYDNPQSFSKAFKKQFSVSPKAYMDKLRARLREET-EKWSNPHDLEVEVCEVDDLDLVYIRIFGKYGEaepYEE 159
Cdd:COG3449   83 AAAAASGYSSSASFRRFFRAFGGSSRSRRRRAKAKLLALPPlDPPRLEPMMDVEIKELPPRRVAYLRHRGPYEE---IGE 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562 160 AWNLLIGFLKENQALSEDTRFIGLSFDDPNVTHPDQCRFYACASVGKEIIPSGMFGTIRLQKGKYAVYTLKGSYAGLQEL 239
Cdd:COG3449  160 AFERLIAWAKARGLLPPDSRTIGIYYDDPDITPPEKLRYDACVTVPEDVALPGGVEVKTIPGGRYAVLRHKGPYEDLGAA 239

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 496047562 240 YNTINIDF----NYTKRHGMAFEEYVSYSEEDDDTQ-VTKIYIPIK 280
Cdd:COG3449  240 WDWLYGEWlpasGYELRDRPCFEIYLNDPRETPEGElITDIYLPLK 285
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 11-118 1.30e-25

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: 102.93  E-value: 1.30e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562  11 RKINQVIDYINANLHLPLRLDIIAGQVNVSERQLLRIMKGALNESLYAYVARQRVERAVLYMHTEDMSLADLASRVGYDN 90
Cdd:COG4977  210 PRLARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGS 289

                         90       100
                 ....*....|....*....|....*...
gi 496047562  91 PQSFSKAFKKQFSVSPKAYMDKLRARLR 118
Cdd:COG4977  290 ASHFRRAFRRRFGVSPSAYRRRFRARAA 317
GyrI-like pfam06445
GyrI-like small molecule binding domain; This family contains the small molecule binding ...
 131-279 4.22e-24

GyrI-like small molecule binding domain; This family contains the small molecule binding domain of a number of different bacterial transcription activators. This family also contains DNA gyrase inhibitors. The GyrI superfamily contains a diad of the SHS2 module, adapted for small-molecule binding. The GyrI superfamily includes a family of secreted forms that is found only in animals and the bacterial pathogen Leptospira.


Pssm-ID: 428947  Cd Length: 153  Bit Score: 94.78  E-value: 4.22e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562  131 EVEVCEVDDLDLVYIRIFGKYGEaEPYEEAWNLLIGFLKENQALSEDTRFIGLSFDDPNVTHPDQCRFYACASVGKEIIP 210
Cdd:pfam06445   1 EVEIVELPAFRVAGLRHRGPYNE-EGIGALWEELCAWASENGLSPAPSPLIGVSYDDPEVTEDEELRYDAGVAVPIPVEG 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 496047562  211 SGMFGTIRLQKGKYAVYTLKGSYAGLQELYNTINIDF----NYTKRHGMAFEEYVS-YSEEDDDTQVTKIYIPI 279
Cdd:pfam06445  80 PEGVEELELPGGEYAVFRHKGPYDDLQETYAKIYGEWlpesGYERRDGPSFEIYLNdPREVPEEELKTEIYIPV 153
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
24-116 1.59e-23

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 96.39  E-value: 1.59e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562  24 LHLPLRLDIIAGQVNVSERQLLRIMKGALNESLYAYVARQRVERAVLYMHTEDMSLADLASRVGYDNPQSFSKAFKKQFS 103
Cdd:COG2207  165 LLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFG 244

                         90
                 ....*....|...
gi 496047562 104 VSPKAYMDKLRAR 116
Cdd:COG2207  245 VTPSEYRKRLRAR 257
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
27-110 1.49e-22

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 88.76  E-value: 1.49e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562    27 PLRLDIIAGQVNVSERQLLRIMKGALNESLYAYVARQRVERAVLYMHTEDMSLADLASRVGYDNPQSFSKAFKKQFSVSP 106
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 496047562   107 KAYM 110
Cdd:smart00342  81 SEYR 84
AraC_E_bind smart00871
Bacterial transcription activator, effector binding domain; This domain is found in the ...
 131-280 1.73e-22

Bacterial transcription activator, effector binding domain; This domain is found in the probable effector binding domain of a number of different bacterial transcription activators.and is also present in some DNA gyrase inhibitors. The absence of a HTH motif in the DNA gyrase inhibitors is thought to indicate the fact that these do not bind DNA.


Pssm-ID: 214874 [Multi-domain]  Cd Length: 158  Bit Score: 91.00  E-value: 1.73e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562   131 EVEVCEVDDLDLVYIRIFGKYGEAEpYEEAWNLLIGFLKENQALSE--DTRFIGLSFDDPNVTHPDQCRFYACASVGKEI 208
Cdd:smart00871   1 EVRIVELPAFKVAGLRHRGPNEDEK-IPELWQRLIQWAKELGLLPVgnSGEPYGVYYDDPDDTPDGEFRYDAGVEVSDEV 79

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 496047562   209 IPSGMFGTIRLQKGKYAVYTLKG-SYAGLQE----LYNTINIDFNYTKRHGMAFEEY--VSYSEEDDDTQVTKIYIPIK 280
Cdd:smart00871  80 EAPEGVETKTIPAGKYAVFTHKGgSYDEIQEaweaIYGEWLPNSGYELRDAGPDFEVylNDPPDTDPEELVTEIYIPVK 158
HTH_18 pfam12833
Helix-turn-helix domain;
33-109 6.16e-20

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 81.87  E-value: 6.16e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 496047562   33 IAGQVNVSERQLLRIMKGALNESLYAYVARQRVERAV-LYMHTEDMSLADLASRVGYDNPQSFSKAFKKQFSVSPKAY 109
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARrLLLEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEY 78
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
12-119 2.79e-15

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 74.24  E-value: 2.79e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562  12 KINQVIDYINANLHLPLRLDIIAGQVNVSERQLLRIMKGALNESLYAYVARQRVERAVLYMHTEDMSLADLASRVGYDNP 91
Cdd:PRK10572 184 RVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQ 263

                         90       100
                 ....*....|....*....|....*...
gi 496047562  92 QSFSKAFKKQFSVSPKAYmdklRARLRE 119
Cdd:PRK10572 264 LYFSRVFKKCTGASPSEF----RARCEE 287
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
8-109 8.37e-15

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 68.80  E-value: 8.37e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562   8 IYQRKINQVIDYINANLHLPLRLDIIAGQVNVSERQLLRIMKGALNESLYAYVARQRVERAVLYMHTEDMSLADLASRVG 87
Cdd:PRK10219   2 SHQKIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLG 81

                         90       100
                 ....*....|....*....|..
gi 496047562  88 YDNPQSFSKAFKKQFSVSPKAY 109
Cdd:PRK10219  82 YVSQQTFSRVFRRQFDRTPSDY 103
ftrA PRK09393
transcriptional activator FtrA; Provisional
 11-118 1.32e-13

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 69.61  E-value: 1.32e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562  11 RKINQVIDYINANLHLPLRLDIIAGQVNVSERQLLRIMKGALNESLYAYVARQRVERAVLYMHTEDMSLADLASRVGYDN 90
Cdd:PRK09393 218 DRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAERAGFGS 297

                         90       100
                 ....*....|....*....|....*...
gi 496047562  91 PQSFSKAFKKQFSVSPKAYmdklRARLR 118
Cdd:PRK09393 298 EESLRHHFRRRAATSPAAY----RKRFG 321
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 13-109 2.39e-13

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: 69.32  E-value: 2.39e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562   13 INQVIDYINANLHLPLRLDIIAGQVNVSERQLLRIMKGALNESLYAYVARQRVERAVlYMHTEDMSLADLASRVGYDNPQ 92
Cdd:TIGR04094 287 IRAVIQYINLNLYDPLKVEEIAKQFFMSESKLRKLFKKEMGISIQEYISKRKIEEAK-YLLRSQIPVSEVSNELGFYDLS 365

                          90
                  ....*....|....*..
gi 496047562   93 SFSKAFKKQFSVSPKAY 109
Cdd:TIGR04094 366 HFSRTFKKHTGVSPKQY 382
Cass2 pfam14526
Integron-associated effector binding protein; This family contains Cass2 from Vibrio cholerae, ...
 133-279 2.85e-12

Integron-associated effector binding protein; This family contains Cass2 from Vibrio cholerae, an integron-associated protein that has been shown to bind cationic drug compounds with submicromolar affinity. Cass2 has been proposed to be representative of a larger family of independent effector-binding proteins associated with lateral gene transfer within Vibrio and other closely-related species.


Pssm-ID: 434016 [Multi-domain]  Cd Length: 149  Bit Score: 63.14  E-value: 2.85e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562  133 EVCEVDDLDLVYIRIFGKYGEAEPYEEAWNLLIGFLKENQ--ALSEDTRFIGLSFDDPNVThpDQCRFYACASVGKEIIP 210
Cdd:pfam14526   1 EIVELPSFTVAGIRYEGPNEYEDHNKEIGKFWEEFNEDGRlpNIKKDDKSYGIYVDYEDEE--NEFDYYAGVEVPSFSEL 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 496047562  211 SGMFGTIRLQKGKYAVYTLKGSYAGL-----QELYNTINIDFNYTKRHGMAFEEYVsySEEDDDTQVTkIYIPI 279
Cdd:pfam14526  79 PEGLVVIEIPGGKYAVFTIEGDFPDAiaeawTRIYGWLLPNSGYERAGGPDFEVYK--ENGDENMKIE-LYIPV 149
PRK15121 PRK15121
MDR efflux pump AcrAB transcriptional activator RobA;
13-280 3.22e-12

MDR efflux pump AcrAB transcriptional activator RobA;


Pssm-ID: 185076 [Multi-domain]  Cd Length: 289  Bit Score: 65.41  E-value: 3.22e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562  13 INQVIDYINANLHLPLRLDIIAGQVNVSERQLLRIMKGALNESLYAYVARQRVERAVLYMHTEDMSLADLASRVGYDNPQ 92
Cdd:PRK15121   7 IRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKAAVALRLTSRPILDIALQYRFDSQQ 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562  93 SFSKAFKKQFSVSPKAYmdklraRLREEtekWSN-----PHDL------EVEVCEVDDLDLVyirifgkyGEAEPYE--- 158
Cdd:PRK15121  87 TFTRAFKKQFAQTPALY------RRSPE---WSAfgirpPIRLgeftlpEHEFVTLPETPLV--------GVTQSYScsl 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562 159 EAW---------NLLIGFLKENQALSEdtRFIGLSFDDPNVTHPD-QCRFYACAsVGKEIIPSGMFGT--IRLQKGKYAV 226
Cdd:PRK15121 150 EQIsdfrhemrvQFWRDFLGNAPTIPP--VLYGLHETRPSQEKDDeQEVFYTTA-LEPDQADGYVQTGhpVMLQGGEYVM 226

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 496047562 227 YTLKGSYAGLQE----LYNTINIDFNYTKRHGMAFEEYVSYSEEDDDTQVTKI----YIPIK 280
Cdd:PRK15121 227 FTYEGLGTGLQEfiltVYGTCMPMLNLTRRKGQDIERYYPAEDAKAGDRPINLrceyLIPIR 288
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 11-118 6.55e-12

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 64.67  E-value: 6.55e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562  11 RKINQVIDyinANLHLP-LRLDIIAGQVNVSERQLLRIMKGAlNESLYAYVARQRVER--AVLYMHTEDMSLADLASRVG 87
Cdd:PRK09685 200 QKVVALID---QSIQEEiLRPEWIAGELGISVRSLYRLFAEQ-GLVVAQYIRNRRLDRcaDDLRPAADDEKITSIAYKWG 275

                         90       100       110
                 ....*....|....*....|....*....|.
gi 496047562  88 YDNPQSFSKAFKKQFSVSPKAYmdklRARLR 118
Cdd:PRK09685 276 FSDSSHFSTAFKQRFGVSPGEY----RRKFR 302
BltR2 COG4978
GyrI-like small molecule binding domain [Signal transduction mechanisms];
132-275 1.37e-07

GyrI-like small molecule binding domain [Signal transduction mechanisms];


Pssm-ID: 444003  Cd Length: 144  Bit Score: 49.61  E-value: 1.37e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562 132 VEVCEVDDLDLVYIRIFGKYGEAEP-YEEAWNLLIGFLKENqalsedtrfiGLSFDDPNVTH-----PDQCRFYACASVG 205
Cdd:COG4978    1 VEVKELPAQPVASIRATVPMDELGElIGEAFGELFAYLAEN----------GIEPAGPPFAIyhdtdEDDVDVEVGVPVA 70

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 496047562 206 KEIIPSGMFGTIRLQKGKYAVYTLKGSYAGLQELYNTInidFNYTKRHG-----MAFEEYVS--YSEEDDDTQVTKI 275
Cdd:COG4978   71 GPLPGTGDIKVGTLPAGKAATATHRGPYDTLDEAYEAL---LAWIEENGlevagPPREVYLTdpGNEPDPEEWVTEI 144
YdeE COG3708
Predicted transcriptional regulator YdeE, contains AraC-type DNA-binding domain [Transcription] ...
 173-280 2.14e-07

Predicted transcriptional regulator YdeE, contains AraC-type DNA-binding domain [Transcription];


Pssm-ID: 442922  Cd Length: 157  Bit Score: 49.63  E-value: 2.14e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562 173 ALSEDTRFIGLSFDDPNVThpDQCRFYACASVGKEI-IPSGMfGTIRLQKGKYAVYTLKGSYA-GLQELYNTINIDF--- 247
Cdd:COG3708   48 NLSNPGGLYGVCTDYESDE--GEFDYLAGVEVSSFDeVPEGL-ETLEIPAGTYAVFTHKGPMPeALQETWQYIYSEWlps 124

                         90       100       110
                 ....*....|....*....|....*....|....
gi 496047562 248 -NYTKRHGMAFEEYVSYSEEDDDTQVtKIYIPIK 280
Cdd:COG3708  125 sGYERADGPDFEVYDERDDPSPDSEV-EIWIPIK 157
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 74-109 1.46e-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: 44.07  E-value: 1.46e-06
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 496047562   74 TEDMSLADLASRVGYDnPQSFSKAFKKQFSVSPKAY 109
Cdd:pfam00165   6 STNLTIADIADELGFS-RSYFSRLFKKYTGVTPSQY 40
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
24-125 1.08e-05

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 45.93  E-value: 1.08e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562  24 LHLPLRLDIIAGQVNVSERQLLRIMKGALNESLYAYVARQRVERAVLYMHTEDMSLADLASRVGYdNPQSFSKAFKKQFS 103
Cdd:COG2207  116 LLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARELGL-SPRTLSRLFKEETG 194

                         90       100
                 ....*....|....*....|....*..
gi 496047562 104 VSPKAYMDKLR-----ARLREETEKWS 125
Cdd:COG2207  195 TSPKQYLRELRlerakRLLAETDLSIS 221
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 65-120 1.73e-05

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: 45.43  E-value: 1.73e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562  65 VERAVLYMHT---EDMSLADLASRVGYDnPQSFSKAFKKQFSVSPKAYMDKLRA-RLREE 120
Cdd:COG2169   86 VARACRLIEAgaeDRPSLEDLAARLGLS-PRHLRRLFKAHTGVTPKAYARARRLlRARQL 144
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
11-107 1.38e-04

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 42.36  E-value: 1.38e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562  11 RKINQVIDYINANLHLPLRLDIIAGQVNVSERQLLRIMKGALNESLYAYVARQRVERAVLYMHTEDMSLADLASRVGYDN 90
Cdd:PRK13503 171 ARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFGD 250

                         90
                 ....*....|....*..
gi 496047562  91 PQSFSKAFKKQFSVSPK 107
Cdd:PRK13503 251 SNHFSTLFRREFSWSPR 267
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
3-109 4.81e-04

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 41.04  E-value: 4.81e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496047562   3 PDTEniyqrKINQVIDYINANLHLPLRLDIIAGQVNVSERQLLRIMKGALNESLYAYVARQRVERAVLYMHTEDMSLADL 82
Cdd:PRK13501 173 PDGE-----QLDLIMSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRISDI 247

                         90       100
                 ....*....|....*....|....*..
gi 496047562  83 ASRVGYDNPQSFSKAFKKQFSVSPKAY 109
Cdd:PRK13501 248 AARCGFEDSNYFSAVFTREAGMTPRDY 274
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
78-116 1.21e-03

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 37.15  E-value: 1.21e-03
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 496047562    78 SLADLASRVGYdNPQSFSKAFKKQFSVSPKAYMDKLRAR 116
Cdd:smart00342   3 TLEDLAEALGV-SPRHLQRLFKKETGTTPKQYLRDRRLE 40
 
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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