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Conserved domains on  [gi|1307851395|gb|AUD72012|]
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Transcriptional regulator LacI family [Bifidobacterium breve]

Protein Classification

LacI family DNA-binding transcriptional regulator( domain architecture ID 11446715)

LacI family DNA-binding transcriptional regulator functions as an activator or repressor by binding a specific effector ligand that either decreases (induction) or increases DNA-binding affinity (co-repression)

CATH:  3.40.50.2300
Gene Ontology:  GO:0003677|GO:0003700|GO:0006355
PubMed:  8543068|12598694

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PurR COG1609
DNA-binding transcriptional regulator, LacI/PurR family [Transcription];
1-350 2.37e-79

DNA-binding transcriptional regulator, LacI/PurR family [Transcription];


:

Pssm-ID: 441217 [Multi-domain]  Cd Length: 335  Bit Score: 245.88  E-value: 2.37e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395   1 MVGMRDVAKTAGVSLSTVSLVVNNTGYVSDDMRAKVEAAMRQLNYIPNELARNLYRNRTNTIGVIMPTIAHPFFATLTAH 80
Cdd:COG1609     3 RVTIKDVARLAGVSVATVSRVLNGPPRVSEETRERVLAAAEELGYRPNAAARSLRTGRTRTIGVVVPDLSNPFFAELLRG 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  81 LQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAAHTEHPGGY--WTSIHRPIVAFDRTL-GEGVPAVRSDH 157
Cdd:COG1609    83 IEEAARERGYQLLLANSDEDPEREREALRLLLSRRVDGLILAGSRLDDARLerLAEAGIPVVLIDRPLpDPGVPSVGVDN 162
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 158 EQGGQLIARQLIDSGARHVVLVGGPRSQFAeattfptiryhlTVERM------LDDAGIACD--YVEAGIVADICAHEAt 229
Cdd:COG1609   163 RAGARLATEHLIELGHRRIAFIGGPADSSS------------ARERLagyreaLAEAGLPPDpeLVVEGDFSAESGYEA- 229
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 230 ARAIFERYSDVDAIV-GSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRLTAVRQDFPAVAAALASRMDSQI 308
Cdd:COG1609   230 ARRLLARGPRPTAIFcANDLMALGALRALREAGLRVPEDVSVVGFDDIPLARYLTPPLTTVRQPIEEMGRRAAELLLDRI 309
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|..
gi 1307851395 309 aadngttsaaaaeggnavaANGGQSTSEDIISVTLIPGETTR 350
Cdd:COG1609   310 -------------------EGPDAPPERVLLPPELVVRESTA 332
 
Name Accession Description Interval E-value
PurR COG1609
DNA-binding transcriptional regulator, LacI/PurR family [Transcription];
1-350 2.37e-79

DNA-binding transcriptional regulator, LacI/PurR family [Transcription];


Pssm-ID: 441217 [Multi-domain]  Cd Length: 335  Bit Score: 245.88  E-value: 2.37e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395   1 MVGMRDVAKTAGVSLSTVSLVVNNTGYVSDDMRAKVEAAMRQLNYIPNELARNLYRNRTNTIGVIMPTIAHPFFATLTAH 80
Cdd:COG1609     3 RVTIKDVARLAGVSVATVSRVLNGPPRVSEETRERVLAAAEELGYRPNAAARSLRTGRTRTIGVVVPDLSNPFFAELLRG 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  81 LQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAAHTEHPGGY--WTSIHRPIVAFDRTL-GEGVPAVRSDH 157
Cdd:COG1609    83 IEEAARERGYQLLLANSDEDPEREREALRLLLSRRVDGLILAGSRLDDARLerLAEAGIPVVLIDRPLpDPGVPSVGVDN 162
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 158 EQGGQLIARQLIDSGARHVVLVGGPRSQFAeattfptiryhlTVERM------LDDAGIACD--YVEAGIVADICAHEAt 229
Cdd:COG1609   163 RAGARLATEHLIELGHRRIAFIGGPADSSS------------ARERLagyreaLAEAGLPPDpeLVVEGDFSAESGYEA- 229
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 230 ARAIFERYSDVDAIV-GSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRLTAVRQDFPAVAAALASRMDSQI 308
Cdd:COG1609   230 ARRLLARGPRPTAIFcANDLMALGALRALREAGLRVPEDVSVVGFDDIPLARYLTPPLTTVRQPIEEMGRRAAELLLDRI 309
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|..
gi 1307851395 309 aadngttsaaaaeggnavaANGGQSTSEDIISVTLIPGETTR 350
Cdd:COG1609   310 -------------------EGPDAPPERVLLPPELVVRESTA 332
PBP1_Qymf-like cd06291
ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing ...
61-348 1.56e-77

ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs; This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380514 [Multi-domain]  Cd Length: 264  Bit Score: 238.57  E-value: 1.56e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAAHTEHPGGYwTSIHRPIV 140
Cdd:cd06291     1 TIGLIVPDISNPFFAELAKYIEKELFKKGYKMILCNSNEDEEKEKEYLEMLKRNKVDGIILGSHSLDIEEY-KKLNIPIV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 141 AFDRTLGEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSqfaeatTFPTIRYHLTVERMLDDAGIACDYVEAGIV 220
Cdd:cd06291    80 SIDRYLSEGIPSVSSDNYQGGRLAAEHLIEKGCKKILHIGGPSN------NSPANERYRGFEDALKEAGIEYEIIEIDEN 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 221 A-DICAHEATARAIFERYSDVDAIVG-SDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRLTAVRQDFPAVAA 298
Cdd:cd06291   154 DfSEEDAYELAKELLEKYPDIDGIFAsNDLLAIGVLKALQKLGIRVPEDVQIIGFDGIEISELLYPELTTIRQPIEEMAK 233
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1307851395 299 ALASRMDSQIaadngttsaaaaeggnavaaNGGQSTSEDII-SVTLIPGET 348
Cdd:cd06291   234 EAVELLLKLI--------------------EGEEIEESRIVlPVELIERET 264
PRK10423 PRK10423
transcriptional repressor RbsR; Provisional
4-291 3.27e-35

transcriptional repressor RbsR; Provisional


Pssm-ID: 182448 [Multi-domain]  Cd Length: 327  Bit Score: 130.97  E-value: 3.27e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395   4 MRDVAKTAGVSLSTVSLVVNNTGYVSDDMRAKVEAAMRQLNYIPNELARNLYRNRTNTIGVIMPTIAHPFFATLTAHLQR 83
Cdd:PRK10423    1 MKDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSALARSLKLNQTRTIGMLITASTNPFYSELVRGVER 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  84 EFAARDLKTLLCSIadadkgEGEYVDM-------LQRHmMDGI-VMAAHTEHPGGywTSIHR----PIVAFDRTLGEGVP 151
Cdd:PRK10423   81 SCFERGYSLVLCNT------EGDEQRMnrnletlMQKR-VDGLlLLCTETHQPSR--EIMQRypsvPTVMMDWAPFDGDS 151
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 152 AVRSDHE-QGGQLIARQLIDSGARHVVLVGGPRSQfaeatTFPTIR---YHLTVER----MLDDAGIACDY-VEAGIVA- 221
Cdd:PRK10423  152 DLIQDNSlLGGDLATQYLIDKGYTRIACITGPLDK-----TPARLRlegYRAAMKRaglnIPDGYEVTGDFeFNGGFDAm 226
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1307851395 222 -DICAHEATARAIFerysdvdaiVGSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRLTAVRQ 291
Cdd:PRK10423  227 qQLLALPLRPQAVF---------TGNDAMAVGVYQALYQAGLSVPQDIAVIGYDDIELARYMTPPLTTIHQ 288
HTH_LACI smart00354
helix_turn _helix lactose operon repressor;
4-71 2.05e-27

helix_turn _helix lactose operon repressor;


Pssm-ID: 197675 [Multi-domain]  Cd Length: 70  Bit Score: 102.67  E-value: 2.05e-27
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1307851395    4 MRDVAKTAGVSLSTVSLVVNNTGYVSDDMRAKVEAAMRQLNYIPNELARNLYRNRTNTIGVIMPTIAH 71
Cdd:smart00354   3 IKDVARLAGVSKATVSRVLNGKGRVSEETREKVLAAMEELGYIPNRVARSLKGKKTKTIGLIVPDITN 70
LacI pfam00356
Bacterial regulatory proteins, lacI family;
4-48 6.46e-17

Bacterial regulatory proteins, lacI family;


Pssm-ID: 306791 [Multi-domain]  Cd Length: 46  Bit Score: 73.44  E-value: 6.46e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1307851395   4 MRDVAKTAGVSLSTVSLVVNNTGYVSDDMRAKVEAAMRQLNYIPN 48
Cdd:pfam00356   2 IKDVARLAGVSKSTVSRVLNNPGRVSEETRERVEAAMEELNYIPN 46
 
Name Accession Description Interval E-value
PurR COG1609
DNA-binding transcriptional regulator, LacI/PurR family [Transcription];
1-350 2.37e-79

DNA-binding transcriptional regulator, LacI/PurR family [Transcription];


Pssm-ID: 441217 [Multi-domain]  Cd Length: 335  Bit Score: 245.88  E-value: 2.37e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395   1 MVGMRDVAKTAGVSLSTVSLVVNNTGYVSDDMRAKVEAAMRQLNYIPNELARNLYRNRTNTIGVIMPTIAHPFFATLTAH 80
Cdd:COG1609     3 RVTIKDVARLAGVSVATVSRVLNGPPRVSEETRERVLAAAEELGYRPNAAARSLRTGRTRTIGVVVPDLSNPFFAELLRG 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  81 LQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAAHTEHPGGY--WTSIHRPIVAFDRTL-GEGVPAVRSDH 157
Cdd:COG1609    83 IEEAARERGYQLLLANSDEDPEREREALRLLLSRRVDGLILAGSRLDDARLerLAEAGIPVVLIDRPLpDPGVPSVGVDN 162
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 158 EQGGQLIARQLIDSGARHVVLVGGPRSQFAeattfptiryhlTVERM------LDDAGIACD--YVEAGIVADICAHEAt 229
Cdd:COG1609   163 RAGARLATEHLIELGHRRIAFIGGPADSSS------------ARERLagyreaLAEAGLPPDpeLVVEGDFSAESGYEA- 229
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 230 ARAIFERYSDVDAIV-GSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRLTAVRQDFPAVAAALASRMDSQI 308
Cdd:COG1609   230 ARRLLARGPRPTAIFcANDLMALGALRALREAGLRVPEDVSVVGFDDIPLARYLTPPLTTVRQPIEEMGRRAAELLLDRI 309
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|..
gi 1307851395 309 aadngttsaaaaeggnavaANGGQSTSEDIISVTLIPGETTR 350
Cdd:COG1609   310 -------------------EGPDAPPERVLLPPELVVRESTA 332
PBP1_Qymf-like cd06291
ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing ...
61-348 1.56e-77

ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs; This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380514 [Multi-domain]  Cd Length: 264  Bit Score: 238.57  E-value: 1.56e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAAHTEHPGGYwTSIHRPIV 140
Cdd:cd06291     1 TIGLIVPDISNPFFAELAKYIEKELFKKGYKMILCNSNEDEEKEKEYLEMLKRNKVDGIILGSHSLDIEEY-KKLNIPIV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 141 AFDRTLGEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSqfaeatTFPTIRYHLTVERMLDDAGIACDYVEAGIV 220
Cdd:cd06291    80 SIDRYLSEGIPSVSSDNYQGGRLAAEHLIEKGCKKILHIGGPSN------NSPANERYRGFEDALKEAGIEYEIIEIDEN 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 221 A-DICAHEATARAIFERYSDVDAIVG-SDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRLTAVRQDFPAVAA 298
Cdd:cd06291   154 DfSEEDAYELAKELLEKYPDIDGIFAsNDLLAIGVLKALQKLGIRVPEDVQIIGFDGIEISELLYPELTTIRQPIEEMAK 233
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1307851395 299 ALASRMDSQIaadngttsaaaaeggnavaaNGGQSTSEDII-SVTLIPGET 348
Cdd:cd06291   234 EAVELLLKLI--------------------EGEEIEESRIVlPVELIERET 264
PBP1_LacI_sugar_binding-like cd06267
ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 ...
61-313 1.60e-42

ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 periplasmic-binding fold protein superfamily; Ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.


Pssm-ID: 380491 [Multi-domain]  Cd Length: 264  Bit Score: 148.43  E-value: 1.60e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAAHTEHPGGYWTSIHR--P 138
Cdd:cd06267     1 TIGLIVPDISNPFFAELLRGIEDAARERGYSLLLCNTDEDPEREREYLRLLLSRRVDGIILAPSSLDDELLEELLAAgiP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 139 IVAFDRTL-GEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSqfaeattFPTIRyhltvERM------LDDAGIA 211
Cdd:cd06267    81 VVLIDRRLdGLGVDSVVVDNYAGAYLATEHLIELGHRRIAFIGGPLD-------LSTSR-----ERLegyrdaLAEAGLP 148
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 212 CD--YVEAGIVADICAHEAtARAIFERYSDVDAIV-GSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRLTA 288
Cdd:cd06267   149 VDpeLVVEGDFSEESGYEA-ARELLALPPRPTAIFaANDLMAIGALRALRELGLRVPEDISVVGFDDIPLAALLTPPLTT 227
                         250       260
                  ....*....|....*....|....*
gi 1307851395 289 VRQDFPAVAAALASRMDSQIAADNG 313
Cdd:cd06267   228 VRQPAYEMGRAAAELLLERIEGEEE 252
PRK10423 PRK10423
transcriptional repressor RbsR; Provisional
4-291 3.27e-35

transcriptional repressor RbsR; Provisional


Pssm-ID: 182448 [Multi-domain]  Cd Length: 327  Bit Score: 130.97  E-value: 3.27e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395   4 MRDVAKTAGVSLSTVSLVVNNTGYVSDDMRAKVEAAMRQLNYIPNELARNLYRNRTNTIGVIMPTIAHPFFATLTAHLQR 83
Cdd:PRK10423    1 MKDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSALARSLKLNQTRTIGMLITASTNPFYSELVRGVER 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  84 EFAARDLKTLLCSIadadkgEGEYVDM-------LQRHmMDGI-VMAAHTEHPGGywTSIHR----PIVAFDRTLGEGVP 151
Cdd:PRK10423   81 SCFERGYSLVLCNT------EGDEQRMnrnletlMQKR-VDGLlLLCTETHQPSR--EIMQRypsvPTVMMDWAPFDGDS 151
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 152 AVRSDHE-QGGQLIARQLIDSGARHVVLVGGPRSQfaeatTFPTIR---YHLTVER----MLDDAGIACDY-VEAGIVA- 221
Cdd:PRK10423  152 DLIQDNSlLGGDLATQYLIDKGYTRIACITGPLDK-----TPARLRlegYRAAMKRaglnIPDGYEVTGDFeFNGGFDAm 226
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1307851395 222 -DICAHEATARAIFerysdvdaiVGSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRLTAVRQ 291
Cdd:PRK10423  227 qQLLALPLRPQAVF---------TGNDAMAVGVYQALYQAGLSVPQDIAVIGYDDIELARYMTPPLTTIHQ 288
PBP1_LacI-like cd06278
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
61-309 2.22e-31

ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380501 [Multi-domain]  Cd Length: 266  Bit Score: 119.18  E-value: 2.22e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADkGEGEYVDMLQRHMMDGIVMAAHTEHPG--GYWTSIHRP 138
Cdd:cd06278     1 LVGVVVGDLSNPFYAELLEELSRALQARGLRPLLFNVDDED-DVDDALRQLLQYRVDGVIVTSATLSSElaEECARRGIP 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 139 IVAFDRTL-GEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRsqfaeaTTFPTIRYHLTVERMLDDAGIACDYVEA 217
Cdd:cd06278    80 VVLFNRVVeDPGVDSVSCDNRAGGRLAADLLLAAGHRRIAFLGGPE------GTSTSRERERGFRAALAELGLPPPAVEA 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 218 GIVADICAHEAtARAIFERYSDVDAIV-GSDLVAsVALQEALRR--GISVPRDLQIIAYDGTFMAETAGMRLTAVRQDFP 294
Cdd:cd06278   154 GDYSYEGGYEA-ARRLLAAPDRPDAIFcANDLMA-LGALDAARQegGLVVPEDISVVGFDDIPMAAWPSYDLTTVRQPIE 231
                         250
                  ....*....|....*
gi 1307851395 295 AVAAALASRMDSQIA 309
Cdd:cd06278   232 EMAEAAVDLLLERIE 246
PRK10703 PRK10703
HTH-type transcriptional repressor PurR;
1-291 2.85e-29

HTH-type transcriptional repressor PurR;


Pssm-ID: 236739 [Multi-domain]  Cd Length: 341  Bit Score: 115.21  E-value: 2.85e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395   1 MVGMRDVAKTAGVSLSTVSLVVNNTGYVSDDMRAKVEAAMRQLNYIPNELARNLYRNRTNTIGVIMPTIAHPFFATLTAH 80
Cdd:PRK10703    1 MATIKDVAKRAGVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLATSSEAPYFAEIIEA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  81 LQREFAARDLKTLLC-SIADADKGEGeYVDMLQRHMMDGI-VMAA-HTEHPGGYWTSI-HRPIVAFDrtLGEgvpaVRSD 156
Cdd:PRK10703   81 VEKNCYQKGYTLILCnAWNNLEKQRA-YLSMLAQKRVDGLlVMCSeYPEPLLAMLEEYrHIPMVVMD--WGE----AKAD 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 157 HE--------QGGQLIARQLIDSGARHVVLVGGPrsqfAEATTFPTiRYhLTVERMLDDAGIAC--DYVEAGIVADICAH 226
Cdd:PRK10703  154 FTdaiidnafEGGYLAGRYLIERGHRDIGVIPGP----LERNTGAG-RL-AGFMKAMEEANIKVpeEWIVQGDFEPESGY 227
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1307851395 227 EATARAIFERYSDVDAIVGSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRLTAVRQ 291
Cdd:PRK10703  228 EAMQQILSQKHRPTAVFCGGDIMAMGAICAADEMGLRVPQDISVIGYDNVRNARYFTPALTTIHQ 292
PBP1_LacI-like cd06284
ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus ...
61-291 3.83e-29

ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria; This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.


Pssm-ID: 380507 [Multi-domain]  Cd Length: 267  Bit Score: 113.02  E-value: 3.83e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAAhTEHPGGYWTSIHR--P 138
Cdd:cd06284     1 TILVLVPNISNPFYSEILRGIEDAAAEAGYDVLLGDTDSDPEREDDLLDMLRSRRVDGVILLS-GRLDAELLSELSKryP 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 139 IV-AFDRTLGEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPrsqfaeattfptIRYHLTVERM------LDDAGIA 211
Cdd:cd06284    80 IVqCCEYIPDSGVPSVSIDNEAAAYDATEYLISLGHRRIAHINGP------------LDNVYARERLegyrraLAEAGLP 147
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 212 CD---YVEAGIVADicAHEATARAIFERYSDVDAIV-GSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRLT 287
Cdd:cd06284   148 VDedlIIEGDFSFE--AGYAAARALLALPERPTAIFcASDELAIGAIKALRRAGLRVPEDVSVIGFDDIEFAEMFSPSLT 225

                  ....
gi 1307851395 288 AVRQ 291
Cdd:cd06284   226 TIRQ 229
PBP1_CcpB-like cd06286
ligand-binding domain of a novel transcription factor implicated in catabolite repression in ...
61-312 1.15e-27

ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species; This group includes the ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. Catabolite control protein B (CcpB) is 30% identical in sequence to CcpA which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. Like CcpA, the DNA-binding protein CcpB exerts its catabolite-repressing effect by a mechanism dependent on the presence of HPr(Ser-P), the small phosphocarrier proteins of the phosphoenolpyruvate-sugar phosphotransferase system, but with a less significant degree.


Pssm-ID: 380509 [Multi-domain]  Cd Length: 262  Bit Score: 109.17  E-value: 1.15e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLC-SIADADKgEGEYVDMLQRHMMDGIVMAAHTEHpggyWTSI---- 135
Cdd:cd06286     1 TIGVVVPYIDHPYFSQLINGIAEAAFKKGYQVLLLqTNYDKEK-ELRALELLKTKQIDGLIITSREND----WEVIepya 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 136 -HRPIVAFDRTLGEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGpRSQFAEATTFPTIRYHLTVermLDDAGIA--- 211
Cdd:cd06286    76 kYGPIVLCEETDSPDIPSVYIDRYEAYLEALEYLKEKGHRKIGYCLG-RPESSSASTQARLKAYQDV---LGEHGLSlre 151
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 212 ------CDYVEAGIVAdicaheatARAIFERYSDVDAI-VGSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETagM 284
Cdd:cd06286   152 ewiftnCHTIEDGYKL--------AKKLLALKERPDAIfTNSDEVAAGIIAEAQKNGIRVPEDLAVIGFDNQPISEL--L 221
                         250       260
                  ....*....|....*....|....*...
gi 1307851395 285 RLTAVRQDFPAVAAALASRMDSQIAADN 312
Cdd:cd06286   222 NLTTIDQPLEEMGKEAFELLLSQLESKE 249
HTH_LACI smart00354
helix_turn _helix lactose operon repressor;
4-71 2.05e-27

helix_turn _helix lactose operon repressor;


Pssm-ID: 197675 [Multi-domain]  Cd Length: 70  Bit Score: 102.67  E-value: 2.05e-27
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1307851395    4 MRDVAKTAGVSLSTVSLVVNNTGYVSDDMRAKVEAAMRQLNYIPNELARNLYRNRTNTIGVIMPTIAH 71
Cdd:smart00354   3 IKDVARLAGVSKATVSRVLNGKGRVSEETREKVLAAMEELGYIPNRVARSLKGKKTKTIGLIVPDITN 70
PBP1_CelR cd06295
ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly ...
57-309 2.90e-27

ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators; This group includes the ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. The binding of CelR to the celE promoter is inhibited specifically by cellobiose. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380518 [Multi-domain]  Cd Length: 273  Bit Score: 108.11  E-value: 2.90e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  57 NRTNTIGVIMPTIAH-------PFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMlQRhmMDGIVMAahtehpg 129
Cdd:cd06295     1 QRSRTIAVVVPMDPHgdqsitdPFFLELLGGISEALTDRGYDMLLSTQDEDANQLARLLDS-GR--ADGLIVL------- 70
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 130 GYWtsihRPIVAFDRTLGEGVP--------------AVRSDHEQGGQLIARQLIDSGARHVVLVGGPRS-QFAEattfpt 194
Cdd:cd06295    71 GQG----LDHDALRELAQQGLPmvvwgapedgqsycSVGSDNVKGGALATEHLIEIGRRRIAFLGDPPHpEVAD------ 140
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 195 iRYHLTVERMlDDAGIACDYVEAGIVADICAHEATA-RAIFERYSDVDAI-VGSDLVASVALQEALRRGISVPRDLQIIA 272
Cdd:cd06295   141 -RLQGYRDAL-AEAGLEADPSLLLSCDFTEESGYAAmRALLDSGTAFDAIfAASDLIAMGAIRALRERGISVPGDVAVVG 218
                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 1307851395 273 YDGTFMAETAGMRLTAVRQDFPAVAAALASRMDSQIA 309
Cdd:cd06295   219 YDDIPLAAYFRPPLTTVRQDLALAGRLLVEKLLALIA 255
PBP1_DegA_Like cd19976
ligand-binding domain of putative DNA transcription regulators highly similar to that of the ...
61-291 8.94e-27

ligand-binding domain of putative DNA transcription regulators highly similar to that of the transcription regulator DegA; This group includes the ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that of the transcription regulator DegA, which is involved in the control of degradation of Bacillus subtilis amidophosphoribosyltransferase (purF). This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.


Pssm-ID: 380631 [Multi-domain]  Cd Length: 268  Bit Score: 106.56  E-value: 8.94e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSiADADKG-EGEYVDMLQRHMMDGIVMAAHTEHPGG---YWTSIH 136
Cdd:cd19976     1 TIGLIVPDISNPFFSELVRGIEDTLNELGYNIILCN-TYNDFErEKKYIQELKERNVDGIIIASSNISDEAiikLLKEEK 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 137 RPIVAFDRTL-GEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSqfaeattfpTIRYHltvERM------LDDAG 209
Cdd:cd19976    80 IPVVVLDRYIeDNDSDSVGVDDYRGGYEATKYLIELGHTRIGCIVGPPS---------TYNEH---ERIegyknaLQDHN 147
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 210 IACD--YVEAGIVADICAHEATARAIfeRYSDVDAIV-GSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRL 286
Cdd:cd19976   148 LPIDesWIYSGESSLEGGYKAAEELL--KSKNPTAIFaGNDLIAMGVYRAALELGLKIPEDLSVIGFDNIILSEYITPAL 225

                  ....*
gi 1307851395 287 TAVRQ 291
Cdd:cd19976   226 TTIAQ 230
PBP1_LacI cd01574
ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of ...
61-311 3.07e-26

ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators; Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380488 [Multi-domain]  Cd Length: 265  Bit Score: 105.36  E-value: 3.07e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGE-GEYVDMLQRHMMDGIVMAAHTE--HPGGYWTSIHR 137
Cdd:cd01574     1 TIGVIATGLSLYGPASTLAGIERAARERGYSVSIATVDEDDPASvREALDRLLSQRVDGIIVIAPDEavLEALRRLPPGL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 138 PIVAFDRTLGEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSQFAEATtfptiRyHLTVERMLDDAGIACDYVEA 217
Cdd:cd01574    81 PVVIVGSGPSPGVPTVSIDQEEGARLATRHLLELGHRRIAHIAGPLDWVDARA-----R-LRGWREALEEAGLPPPPVVE 154
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 218 GivaDICA---HEATARaiFERYSDVDAI-VGSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRLTAVRQDF 293
Cdd:cd01574   155 G---DWSAasgYRAGRR--LLDDGPVTAVfAANDQMALGALRALHERGLRVPEDVSVVGFDDIPEAAYFVPPLTTVRQDF 229
                         250
                  ....*....|....*...
gi 1307851395 294 PAVAAALASRMDSQIAAD 311
Cdd:cd01574   230 AELGRRAVELLLALIEGP 247
PBP1_LacI-like cd06285
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
61-314 8.95e-26

ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380508 [Multi-domain]  Cd Length: 269  Bit Score: 104.23  E-value: 8.95e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAAHTEHPGgyWTSIHR--- 137
Cdd:cd06285     1 TIGVLVSDLSNPFYAELVEGIEDAARERGYTVLLADTGDDPERELAALDSLLSRRVDGLIITPARDDAP--DLQELAarg 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 138 -PIVAFDRTLGEGV-PAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSqfaeatTFPTIRYHLTVERMLDDAGI---AC 212
Cdd:cd06285    79 vPVVLVDRRIGDTAlPSVTVDNELGGRLATRHLLELGHRRIAVVAGPLN------ASTGRDRLRGYRRALAEAGLpvpDE 152
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 213 DYVEAGIVADicAHEATARAIFERYSDVDAIVG-SDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRLTAVRQ 291
Cdd:cd06285   153 RIVPGGFTIE--AGREAAYRLLSRPERPTAVFAaNDLMAIGVLRAARDLGLRVPEDLSVVGFDDIPLAAFLPPPLTTVRQ 230
                         250       260
                  ....*....|....*....|...
gi 1307851395 292 DFPAVAAALASRMDSQIAADNGT 314
Cdd:cd06285   231 PKYEMGRRAAELLLQLIEGGGRP 253
PBP1_LacI-like cd06293
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
61-310 5.76e-25

ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380516 [Multi-domain]  Cd Length: 270  Bit Score: 101.96  E-value: 5.76e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAAHTEHPGgYWTSI---HR 137
Cdd:cd06293     1 TIGLVVPDVSNPFFAEVARGVEDAARERGYAVVLCNSGRDPERERRYLEMLESQRVRGLIVTPSDDDLS-HLARLrarGT 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 138 PIVAFDR-TLGEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSQFAEATTFPTIRyhltveRMLDDAGIACDYVE 216
Cdd:cd06293    80 AVVLLDRpAPGPAGCSVSVDDVQGGALAVDHLLELGHRRIAFVSGPLRTRQVAERLAGAR------AAVAEAGLDPDEVV 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 217 AGIVADIC---AHEATARAIFERYSDVDAIV-GSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRLTAVRQD 292
Cdd:cd06293   154 RELSAPDAnaeLGRAAAAQLLAMPPRPTAVFaANDLLALGLLAGLRRAGLRVPDDVSVVGYDDLPFAAAANPPLTTVRQP 233
                         250
                  ....*....|....*...
gi 1307851395 293 FPAVAAALASRMDSQIAA 310
Cdd:cd06293   234 SYELGRAAADLLLDEIEG 251
PBP1_AglR_RafR-like cd06292
Ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that ...
61-308 8.21e-25

Ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that of the repressors specific raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins highly similar to DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR). Members of this group belong to the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380515 [Multi-domain]  Cd Length: 273  Bit Score: 101.58  E-value: 8.21e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTI----AHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAaHTEHPGG---YWT 133
Cdd:cd06292     1 LIGYVVPELpggfSDPFFDEFLAALGHAAAARGYDVLLFTASGDEDEIDYYRDLVRSRRVDGFVLA-STRHDDPrvrYLH 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 134 SIHRPIVAFDRTLGE-GVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSqfaeattfptirYHLTVERM------LD 206
Cdd:cd06292    80 EAGVPFVAFGRANPDlDFPWVDVDGAAGMRQAVRHLIALGHRRIGLIGGPEG------------SVPSDDRLagyraaLE 147
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 207 DAGI--ACDYVEAGIVaDICAHEATARAIFERYSDVDAIV-GSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAG 283
Cdd:cd06292   148 EAGLpfDPGLVVEGEN-TEEGGYAAAARLLDLGPPPTAIVcVSDLLALGAMRAARERGLRVGRDVSVVGFDDSPLAAFTH 226
                         250       260
                  ....*....|....*....|....*
gi 1307851395 284 MRLTAVRQDFPAVAAALASRMDSQI 308
Cdd:cd06292   227 PPLTTVRQPIDEIGRAVVDLLLAAI 251
PBP1_LacI-like cd06299
ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum ...
61-316 1.49e-24

ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum produces significant amounts of L-glutamate directly from cheap sugar and ammonia; This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380522 [Multi-domain]  Cd Length: 268  Bit Score: 100.82  E-value: 1.49e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIvMAAHTEHPGGYWTSIHR--- 137
Cdd:cd06299     1 TIGLLVPDIRNPFFAELASGIEDEARAHGYSVILGNSDEDPEREDESLEMLLSQRVDGI-IAVPTGENSEGLQALIAqgl 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 138 PIVAFDRTLGE--GVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSqfaeattFPTIRyhltvERM------LDDAG 209
Cdd:cd06299    80 PVVFVDREVEGlgGVPVVTSDNRPGAREAVEYLVSLGHRRIGYISGPLS-------TSTGR-----ERLaafraaLTAAG 147
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 210 IACD---YVEAGIVADICAhEATARaIFERYSDVDAIVGSD-LVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMR 285
Cdd:cd06299   148 IPIDeelVAFGDFRQDSGA-AAAHR-LLSRGDPPTALIAGDsLMALGAIQALRELGLRIGDDVSLISFDDVPWFELLSPP 225
                         250       260       270
                  ....*....|....*....|....*....|.
gi 1307851395 286 LTAVRQDFPAVAAALASRMDSQIAADNGTTS 316
Cdd:cd06299   226 LTVIAQPVERIGRRAVELLLALIENGGRATS 256
PBP1_EndR-like cd19977
periplasmic ligand-binding domain of putative repressor of the endoglucanase operon and its ...
61-291 2.03e-24

periplasmic ligand-binding domain of putative repressor of the endoglucanase operon and its close homologs; This group includes the ligand-binding domain of putative repressor of the endoglucanase operon from Paenibacillus polymyxa and its close homologs from other bacteria. This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.


Pssm-ID: 380632 [Multi-domain]  Cd Length: 264  Bit Score: 100.30  E-value: 2.03e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSI-ADADKGEgEYVDMLQRHMMDGIVMAAhTEHPGGYWTSI---H 136
Cdd:cd19977     1 TIGLIVADILNPFFTSVVRGIEDEAYKNGYHVILCNTdEDPEKEK-KYIEMLRAKQVDGIIIAP-TGGNEDLIEKLvksG 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 137 RPIVAFDRTLGE-GVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPrsqfAEATTfptiryhlTVERM------LDDAG 209
Cdd:cd19977    79 IPVVFVDRYIPGlDVDTVVVDNFKGAYQATEHLIELGHKRIAFITYP----LELST--------RQERLegykaaLADHG 146
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 210 I--------ACDYVEAGIVAdicaheatARAIFERYSDVDAI-VGSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAE 280
Cdd:cd19977   147 LpvdeelikHVDRQDDVRKA--------ISELLKLEKPPDAIfAANNLITLEVLKAIKELGLRIPDDIALIGFDDIPWAD 218
                         250
                  ....*....|.
gi 1307851395 281 TAGMRLTAVRQ 291
Cdd:cd19977   219 LFNPPLTVIAQ 229
PBP1_LacI-like cd06273
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
61-312 4.71e-24

ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380497 [Multi-domain]  Cd Length: 268  Bit Score: 99.51  E-value: 4.71e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLL-CSIADADKgEGEYVDMLQRHMMDGIVMAAHTEHPGGY--WTSIHR 137
Cdd:cd06273     1 TIGAIVPTLDNAIFARAIQALQQTLAEAGYTLLLaTSEYDPAR-ELEQVRALIERGVDGLILVGSDHDPELFelLEQRQV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 138 PIVA-FDRTLGEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRsqfaeATTFPTIRYHLTVERMLDDAGIA----- 211
Cdd:cd06273    80 PYVLtWSYDEDSPHPSIGFDNRAAAARAAQHLLDLGHRRIAVISGPT-----AGNDRARARLAGIRDALAERGLElpeer 154
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 212 ---CDY-VEAGIVAdicaheatARAIFERYSDVDAIV-GSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRL 286
Cdd:cd06273   155 vveAPYsIEEGREA--------LRRLLARPPRPTAIIcGNDVLALGALAECRRLGISVPEDLSITGFDDLELAAHLSPPL 226
                         250       260       270
                  ....*....|....*....|....*....|..
gi 1307851395 287 TAVRqdFPAV------AAALASRMDSQIAADN 312
Cdd:cd06273   227 TTVR--VPAReigelaARYLLALLEGGPPPKS 256
PBP1_LacI-like cd06281
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
61-309 1.59e-23

ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380504 [Multi-domain]  Cd Length: 270  Bit Score: 98.08  E-value: 1.59e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAAHTEHPGGYWTSIHR--- 137
Cdd:cd06281     1 TVGCLVSDISNPLYARIVKAAEARLRAAGYTLLLASTGNDEERELELLSLFQRRRVDGLILTPGDEDDPELAAALARldi 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 138 PIVAFDRTLGEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPrsqfaeattfPTIRyhLTVERMlddAGIACDYVEA 217
Cdd:cd06281    81 PVVLIDRDLPGDIDSVLVDHRSGVRQATEYLLSLGHRRIALLTGG----------PDIR--PGRERI---AGFKAAFAAA 145
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 218 GIVAD----------ICAHEATARAIFERYSDVDAIV--GSDLVASVaLQEALRRGISVPRDLQIIAYDGTFMAETAGMR 285
Cdd:cd06281   146 GLPPDpdlvrlgsfsADSGFREAMALLRQPRPPTAIIalGTQLLAGV-LRAVRAAGLRIPGDLSVVSIGDSDLAELHDPP 224
                         250       260
                  ....*....|....*....|....*...
gi 1307851395 286 LTAVRQDFPAVAAALAS----RMDSQIA 309
Cdd:cd06281   225 ITAIRWDLDAVGRAAAEllldRIEGPPA 252
lacI PRK09526
lac repressor; Reviewed
6-304 5.02e-23

lac repressor; Reviewed


Pssm-ID: 181929 [Multi-domain]  Cd Length: 342  Bit Score: 98.14  E-value: 5.02e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395   6 DVAKTAGVSLSTVSLVVNNTGYVSDDMRAKVEAAMRQLNYIPNELARNLYRNRTNTIGVIMPTIAHPFFATLTAHLQREF 85
Cdd:PRK09526   10 DVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVPNRVAQQLAGKQSLTIGLATTSLALHAPSQIAAAIKSRA 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  86 AARDLKTLLCSIADADkGEG--EYVDMLQRHMMDGIVM-----AAHTEHPGGYWTSIhrPIVAFDRTLGEGVPAVRSDHE 158
Cdd:PRK09526   90 DQLGYSVVISMVERSG-VEAcqAAVNELLAQRVSGVIInvpleDADAEKIVADCADV--PCLFLDVSPQSPVNSVSFDPE 166
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 159 QGGQLIARQLIDSGARHVVLVGGPRSQFAEattfpTIRYHLTVERmLDDAGIACDYVEAGIVADICAHEATARAIFERyS 238
Cdd:PRK09526  167 DGTRLGVEHLVELGHQRIALLAGPESSVSA-----RLRLAGWLEY-LTDYQLQPIAVREGDWSAMSGYQQTLQMLREG-P 239
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1307851395 239 DVDAI-VGSDLVASVALQEALRRGISVPRDLQIIAYDGTfmAETAGMR--LTAVRQDFPAVAAALASRM 304
Cdd:PRK09526  240 VPSAIlVANDQMALGVLRALHESGLRVPGQISVIGYDDT--EDSSYFIppLTTIKQDFRLLGKEAVDRL 306
PBP1_CcpA-like cd19975
ligand-binding domain of putative DNA transcription regulators highly similar to that of the ...
61-293 1.33e-22

ligand-binding domain of putative DNA transcription regulators highly similar to that of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation; This group includes the ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.


Pssm-ID: 380630 [Multi-domain]  Cd Length: 269  Bit Score: 95.32  E-value: 1.33e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAAH--TEHPGGYWTSIHRP 138
Cdd:cd19975     1 TIGVIIPDISNSFFAEILKGIEDEARENGYSVILCNTGSDEEREKKYLQLLKEKRVDGIIFASGtlTEENKQLLKNMNIP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 139 IVAFDR-TLGEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPrsqfaeaTTFPTIRY--HLTVERMLDDAGIACD-- 213
Cdd:cd19975    81 VVLVSTeSEDPDIPSVKIDDYQAAYDATNYLIKKGHRKIAMISGP-------LDDPNAGYprYEGYKKALKDAGLPIKen 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 214 -------YVEAGIVAdicaheatARAIFERYSDVDAIV-GSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMR 285
Cdd:cd19975   154 livegdfSFKSGYQA--------MKRLLKNKKLPTAVFaASDEMALGVISAAYDHGIRVPEDISVIGFDNTEIAEMSIPP 225

                  ....*...
gi 1307851395 286 LTAVRQDF 293
Cdd:cd19975   226 LTTVSQPF 233
PBP1_LacI-like cd06279
ligand-binding domain of an uncharacterized transcription regulator from Corynebacterium ...
61-292 2.59e-22

ligand-binding domain of an uncharacterized transcription regulator from Corynebacterium glutamicum and its close homologs from other bacteria; This group includes the ligand-binding domain of an uncharacterized transcription regulator from Corynebacterium glutamicum and its close homologs from other bacteria. This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.


Pssm-ID: 380502 [Multi-domain]  Cd Length: 284  Bit Score: 94.97  E-value: 2.59e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPT-----IAHPFFATLTAHLQREFAARDLKTLLCSiadaDKGEGEYVDMLQRHMMDG-IVMAAHTEHPggYWTS 134
Cdd:cd06279     1 AIGVLLPDdlsyaFSDPVAAQFLRGVAEVCEEEGLGLLLLP----ATDEGSAAAAVRNAAVDGfIVYGLSDDDP--AVAA 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 135 I---HRPIVAFDRTLGEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSQ-----FAEATTFPTIRYHLTVERMld 206
Cdd:cd06279    75 LrrrGLPLVVVDGPAPPGIPSVGIDDRAAARAAARHLLDLGHRRIAILSLRLDRgrergPVSAERLAAATNSVARERL-- 152
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 207 dAGIACDYVEAGIVADICAH-----------EATARAIFERYSDVDAIVG-SDLVASVALQEALRRGISVPRDLQIIAYD 274
Cdd:cd06279   153 -AGYRDALEEAGLDLDDVPVveapgnteeagRAAARALLALDPRPTAILCmSDVLALGALRAARERGLRVPEDLSVTGFD 231
                         250
                  ....*....|....*...
gi 1307851395 275 GTFMAETAGMRLTAVRQD 292
Cdd:cd06279   232 DIPEAAAADPGLTTVRQP 249
PBP1_LacI-like cd06290
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
61-291 6.51e-22

ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380513 [Multi-domain]  Cd Length: 267  Bit Score: 93.45  E-value: 6.51e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVM-AAHTEHPGGYWTSIHRPI 139
Cdd:cd06290     1 TIGVLVPDIDSPFYSEILNGIEEVLAESGYTLIVSTSHWNADRELEILRLLLARKVDGIIVvGGFGDEELLKLLAEGIPV 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 140 VAFDRTLGEG-VPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSQFAeattfptiryhlTVERM------LDDAGIAC 212
Cdd:cd06290    81 VLVDRELEGLnLPVVNVDNEQGGYNATNHLIDLGHRRIVHISGPEDHPD------------AQERYagyrraLEDAGLEV 148
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 213 D--YVEAGIVADICAHEATaRAIFERYSDVDAI-VGSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRLTAV 289
Cdd:cd06290   149 DprLIVEGDFTEESGYEAM-KKLLKRGGPFTAIfAANDLMALGAMKALREAGIRVPDDVSVIGFDDLPFSKYTTPPLTTV 227

                  ..
gi 1307851395 290 RQ 291
Cdd:cd06290   228 RQ 229
PBP1_GalS-like cd06270
ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory ...
61-291 1.11e-20

ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism; Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type 1 periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar binding of ABC-type transport systems.


Pssm-ID: 380494 [Multi-domain]  Cd Length: 266  Bit Score: 89.89  E-value: 1.11e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMaaHTEHPG----GYWTSIH 136
Cdd:cd06270     1 TIGLVVPDLSGPFFGSLLKGAERVARAHGKQLLITSGHHDAEEEREAIEFLLDRRCDAIIL--HSRALSdeelILIAEKI 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 137 RPIVAFDRTLgEGVP--AVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSQFAeattfPTIRyHLTVERMLDDAGI---- 210
Cdd:cd06270    79 PPLVVINRYI-PGLAdrCVWLDNEQGGRLAAEHLLDLGHRRIACITGPLDIPD-----ARER-LAGYRDALAEAGIpldp 151
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 211 ----ACDYVEAGivadicaHEATARAIFERYSDVDAIV-GSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMR 285
Cdd:cd06270   152 sliiEGDFTIEG-------GYAAAKQLLARGLPFTALFaYNDDMAIGALAALHEAGIKVPEDVSVIGFDDVPLARYLSPK 224

                  ....*.
gi 1307851395 286 LTAVRQ 291
Cdd:cd06270   225 LTTVHY 230
PBP1_sucrose_transcription_regulator cd06288
ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members ...
61-274 1.67e-20

ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380511 [Multi-domain]  Cd Length: 268  Bit Score: 89.53  E-value: 1.67e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAH-PFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAAHTEHPggywtsIHRPI 139
Cdd:cd06288     1 TIGLITDDIATtPFAGDIIRGAQDAAEEHGYLLLLANTGGDPELEAEAIRELLSRRVDGIIYASMHHRE------VTLPP 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 140 VAFD--------RTLGEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSQFAeattfptiryhlTVERM------L 205
Cdd:cd06288    75 ELTDiplvllncFDDDPSLPSVVPDDEQGGYLATRHLIEAGHRRIAFIGGPEDSLA------------TRLRLagyraaL 142
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1307851395 206 DDAGIACD--YVEAGIVADICAHEAtARAIFERYSDVDAIV-GSDLVASVALQEALRRGISVPRDLQIIAYD 274
Cdd:cd06288   143 AEAGIPYDpsLVVHGDWGRESGYEA-AKRLLSAPDRPTAIFcGNDRMAMGVYQAAAELGLRVPEDLSVVGFD 213
PRK10014 PRK10014
DNA-binding transcriptional repressor MalI; Provisional
6-189 4.70e-20

DNA-binding transcriptional repressor MalI; Provisional


Pssm-ID: 182193 [Multi-domain]  Cd Length: 342  Bit Score: 89.77  E-value: 4.70e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395   6 DVAKTAGVSLSTVSLVVNNTGYVSDDMRAKVEAAMRQLNYIPNELARNLYRNRTNTIGVIMPTIAHPFFATLTAHLQREF 85
Cdd:PRK10014   11 DVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVRNRQASALRGGQSGVIGLIVRDLSAPFYAELTAGLTEAL 90
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  86 AARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAAHTEHPGGYWTSIHR---PIVAFDR-TLGEGVPAVRSDHEQGG 161
Cdd:PRK10014   91 EAQGRMVFLLQGGKDGEQLAQRFSTLLNQGVDGVVIAGAAGSSDDLREMAEEkgiPVVFASRaSYLDDVDTVRPDNMQAA 170
                         170       180
                  ....*....|....*....|....*...
gi 1307851395 162 QLIARQLIDSGARHVVLVGGPRSQFAEA 189
Cdd:PRK10014  171 QLLTEHLIRNGHQRIAWLGGQSSSLTRA 198
PBP1_PurR cd06275
ligand-binding domain of purine repressor, PurR, which functions as the master regulatory ...
61-291 5.14e-20

ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli; Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the purine transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380499 [Multi-domain]  Cd Length: 269  Bit Score: 88.08  E-value: 5.14e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDG-IVMaaHTEHPGGYWTSIHR-- 137
Cdd:cd06275     1 TIGLLVTSSENPFFAEVVRGVEDACFRAGYSLILCNSDNDPEKQRAYLDMLAEKRVDGlLLM--CSEMTDDDAELLAAlr 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 138 --PIVAFDRTL-GEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSqfaeattFPTIRYHLT-VERMLDDAGIAcd 213
Cdd:cd06275    79 siPVVVLDREIaGDNADAVLDDSFQGGYLATRHLIELGHRRIGCITGPLE-------HSVSRERLAgFRRALAEAGIE-- 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 214 yVEAGIVADICAHEATARAIFERY----SDVDAI-VGSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRLTA 288
Cdd:cd06275   150 -VPPSWIVEGDFEPEGGYEAMQRLlsqpPRPTAVfACNDMMALGALRAAQEQGLRVPQDISIIGYDDIELARYFSPALTT 228

                  ...
gi 1307851395 289 VRQ 291
Cdd:cd06275   229 IHQ 231
PBP1_MalI-like cd06289
ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia ...
61-274 1.79e-19

ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria; This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380512 [Multi-domain]  Cd Length: 268  Bit Score: 86.85  E-value: 1.79e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVM--AAHTehPGGYWTSIHR- 137
Cdd:cd06289     1 TVGLIVPDLSNPFFAELLAGIEEALEEAGYLVFLANTGEDPERQRRFLRRMLEQGVDGLILspAAGT--TAELLRRLKAw 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 138 --PIVAFDRTL-GEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSqfaeATTfptiryhlTVERM------LDDA 208
Cdd:cd06289    79 giPVVLALRDVpGSDLDYVGIDNRLGAQLATEHLIALGHRRIAFLGGLSD----SST--------RRERLagfraaLAEA 146
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1307851395 209 GIAcdyVEAGIVADICA-HEA---TARAIFERYSDVDAIV-GSDLVASVALQEALRRGISVPRDLQIIAYD 274
Cdd:cd06289   147 GLP---LDESLIVPGPAtREAgaeAARELLDAAPPPTAVVcFNDLVALGAMLALRRRGLEPGRDIAVVGFD 214
PBP1_GntR cd01575
ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of ...
61-290 1.32e-18

ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators; This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding, which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380489 [Multi-domain]  Cd Length: 269  Bit Score: 84.08  E-value: 1.32e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLL-CSIADADKgEGEYVDMLQRHMMDGIVMaahtehpggywTSIHRPI 139
Cdd:cd01575     1 LVAVVVPSLSNSVFAETLQGLSDVLEPAGYQLLLgNTGYSPER-EEELIRALLSRRPAGLIL-----------TGTEHTP 68
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 140 VAFDRTLGEGVP--------------AVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSQFAEATtfptIRYHLTVERML 205
Cdd:cd01575    69 ATRKLLRAAGIPvvetwdlpddpidmAVGFSNFAAGRAMARHLIERGYRRIAFVGARLDGDSRAR----QRLEGFRDALA 144
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 206 DdAGIACDYVEAGIVADICAHEATA-RAIFERYSDVDAIV-GSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAG 283
Cdd:cd01575   145 E-AGLPLPLVLLVELPSSFALGREAlAELLARHPDLDAIFcSNDDLALGALFECQRRGIRVPGDIAIAGFGDLDIAAALP 223

                  ....*..
gi 1307851395 284 MRLTAVR 290
Cdd:cd01575   224 PALTTVR 230
PBP1_AglR-like cd20010
Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) and ...
61-312 1.37e-18

Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) and similar proteins; Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380665 [Multi-domain]  Cd Length: 269  Bit Score: 84.14  E-value: 1.37e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPT----IAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAAHTEH-PggywtSI 135
Cdd:cd20010     1 AIGLVLPLdpgdLGDPFFLEFLAGLSEALAERGLDLLLAPAPSGEDELATYRRLVERGRVDGFILARTRVNdP-----RI 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 136 HR------PIVAFDRTLGEG-VPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPrsqfaEATTFPTIRYHlTVERMLDDA 208
Cdd:cd20010    76 AYllergiPFVVHGRSESGApYAWVDIDNEGAFRRATRRLLALGHRRIALLNGP-----EELNFAHQRRD-GYRAALAEA 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 209 GIACD--YVEAGIVADICAHEAtARAIFERYSDVDAIV-GSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGM- 284
Cdd:cd20010   150 GLPVDpaLVREGPLTEEGGYQA-ARRLLALPPPPTAIVcGSDLLALGAYRALREAGLSPGKDVSVIGHDDLLPALEYFSp 228
                         250       260
                  ....*....|....*....|....*...
gi 1307851395 285 RLTAVRQDFPAVAAALASRMDSQIAADN 312
Cdd:cd20010   229 PLTTTRSSLRDAGRRLAEMLLALIDGEP 256
PBP1_LacI-like cd06282
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
61-317 1.11e-17

ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380505 [Multi-domain]  Cd Length: 267  Bit Score: 81.56  E-value: 1.11e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMA---AHTEHPGGYWTSIHR 137
Cdd:cd06282     1 TIGVLIPSLNNPVFAEAAQGIQRAARAAGYSLLIATTDYDPARELDAVETLLEQRVDGLILTvgdAQGSEALELLEEEGV 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 138 PIV-AFDRTLGEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSQFAEAttfptIRYHLTVERMLDDAGI-ACDYV 215
Cdd:cd06282    81 PYVlLFNQTENSSHPFVSVDNRLASYDVAEYLIALGHRRIAMVAGDFSASDRA-----RLRYQGYRDALKEAGLkPIPIV 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 216 EAGIVADicAHEATARAIFERYSDVDAIVGS-DLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRLTAVRQDFP 294
Cdd:cd06282   156 EVDFPTN--GLEEALTSLLSGPNPPTALFCSnDLLALSVISALRRLGIRVPDDVSVIGFDGIAIGELLTPTLATVVQPSR 233
                         250       260
                  ....*....|....*....|...
gi 1307851395 295 AVAAALASRMDSQIAADNGTTSA 317
Cdd:cd06282   234 DMGRAAADLLLAEIEGESPPTSI 256
PRK11303 PRK11303
catabolite repressor/activator;
6-180 1.30e-17

catabolite repressor/activator;


Pssm-ID: 236897 [Multi-domain]  Cd Length: 328  Bit Score: 82.23  E-value: 1.30e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395   6 DVAKTAGVSLSTVSLVVNNTG--Y-VSDDMRAKVEAAMRQLNYIPNELARNLYRNRTNTIGVIMPTIAHPFFATLTAHLQ 82
Cdd:PRK11303    5 EIARLAGVSRTTASYVINGKAkqYrVSDKTVEKVMAVVREHNYHPNAVAAGLRAGRTRSIGLIIPDLENTSYARIAKYLE 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  83 REFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAAH--TEHPgGY--WTSIHRPIVAFDRTLG-EGVPAVRSDH 157
Cdd:PRK11303   85 RQARQRGYQLLIACSDDQPDNEMRCAEHLLQRQVDALIVSTSlpPEHP-FYqrLQNDGLPIIALDRALDrEHFTSVVSDD 163
                         170       180
                  ....*....|....*....|...
gi 1307851395 158 EQGGQLIARQLIDSGARHVVLVG 180
Cdd:PRK11303  164 QDDAEMLAESLLKFPAESILLLG 186
HTH_LacI cd01392
Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; ...
5-54 1.37e-17

Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repressor binds its ligand, it undergoes a conformational change which affects the DNA-binding affinity of the repressor. In Escherichia coli, LacI represses transcription by binding with high affinity to the lac operon at a specific operator DNA sequence until it interacts with the physiological inducer allolactose or a non-degradable analog IPTG (isopropyl-beta-D-thiogalactopyranoside). Induction of the repressor lowers its affinity for the operator sequence, thereby allowing transcription of the lac operon structural genes (lacZ, lacY, and LacA). The lac repressor occurs as a tetramer made up of two functional dimers. Thus, two DNA binding domains of a dimer are required to bind the inverted repeat sequences of the operator DNA binding sites.


Pssm-ID: 143331 [Multi-domain]  Cd Length: 52  Bit Score: 75.52  E-value: 1.37e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1307851395   5 RDVAKTAGVSLSTVSLVVNNTGYVSDDMRAKVEAAMRQLNYIPNELARNL 54
Cdd:cd01392     1 KDIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYRPNAAARSL 50
PBP1_LacI-like cd06280
ligand-binding domain of an uncharacterized transcription regulator from Staphylococcus ...
61-292 1.74e-17

ligand-binding domain of an uncharacterized transcription regulator from Staphylococcus saprophyticus and its close homologs from other bacteria; This group includes the ligand-binding domain of an uncharacterized transcription regulator from Staphylococcus saprophyticus and its close homologs from other bacteria. This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.


Pssm-ID: 380503 [Multi-domain]  Cd Length: 266  Bit Score: 81.15  E-value: 1.74e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMA----AHTEHPGGYWTSIh 136
Cdd:cd06280     1 TIGLIVPDITNPFFTTIARGIEDAAEKHGYQVILANTDEDPEKEKRYLDSLLSKQVDGIILApsagPSRELKRLLKHGI- 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 137 rPIVAFDRTL-GEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRsqfaEATTfptiryhlTVERM------LDDAG 209
Cdd:cd06280    80 -PIVLIDREVeGLELDLVAGDNREGAYKAVKHLIELGHRRIGLITGPL----EIST--------TRERLagyreaLAEAG 146
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 210 IACD---------YVEAGIVAdicaheatARAIFERYSDVDAIV-GSDLVASVALQEALRRGISVPRDLQIIAYDGTFMA 279
Cdd:cd06280   147 IPVDeslifegdsTIEGGYEA--------VKALLDLPPRPTAIFaTNNLMAVGALRALRERGLEIPQDISVVGFDDSDWF 218
                         250
                  ....*....|...
gi 1307851395 280 ETAGMRLTAVRQD 292
Cdd:cd06280   219 EIVDPPLTVVAQP 231
LacI pfam00356
Bacterial regulatory proteins, lacI family;
4-48 6.46e-17

Bacterial regulatory proteins, lacI family;


Pssm-ID: 306791 [Multi-domain]  Cd Length: 46  Bit Score: 73.44  E-value: 6.46e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1307851395   4 MRDVAKTAGVSLSTVSLVVNNTGYVSDDMRAKVEAAMRQLNYIPN 48
Cdd:pfam00356   2 IKDVARLAGVSKSTVSRVLNNPGRVSEETRERVEAAMEELNYIPN 46
PRK10727 PRK10727
HTH-type transcriptional regulator GalR;
1-299 1.99e-16

HTH-type transcriptional regulator GalR;


Pssm-ID: 182681 [Multi-domain]  Cd Length: 343  Bit Score: 79.03  E-value: 1.99e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395   1 MVGMRDVAKTAGVSLSTVSLVVNNTGYVSDDMRAKVEAAMRQLNYIPNELARNLYRNRTNTIGVIMPTIAHPFFATLTAH 80
Cdd:PRK10727    1 MATIKDVARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLSYHPNANARALAQQSTETVGLVVGDVSDPFFGAMVKA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  81 LQrEFAARDLKTLLC--SIADADKgEGEYVDMLQRHMMDGIVMAAHTeHPGGYWTSIHRPI---VAFDRTL-GEGVPAVR 154
Cdd:PRK10727   81 VE-QVAYHTGNFLLIgnGYHNEQK-ERQAIEQLIRHRCAALVVHAKM-IPDAELASLMKQIpgmVLINRILpGFENRCIA 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 155 SDHEQGGQLIARQLIDSGARHVVLVGGpRSQFAEATtfptiryhltvERM------LDDAGIACDyveAGIVA----DIC 224
Cdd:PRK10727  158 LDDRYGAWLATRHLIQQGHTRIGYLCS-NHSISDAE-----------DRLqgyydaLAESGIPAN---DRLVTfgepDES 222
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1307851395 225 AHEATARAIFERYSDVDAIVG-SDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRLTAVRqdFPAVAAA 299
Cdd:PRK10727  223 GGEQAMTELLGRGRNFTAVACyNDSMAAGAMGVLNDNGIDVPGEISLIGFDDVLVSRYVRPRLTTVR--YPIVTMA 296
PBP1_FruR cd06274
ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its ...
61-313 3.86e-16

ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs; Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs, all of which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to members of the type 1 periplasmic binding protein superfamily. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor


Pssm-ID: 380498 [Multi-domain]  Cd Length: 264  Bit Score: 77.25  E-value: 3.86e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAAHTEHPGGY--WTSIHRP 138
Cdd:cd06274     1 TIGLIVPDLANRFFARLAEALERLARERGLQLLIACSDDDPEQERRLVENLIARQVDGLIVAPSTPPDDIYylCQAAGLP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 139 IVAFDRTL-GEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSQfaeattfPTIRyhltvERMlddAGIACDYVEA 217
Cdd:cd06274    81 VVFLDRPFsGSDAPSVVSDNRAGARALTEKLLAAGPGEIYFLGGRPEL-------PSTA-----ERI---RGFRAALAEA 145
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 218 GIVADICAHEA------TARAIFERYSDV-----DA-IVGSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMR 285
Cdd:cd06274   146 GITEGDDWILAegydreSGYQLMAELLARlgglpQAlFTSSLTLLEGVLRFLRERLGAIPSDLVLGTFDDHPLLDFLPNP 225
                         250       260
                  ....*....|....*....|....*...
gi 1307851395 286 LTAVRQDFPAVAAALASRMDSQIAADNG 313
Cdd:cd06274   226 VDSVRQDHDEIAEHAFELLDALIEGQPE 253
PBP1_RegR_EndR_KdgR-like cd06283
ligand-binding domain of DNA transcription repressor RegR and other putative regulators such ...
61-314 1.91e-15

ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR; Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR, all of which are members of the LacI-GalR family of bacterial transcription regulators. RegR regulates bacterial competence and the expression of virulence factors, including hyaluronidase. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380506 [Multi-domain]  Cd Length: 266  Bit Score: 75.28  E-value: 1.91e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAAHTEHPGGYWTSIHR--P 138
Cdd:cd06283     1 LIGVIVADITNPFSSLLLKGIEDVCREAGYQLLICNSNNDPEKERDYIESLLSQRVDGLILQPTGNNNDAYLELAQKglP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 139 IVAFDRTLGE-GVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGP---------RSQ-FAEATTFPTIRYHLTVermLDD 207
Cdd:cd06283    81 VVLVDRQIEPlNWDTVVTDNYDATYEATEHLKEQGYERIVFVTEPikgistrreRLQgFLDALARYNIEGDVYV---IEI 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 208 AGIacDYVEAGIVADICAHEATARAIFerysdvdaIVGSDLVASVAlqEALRR-GISVPRDLQIIAYDGTFMAETAGMRL 286
Cdd:cd06283   158 EDT--EDLQQALAAFLSQHDGGKTAIF--------AANGVVLLRVL--RALKAlGIRIPDDVGLCGFDDWDWADLIGPGI 225
                         250       260
                  ....*....|....*....|....*...
gi 1307851395 287 TAVRQDFPAVAAALASRMDSQIAADNGT 314
Cdd:cd06283   226 TTIRQPTYEIGKAAAEILLERIEGDSGE 253
PBP1_CatR-like cd06296
ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in ...
61-304 1.92e-15

ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation; This group includes the ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group belongs to the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380519 [Multi-domain]  Cd Length: 270  Bit Score: 75.39  E-value: 1.92e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIV--MAAHTEHPGGYWTSIHRP 138
Cdd:cd06296     1 LIDLVLPQLDSPYALEVLRGVERAAAAAGLDLVVTATRAGRAPVDDWVRRAVARGSAGVVlvTSDPTSRQLRLLRSAGIP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 139 IVAFD--RTLGEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPrsqfaeattfptIRYHLTVERM------LDDAGI 210
Cdd:cd06296    81 FVLIDpvGEPDPDLPSVGATNWAGGRLATEHLLDLGHRRIAVITGP------------PRSVSGRARLagyraaLAEAGI 148
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 211 A--------CDY-VEAG--IVADICAHEATARAIFerysdvdaiVGSDLVASVALQEALRRGISVPRDLQIIAYDGTFMA 279
Cdd:cd06296   149 AvdpdlvreGDFtYEAGyrAARELLELPDPPTAVF---------AGNDEQALGVYRAARALGLRVPDDLSVIGFDDTPPA 219
                         250       260
                  ....*....|....*....|....*
gi 1307851395 280 ETAGMRLTAVRQDFPAVAAAlASRM 304
Cdd:cd06296   220 RWTSPPLTTVHQPLREMGAV-AVRL 243
PRK11041 PRK11041
DNA-binding transcriptional regulator CytR; Provisional
28-291 7.91e-15

DNA-binding transcriptional regulator CytR; Provisional


Pssm-ID: 182923 [Multi-domain]  Cd Length: 309  Bit Score: 73.88  E-value: 7.91e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  28 VSDDMRAKVEAAMRQLNYIPNELARNLYRNRTNTIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEY 107
Cdd:PRK11041    4 VSQATRQRVEQAVLEVGYSPQSLGRNLKRNESRTILVIVPDICDPFFSEIIRGIEVTAAEHGYLVLIGDCAHQNQQEKTF 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 108 VDMLQRHMMDGI----------------------VMAAHtehpggYWTSIHRPIVAFDrTLGEGVPAVRSDHEQGGQLIA 165
Cdd:PRK11041   84 VNLIITKQIDGMlllgsrlpfdaskeeqrnlppmVMANE------FAPELELPTVHID-NLTAAFEAVNYLHELGHKRIA 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 166 rqlidsgarhvvLVGGPRSqfaeattFPTIRYHLT-VERMLDDAGIACDyvEAGIVADICAHEATARAI---FERYSDVD 241
Cdd:PRK11041  157 ------------CIAGPEE-------MPLCHYRLQgYVQALRRCGITVD--PQYIARGDFTFEAGAKALkqlLDLPQPPT 215
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1307851395 242 AI-VGSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRLTAVRQ 291
Cdd:PRK11041  216 AVfCHSDVMALGALSQAKRMGLRVPQDLSIIGFDDIDLAQYCDPPLTTVAQ 266
PBP1_CcpA_TTHA0807 cd06297
ligand-binding domain of TTHA0807, a CcpA regulator, from Thermus thermophilus HB8 and its ...
61-301 1.14e-14

ligand-binding domain of TTHA0807, a CcpA regulator, from Thermus thermophilus HB8 and its close homologs; Ligand-binding domain of the uncharacterized transcription regulator TTHA0807 from the extremely thermophilic organism Thermus thermophilus HB8 and close homologs from other bacteria. Although its exact biological function is not known, the TTHA0807 belongs to the catabolite control protein A (CcpA)family of regulatory proteins. The CcpA functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.


Pssm-ID: 380520 [Multi-domain]  Cd Length: 268  Bit Score: 72.88  E-value: 1.14e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAA--HTEHPGGYWTSIHRP 138
Cdd:cd06297     1 TISLLVPEVMTPFYMRLLTGVERALDENRYDLAIFPLLSEYRLEKYLRNSTLAYQCDGLVMASldLTELFEEVIVPTEKP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 139 IVAFDRTlGEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVG-GPRSQFAEATTFPTIRYHLTVermLDDAGIACDyVEA 217
Cdd:cd06297    81 VVLIDAN-SMGYDCVYVDNVKGGFMATEYLAGLGEREYVFFGiEEDTVFTETVFREREQGFLEA---LNKAGRPIS-SSR 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 218 GIVADICAH--EATARAIFERYSDVDAIV-GSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGmrLTAVRQDFP 294
Cdd:cd06297   156 MFRIDNSSKkaECLARELLKKADNPAAFFaAADLVALGLIRAAQSLGLRVGEDVAVIGFDGQPWAASPG--LTTVRQPVE 233

                  ....*..
gi 1307851395 295 AVAAALA 301
Cdd:cd06297   234 EMGEAAA 240
PBP1_SalR cd01545
ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of ...
98-321 1.25e-14

ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380487 [Multi-domain]  Cd Length: 270  Bit Score: 72.97  E-value: 1.25e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  98 ADADKGEGEYVDMLQRHMMDGIVMAA-HTEHPGGywtsihrpIVAFDR-----------TLGEGVPAVRSDHEQGGQLIA 165
Cdd:cd01545    39 SDDEDLADRLRRFLSRSRPDGVILTPpLSDDPAL--------LDALDElgipyvriapgTDDDRSPSVRIDDRAAAREMT 110
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 166 RQLIDSGARHVVLVGGPRSQFAeattfpTIRYHLTVERMLDDAGIACD--YVEAGIVADICAHEAtARAIFERYSDVDAI 243
Cdd:cd01545   111 RHLIALGHRRIGFIAGPPDHGA------SAERLEGFRDALAEAGLPLDpdLVVQGDFTFESGLEA-AEALLDLPDRPTAI 183
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1307851395 244 VGS-DLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRLTAVRQDFPAVAAALASRMdsqIAADNGTTSAAAAE 321
Cdd:cd01545   184 FASnDEMAAGVLAAAHRLGLRVPDDLSVAGFDDSPIARLVWPPLTTVRQPIAEMARRAVELL---IAAIRGAPAGPERE 259
PRK10401 PRK10401
HTH-type transcriptional regulator GalS;
1-77 1.41e-13

HTH-type transcriptional regulator GalS;


Pssm-ID: 236681 [Multi-domain]  Cd Length: 346  Bit Score: 70.58  E-value: 1.41e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1307851395   1 MVGMRDVAKTAGVSLSTVSLVVNNTGYVSDDMRAKVEAAMRQLNYIPNELARNLYRNRTNTIGVIMPTIAHPFFATL 77
Cdd:PRK10401    1 MITIRDVARQAGVSVATVSRVLNNSALVSADTREAVMKAVSELGYRPNANAQALATQVSDTIGVVVMDVSDAFFGAL 77
Peripla_BP_1 pfam00532
Periplasmic binding proteins and sugar binding domain of LacI family; This family includes the ...
59-261 3.85e-13

Periplasmic binding proteins and sugar binding domain of LacI family; This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (pfam00356).


Pssm-ID: 395423 [Multi-domain]  Cd Length: 281  Bit Score: 68.69  E-value: 3.85e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  59 TNTIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAAhtehPGGYWTSIHR- 137
Cdd:pfam00532   1 TLKLGALVPQLDEPFFQDLVKGITKAAKDHGFDVFLLAVGDGEDTLTNAIDLLLASGADGIIITT----PAPSGDDITAk 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 138 ------PIVAFDRT--LGEGVPAVRSDHEQGGQLIARQLIDSGARHVVLV-GGPRSqfaeattfptiryHLTVERM---- 204
Cdd:pfam00532  77 aegygiPVIAADDAfdNPDGVPCVMPDDTQAGYESTQYLIAEGHKRPIAVmAGPAS-------------ALTARERvqgf 143
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1307851395 205 ---LDDAGIAC-DYVEAGIVADICAHEATARAIFERYSDVDAIVG-SDLVASVALQEALRRG 261
Cdd:pfam00532 144 maaLAAAGREVkIYHVATGDNDIPDAALAANAMLVSHPTIDAIVAmNDEAAMGAVRALLKQG 205
PBP1_CcpA cd06298
ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major ...
61-297 7.15e-13

ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation; Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.


Pssm-ID: 380521 [Multi-domain]  Cd Length: 268  Bit Score: 67.70  E-value: 7.15e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQrEFAARDLKTLLCSIADADKgEGEyVDMLQRHMM---DGIVMAAH--TEhpgGYWTSI 135
Cdd:cd06298     1 TVGVIIPDISNLYYAELARGID-DIATMYKYNIILSNSDNNV-DKE-LDLLNTMLSkqvDGIIFMGDelTE---EIREEF 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 136 HR---PIVAFDRTLGEG-VPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSqfaeattFPTIRYHLTV--ERMLDDAG 209
Cdd:cd06298    75 KRspvPVVLAGTVDSDHeIPSVNIDYEQAAYDATKSLIDKGHKKIAFVSGPLK-------EYINNDKKLQgyKRALEEAG 147
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 210 IACD---YVEAGivADICAHEATARAIFER-YSDVdAIVGSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMR 285
Cdd:cd06298   148 LEFNeplIFEGD--YDYDSGYELYEELLESgEPDA-AIVVRDEIAVGLLNAAQDRGLKVPEDLEIIGFDNTRYATMSRPQ 224
                         250
                  ....*....|....*
gi 1307851395 286 LTAVRQ---DFPAVA 297
Cdd:cd06298   225 LTSINQplyDIGAVA 239
PBP1_AraR cd01541
ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a ...
61-312 1.20e-12

ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators; Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of AraR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380483 [Multi-domain]  Cd Length: 274  Bit Score: 67.20  E-value: 1.20e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYV-DMLQRHMmDGI----VMAAHtEHPG-GYWTS 134
Cdd:cd01541     1 TIGVITTYIDDYIFPSIIQGIESVLSENGYSLLLALTNNDVEKEREILeSLLDQNV-DGLiiepTKSAL-PNPNlDLYEE 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 135 IHR---PIVAFDRTL-GEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVggprsqfaeattFPTirYHLT-VERM----- 204
Cdd:cd01541    79 LQKkgiPVVFINSYYpELDAPSVSLDDEKGGYLATKHLIDLGHRRIAGI------------FKS--DDLQgVERYqgfik 144
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 205 -LDDAGIACD------YVEAGIVADICAHEAtaRAIFERYSDVDAIVG-SDLVASVALQEALRRGISVPRDLQIIAYDGT 276
Cdd:cd01541   145 aLREAGLPIDddrilwYSTEDLEDRFFAEEL--REFLRRLSRCTAIVCyNDEIALRLIQALREAGLRVPEDLSVVGFDDS 222
                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 1307851395 277 FMAETAGMRLTAVRQDFPAVAAALASRMDSQIAADN 312
Cdd:cd01541   223 YLASLSEPPLTSVVHPKEELGRKAAELLLRMIEEGR 258
PRK14987 PRK14987
HTH-type transcriptional regulator GntR;
4-314 1.64e-12

HTH-type transcriptional regulator GntR;


Pssm-ID: 184949 [Multi-domain]  Cd Length: 331  Bit Score: 67.36  E-value: 1.64e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395   4 MRDVAKTAGVSLSTVSLVVNNTGYVSDDMRAKVEAAMRQLNYIPNELARNLYRNRTNTIGVIMPTIAHPFFATLTAHLQR 83
Cdd:PRK14987    8 LQDVADRVGVTKMTVSRFLRNPEQVSVALRGKIAAALDELGYIPNRAPDILSNATSRAIGVLLPSLTNQVFAEVLRGIES 87
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  84 EFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAAHTEHPggywtsihrpivafdRTLG----EGVP-------- 151
Cdd:PRK14987   88 VTDAHGYQTMLAHYGYKPEMEQERLESMLSWNIDGLILTERTHTP---------------RTLKmievAGIPvvelmdsq 152
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 152 ------AVRSDHEQGGQLIARQLIDSGARHVVLVGgprSQFAEATTFPTIRYhltvERMLDDAGIACDYVEAGIVADICA 225
Cdd:PRK14987  153 spcldiAVGFDNFEAARQMTTAIIARGHRHIAYLG---ARLDERTIIKQKGY----EQAMLDAGLVPYSVMVEQSSSYSS 225
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 226 HEATARAIFERYSDVDAI--VGSDLVASVALqEALRRGISVPRDLQIIAYDGTFMAETAGMRLTAVRQDFPAVAAALASR 303
Cdd:PRK14987  226 GIELIRQARREYPQLDGVfcTNDDLAVGAAF-ECQRLGLKVPDDMAIAGFHGHDIGQVMEPRLASVLTPRERMGSIGAER 304
                         330
                  ....*....|.
gi 1307851395 304 MDSQIAADNGT 314
Cdd:PRK14987  305 LLARIRGESVT 315
Peripla_BP_3 pfam13377
Periplasmic binding protein-like domain; This domain is found in a variety of transcriptional ...
167-312 4.14e-12

Periplasmic binding protein-like domain; This domain is found in a variety of transcriptional regulatory proteins. It is related to bacterial periplasmic binding proteins, although this domain is unlikely to be found in the periplasm. This domain acts as a sensor binding small molecule ligands that the DNA-binding domain responds to. This domain recognizes Sugars, sugar phosphates, sugar acids and purines (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 433159 [Multi-domain]  Cd Length: 160  Bit Score: 63.51  E-value: 4.14e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 167 QLIDSGARHVVLVGGPRSQFAEattFPTIRYHLTVERMLDdAGIACDYVEaGIVADICAHEATARAIFERYSDVDA-IVG 245
Cdd:pfam13377   1 HLAELGHRRIALIGPEGDRDDP---YSDLRERGFREAARE-LGLDVEPTL-YAGDDEAEAAAARERLRWLGALPTAvFVA 75
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1307851395 246 SDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRLTAVRQDFPAVAAALASRMDSQIAADN 312
Cdd:pfam13377  76 NDEVALGVLQALREAGLRVPEDLSVIGFDDSPLAALVSPPLTTVRVDAEELGRAAAELLLDLLNGEP 142
PBP1_MalR-like cd06294
ligand-binding domain of maltose transcription regulator MalR which is a member of the ...
61-290 8.67e-11

ligand-binding domain of maltose transcription regulator MalR which is a member of the LacI-GalR family repressors; This group includes the ligand-binding domain of maltose transcription regulator MalR which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380517 [Multi-domain]  Cd Length: 269  Bit Score: 61.83  E-value: 8.67e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAH-----PFFATLTAHLQREFAARDLKTLLcsiaDADKGEGE----YVDMLQRHMMDG-IVMAAHTEHPgg 130
Cdd:cd06294     1 TIGLVLPSSAEelfqnPFFSEVLRGISQVANENGYSLLL----ATGNTEEElleeVKRMVRGRRVDGfILLYSKEDDP-- 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 131 ywtSIHR------PIVAFDRTLG-EGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRsqfaeattfptiRYHLTVER 203
Cdd:cd06294    75 ---LIEYlkeegfPFVVIGKPLDdNDVLYVDNDNVQAGYEATEYLIDKGHKRIAFIGGDK------------NLVVSIDR 139
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 204 M------LDDAGIAcdYVEAGIVADICAHEATARAI---FERYSDVDAIVGSDLVASVALQEALR-RGISVPRDLQIIAY 273
Cdd:cd06294   140 LqgykqaLKEAGLP--LDDDYILLLDFSEEDGYDALqelLSKPPPPTAIVATDDLLALGVLRYLQeLGLRVPEDVSIISF 217
                         250
                  ....*....|....*..
gi 1307851395 274 DGTFMAETAGMRLTAVR 290
Cdd:cd06294   218 NNSPLAELASPPLTSVD 234
PBP1_RafR-like cd20009
Ligand-binding domain of DNA transcription repressor specific for raffinose (RafR) and similar ...
62-309 2.24e-09

Ligand-binding domain of DNA transcription repressor specific for raffinose (RafR) and similar proteins; Ligand-binding domain of DNA transcription repressor specific for raffinose (RafR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380664 [Multi-domain]  Cd Length: 266  Bit Score: 57.55  E-value: 2.24e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  62 IGVIMPT--IAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAaHTEHPG---GYWTSIH 136
Cdd:cd20009     2 IALVLPTedEIDGFTSQLISGISEALRGTPYHLVVTPEFPGDDPLEPVRYIVENRLADGIIIS-HTEPQDprvRYLLERG 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 137 RPIVAFDRT-LGEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSQ-FAEattfptiryHLT--VERMLDDAGIAC 212
Cdd:cd20009    81 FPFVTHGRTeLSTPHAYFDFDNEAFAYEAVRRLAARGRRRIALVAPPRELtYAQ---------HRLrgFRRALAEAGLEV 151
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 213 DyVEAGIVADICAHE--ATARAIFERYSDVDAIVGSDLVASVALQEALR-RGISVPRDLQIIAYDGTFMAETAGMRLTAV 289
Cdd:cd20009   152 E-PLLIVTLDSSAEAirAAARRLLRQPPRPDGIICASEIAALGALAGLEdAGLVVGRDVDVVAKETSPILDYFRPPIDTL 230
                         250       260
                  ....*....|....*....|
gi 1307851395 290 RQDFPAVAAALASRMDSQIA 309
Cdd:cd20009   231 YEDIEEAGRFLAEALLRRIE 250
PBP1_TreR-like cd01542
ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a ...
61-293 2.39e-09

ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators; Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380484 [Multi-domain]  Cd Length: 259  Bit Score: 57.12  E-value: 2.39e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKTLL-CSIADADKgEGEYVDMLQRHMMDGIV-MAAHTehpggywTSIHR- 137
Cdd:cd01542     1 LIGVIVPRLDSYSTSRVLEGIDEVLKENGYQPLIaNTNLDEER-EIEYLETLARQKVDGIIlFATEI-------TDEHRk 72
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 138 -------PIVafdrTLG---EGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSQFAEAttfptIRYHLTVERMLDD 207
Cdd:cd01542    73 alkklkiPVV----VLGqehEGFSCVYHDDYGAGKLLGEYLLKKGHKNIAYIGVDEEDIAVG-----VARKQGYLDALKE 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 208 AGIAC-DYVEAGIvaDICAHEATARAIFERYsDVDAIVG-SDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMR 285
Cdd:cd01542   144 HGIDEvEIVETDF--SMESGYEAAKELLKEN-KPDAIICaTDNIALGAIKALRELGIKIPEDISVAGFGGYDLSEFVSPS 220

                  ....*...
gi 1307851395 286 LTAVRQDF 293
Cdd:cd01542   221 LTTVKFDY 228
PBP1_LacI-like cd19974
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
61-308 1.07e-08

ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380629 [Multi-domain]  Cd Length: 270  Bit Score: 55.25  E-value: 1.07e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHP---FFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDGIVMAAHTehPGGYWTSIHR 137
Cdd:cd19974     1 NIAVLIPERFFGdnsFYGKIYQGIEKELSELGYNLVLEIISDEDEEELNLPSIISEEKVDGIIILGEI--SKEYLEKLKE 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 138 ---PIVAFDrTLGEGVP--AVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSqfaeATTFpTIRYhLTVERMLDDAGIAC 212
Cdd:cd19974    79 lgiPVVLVD-HYDEELNadSVLSDNYYGAYKLTSYLIEKGHKKIGFVGDINY----TSSF-MDRY-LGYRKALLEAGLPP 151
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 213 DYVEAgIVADICAHEATARAI--FERYSDVDAIV-GSDLVAsVALQEALR-RGISVPRDLQIIAYDGTFMAETAGMRLTA 288
Cdd:cd19974   152 EKEEW-LLEDRDDGYGLTEEIelPLKLMLPTAFVcANDSIA-IQLIKALKeKGYRVPEDISVVGFDNIELAELSTPPLTT 229
                         250       260
                  ....*....|....*....|
gi 1307851395 289 VRQDFPAVAAALASRMDSQI 308
Cdd:cd19974   230 VEVDKEAMGRRAVEQLLWRI 249
PBP1_hexuronate_repressor-like cd06272
ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon ...
61-274 3.91e-08

ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and close homologs, all members of the LacI-GalR family of bacterial transcription regulators; Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380496 [Multi-domain]  Cd Length: 266  Bit Score: 53.53  E-value: 3.91e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHP-FFATLTAHLQREFAARDLKTLLcSIADADKGE-GEYVDMLQRHMMDGIVMA----AHTEHPGGYWTS 134
Cdd:cd06272     1 TIGLYWPSVGERvALTRLLSGINEAISKQGYNINL-SICPYKVGHlCTAKGLFSENRFDGVIVFgisdSDIEYLNKNKPK 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 135 IhrPIVAFDRtLGEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGP---RSQFAEATTF-PTIR---YHLTVERMLDD 207
Cdd:cd06272    80 I--PIVLYNR-ESPKYSTVNVDNEKAGRLAVLLLIQKGHKSIAYIGNPnsnRNQTLRGKGFiETCEkhgIHLSDSIIDSR 156
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1307851395 208 AGIACDYVEAgivadicaheatARAIFERYSDVDAIV-GSDLVASVALQEALRRGISVPRDLQIIAYD 274
Cdd:cd06272   157 GLSIEGGDNA------------AKKLLKKKTLPKAIFcNSDDIALGVLRVLKENGISIPEDISIVSYD 212
PBP1_GalR cd01544
ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory ...
134-290 4.71e-08

ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism; Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalR is a dimeric protein like GalS and is exclusively involved in the regulation of galactose permease, the low-affinity galactose transporter. GalS is involved in regulating expression of the high-affinity galactose transporter encoded by the mgl operon. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type 1 periplasmic binding protein-like fold. Hence, they are structurally homologous to the periplasmic sugar binding of ABC-type transport systems.


Pssm-ID: 380486 [Multi-domain]  Cd Length: 269  Bit Score: 53.30  E-value: 4.71e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 134 SIHRPIVAFD-RTLGEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSQFAEATTFPTIRYHlTVERMLDDAGIA- 211
Cdd:cd01544    73 KLNPNIVFVDsNPDPDGFDSVVPDFEQAVRQALDYLIELGHRRIGFIGGKEYTSDDGEEIEDPRLR-AFREYMKEKGLYn 151
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 212 CDYVEAGIVADICAHEATARAIfERYSDVDAI-VGSDLVASVALQeALR-RGISVPRDLQIIAYDGTFMAETAGMRLTAV 289
Cdd:cd01544   152 EEYIYIGEFSVESGYEAMKELL-KEGDLPTAFfVASDPMAIGALR-ALQeAGIKVPEDISIISFNDIEVAKYVTPPLTTV 229

                  .
gi 1307851395 290 R 290
Cdd:cd01544   230 H 230
PBP1_repressor_sugar_binding-like cd01537
Ligand-binding domain of the LacI-GalR family of transcription regulators and the ...
62-299 8.85e-08

Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems; Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type 1 periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain. The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type 1, which has six beta strands, and type 2, which has five beta strands. These two distinct structural arrangements may have originated from a common ancestor.


Pssm-ID: 380479 [Multi-domain]  Cd Length: 265  Bit Score: 52.63  E-value: 8.85e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  62 IGVIMPTIAHPFFATLTAHLQREFAARDLKTLLCSIADADKGEGEYVDMLQRHMMDG-IVMAAHTEHPGGYWTS--IHRP 138
Cdd:cd01537     2 IGVTIYSYDDNFMSVIRKAIEQDAKQPGVQLLMNDSQNDQEKQNDQIDVLLAKRVKGlAINLVDPAAAGVAEKArgQNVP 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 139 IVAFDRTLGEGVPA--VRSDHEQGGQLIARQLIDSGARHVVLVGGPRSQfaeattfPTIRYHLT-VERMLDDAGIACD-- 213
Cdd:cd01537    82 VVFFDKEPSRYDKAyyVITDSKEGGIIQGDLLAKHGHIQIVLLKGPLGH-------PDAEARLAgVIKELNDKGIKTEql 154
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 214 YVEAGIVADICAHEATARAIFERYSDVDAIVGSDLVASVALQEALRRGISVPRDLQIIAYDGTFMAETAGMRLTAVRQDF 293
Cdd:cd01537   155 QLDTGDWDTASGKDKMDQWLSGPNKPTAVIANNDAMAMGAVEALKEHGLRVPSDISVFGYDALPEALKSGPLLTTILQDA 234

                  ....*.
gi 1307851395 294 PAVAAA 299
Cdd:cd01537   235 NNLGKT 240
PBP1_LacI-like cd06287
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
138-320 3.20e-07

ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380510 [Multi-domain]  Cd Length: 268  Bit Score: 50.88  E-value: 3.20e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 138 PIVAFDRTLG--EGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSQFAEATTFPTIRyHLTVERMLDDAGIACDyv 215
Cdd:cd06287    81 PVVSIGRAPGtdEPVPYVDLQSAATARLLLEHLHGAGARQVALLTGSSRRNSSLESEAAYL-RFAQEYGTTPVVYKVP-- 157
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 216 EAGivADICAHEATArAIFERYSDVDAI-VGSDLVASVALQEALRRGISVPRDLQIIA-YDGtFMAETAGMRLTAVRQDF 293
Cdd:cd06287   158 ESE--GERAGYEAAA-ALLAAHPDIDAVcVPVDAFAVGAMRAARDSGRSVPEDLMVVTrYDG-IRARTADPPLTAVDLHL 233
                         170       180
                  ....*....|....*....|....*..
gi 1307851395 294 PAVAAALASRMDSQIAADNGTTSAAAA 320
Cdd:cd06287   234 DRVARTAIDLLFASLSGEERSVEVGPA 260
PBP1_XylR cd01543
ligand-binding domain of DNA transcription repressor specific for xylose (XylR); ...
117-304 2.14e-04

ligand-binding domain of DNA transcription repressor specific for xylose (XylR); Ligand-binding domain of DNA transcription repressor specific for xylose (XylR), a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of XylR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380485 [Multi-domain]  Cd Length: 265  Bit Score: 42.19  E-value: 2.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 117 DGIVMAAHTEHPGGYWTSIHRPIVAFD-RTLGEGVPAVRSDHEQGGQLIARQLIDSGARHVVLVGGPRSQFAEAttfpti 195
Cdd:cd01543    52 DGIIARLDDPELAEALRRLGIPVVNVSgSRPEPGFPRVTTDNEAIGRMAAEHLLERGFRHFAFCGFRNAAWSRE------ 125
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 196 RYHlTVERMLDDAGIACDYVEagivADICAHEATARAIFERYSD--------VDAIVGSDLVASVALQEALRRGISVPRD 267
Cdd:cd01543   126 RGE-GFREALREAGYECHVYE----SPPSGSSRSWEEEREELADwlkslpkpVGIFACNDDRARQVLEACREAGIRVPEE 200
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1307851395 268 LQIIAYDG-TFMAETAGMRLTAVRQDFPAV---AAALASRM 304
Cdd:cd01543   201 VAVLGVDNdELICELSSPPLSSIALDAEQIgyeAAELLDRL 241
PBP1_ABC_sugar_binding-like cd01536
periplasmic sugar-binding domain of active transport systems that are members of the type 1 ...
61-276 4.28e-04

periplasmic sugar-binding domain of active transport systems that are members of the type 1 periplasmic binding protein (PBP1) superfamily; Periplasmic sugar-binding domain of active transport systems that are members of the type 1 periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2) receptors such as LsrB and LuxP which are highly homologous to periplasmic pentose/hexose sugar-binding proteins.


Pssm-ID: 380478 [Multi-domain]  Cd Length: 268  Bit Score: 41.40  E-value: 4.28e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLK-TLLCSIADADKGEGEYVDMLQRHMmDGIVMAAHTehPGGYWTSIHR-- 137
Cdd:cd01536     1 KIGVVVKDLTNPFWVAVKKGAEAAAKELGVElVVLDAQGDVAKQISQIEDLIAQGV-DAIIIAPVD--SEALVPAVKKan 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 138 ----PIVAFDRTLGEGVPA---VRSDHEQGGQLIARQL---IDSGARhVVLVGGPRSQFAeattfptiryhlTVERM--L 205
Cdd:cd01536    78 aagiPVVAVDTDIDGGGDVvafVGTDNYEAGKLAGEYLaeaLGGKGK-VAILEGPPGSST------------AIDRTkgF 144
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 206 DDAgIAcDYVEAGIVADICAH--EATARAIFE----RYSDVDAIVGSD----LVASVALQEALRRGisvprDLQIIAYDG 275
Cdd:cd01536   145 KEA-LK-KYPDIEIVAEQPANwdRAKALTVTEnllqANPDIDAVFAANddmaLGAAEALKAAGRTG-----DIKIVGVDG 217

                  .
gi 1307851395 276 T 276
Cdd:cd01536   218 T 218
RbsB COG1879
ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH ...
61-276 1.09e-03

ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH domain [Carbohydrate transport and metabolism];


Pssm-ID: 441483 [Multi-domain]  Cd Length: 307  Bit Score: 40.29  E-value: 1.09e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  61 TIGVIMPTIAHPFFATLTAHLQREFAARDLKtllCSIADADKGEGEYVDMLQRHM---MDGIVMAAHTehPGGYWTSIHR 137
Cdd:COG1879    35 TIGFVVKTLGNPFFVAVRKGAEAAAKELGVE---LIVVDAEGDAAKQISQIEDLIaqgVDAIIVSPVD--PDALAPALKK 109
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395 138 ------PIVAFDRTLGEGVPA--VRSDHEQGGQLIARQLID---SGARHVVLVGGPRSQFAEAttfptiRYHLTVERMLD 206
Cdd:COG1879   110 akaagiPVVTVDSDVDGSDRVayVGSDNYAAGRLAAEYLAKalgGKGKVAILTGSPGAPAANE------RTDGFKEALKE 183
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1307851395 207 DAGIacdYVEAGIVADICAHEA--TARAIFERYSDVDAIVGSDLVASVALQEALR-RGIsvPRDLQIIAYDGT 276
Cdd:COG1879   184 YPGI---KVVAEQYADWDREKAleVMEDLLQAHPDIDGIFAANDGMALGAAQALKaAGR--KGDVKVVGFDGS 251
PKS_KR smart00822
This enzymatic domain is part of bacterial polyketide synthases; It catalyses the first step ...
161-244 3.20e-03

This enzymatic domain is part of bacterial polyketide synthases; It catalyses the first step in the reductive modification of the beta-carbonyl centres in the growing polyketide chain. It uses NADPH to reduce the keto group to a hydroxy group.


Pssm-ID: 214833 [Multi-domain]  Cd Length: 180  Bit Score: 37.85  E-value: 3.20e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1307851395  161 GQLIARQLIDSGARHVVLVGgpRSQFAEATTFPTIryhltveRMLDDAGIACDYVeAGIVADICAHEATARAIFERYSDV 240
Cdd:smart00822  13 GRALARWLAERGARRLVLLS--RSGPDAPGAAALL-------AELEAAGARVTVV-ACDVADRDALAAVLAAIPAVEGPL 82

                   ....
gi 1307851395  241 DAIV 244
Cdd:smart00822  83 TGVI 86
 
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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