NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|492535981|ref|WP_005877467|]
View 

ribose utilization transcriptional repressor RbsR [Enterococcus durans]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PurR COG1609
DNA-binding transcriptional regulator, LacI/PurR family [Transcription];
3-337 3.08e-124

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


:

Pssm-ID: 441217 [Multi-domain]  Cd Length: 335  Bit Score: 359.90  E-value: 3.08e-124
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981   3 KKKITIKDVAKHSGVSIATVSLILNGNEaKFSPKTVEKVFASKKELGYQPDYLARQMITKETKTIGVLVPDITNPFFNIL 82
Cdd:COG1609    1 RKRVTIKDVARLAGVSVATVSRVLNGPP-RVSEETRERVLAAAEELGYRPNAAARSLRTGRTRTIGVVVPDLSNPFFAEL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  83 MRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAINEnLKKHGRPYIVLDQKKSHGFSDSV 162
Cdd:COG1609   80 LRGIEEAARERGYQLLLANSDEDPEREREALRLLLSRRVDGLILAGSRLDDARLER-LAEAGIPVVLIDRPLPDPGVPSV 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 163 RTDDFRGGYLAGVHLLSLGHENIALVypeNPPENI---QLRIEGFKHALDFYQYSHDQLLLLPTLFSKQGGYQAVPSIIE 239
Cdd:COG1609  159 GVDNRAGARLATEHLIELGHRRIAFI---GGPADSssaRERLAGYREALAEAGLPPDPELVVEGDFSAESGYEAARRLLA 235

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 240 SAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKASAKLLLSRIQSPTKE 317
Cdd:COG1609  236 RGPrpTAIFCANDLMALGALRALREAGLRVPEDVSVVGFDDIPLARYLTPPLTTVRQPIEEMGRRAAELLLDRIEGPDAP 315

                        330       340
                 ....*....|....*....|
gi 492535981 318 WEEELLPVKLEKRASTAPLK 337
Cdd:COG1609  316 PERVLLPPELVVRESTAPAP 335
 
Name Accession Description Interval E-value
PurR COG1609
DNA-binding transcriptional regulator, LacI/PurR family [Transcription];
3-337 3.08e-124

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


Pssm-ID: 441217 [Multi-domain]  Cd Length: 335  Bit Score: 359.90  E-value: 3.08e-124
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981   3 KKKITIKDVAKHSGVSIATVSLILNGNEaKFSPKTVEKVFASKKELGYQPDYLARQMITKETKTIGVLVPDITNPFFNIL 82
Cdd:COG1609    1 RKRVTIKDVARLAGVSVATVSRVLNGPP-RVSEETRERVLAAAEELGYRPNAAARSLRTGRTRTIGVVVPDLSNPFFAEL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  83 MRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAINEnLKKHGRPYIVLDQKKSHGFSDSV 162
Cdd:COG1609   80 LRGIEEAARERGYQLLLANSDEDPEREREALRLLLSRRVDGLILAGSRLDDARLER-LAEAGIPVVLIDRPLPDPGVPSV 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 163 RTDDFRGGYLAGVHLLSLGHENIALVypeNPPENI---QLRIEGFKHALDFYQYSHDQLLLLPTLFSKQGGYQAVPSIIE 239
Cdd:COG1609  159 GVDNRAGARLATEHLIELGHRRIAFI---GGPADSssaRERLAGYREALAEAGLPPDPELVVEGDFSAESGYEAARRLLA 235

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 240 SAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKASAKLLLSRIQSPTKE 317
Cdd:COG1609  236 RGPrpTAIFCANDLMALGALRALREAGLRVPEDVSVVGFDDIPLARYLTPPLTTVRQPIEEMGRRAAELLLDRIEGPDAP 315

                        330       340
                 ....*....|....*....|
gi 492535981 318 WEEELLPVKLEKRASTAPLK 337
Cdd:COG1609  316 PERVLLPPELVVRESTAPAP 335
PBP1_DegA_Like cd19976
ligand-binding domain of putative DNA transcription regulators highly similar to that of the ...
 66-332 1.15e-123

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: 355.79  E-value: 1.15e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAINENLKKHGR 145
Cdd:cd19976    1 TIGLIVPDISNPFFSELVRGIEDTLNELGYNIILCNTYNDFEREKKYIQELKERNVDGIIIASSNISDEAIIKLLKEEKI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVYPENPPENIQLRIEGFKHALDFYQYSHDQLLLLPTLF 225
Cdd:cd19976   81 PVVVLDRYIEDNDSDSVGVDDYRGGYEATKYLIELGHTRIGCIVGPPSTYNEHERIEGYKNALQDHNLPIDESWIYSGES 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 226 SKQGGYQAVPSIIESAT-TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKASA 304
Cdd:cd19976  161 SLEGGYKAAEELLKSKNpTAIFAGNDLIAMGVYRAALELGLKIPEDLSVIGFDNIILSEYITPALTTIAQPIFEMGQEAA 240

                        250       260
                 ....*....|....*....|....*...
gi 492535981 305 KLLLSRIQSPTKEWEEELLPVKLEKRAS 332
Cdd:cd19976  241 KLLLKIIKNPAKKKEEIVLPPELIKRDS 268
PRK10423 PRK10423
transcriptional repressor RbsR; Provisional
 8-332 3.14e-63

transcriptional repressor RbsR; Provisional


Pssm-ID: 182448 [Multi-domain]  Cd Length: 327  Bit Score: 203.78  E-value: 3.14e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981   8 IKDVAKHSGVSIATVSLILNGNeaKF-SPKTVEKVFASKKELGYQPDYLARQMITKETKTIGVLVPDITNPFFNILMRGI 86
Cdd:PRK10423   1 MKDVARLAGVSTSTVSHVINKD--RFvSEAITAKVEAAIKELNYAPSALARSLKLNQTRTIGMLITASTNPFYSELVRGV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  87 EEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFII-ATSAISTSAinENLKKH-GRPYIVLDQKKSHGFSDSVRT 164
Cdd:PRK10423  79 ERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLlCTETHQPSR--EIMQRYpSVPTVMMDWAPFDGDSDLIQD 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 165 DDFRGGYLAGVHLLSLGHENIALVYPENPPENIQLRIEGFKHALDFYQYSHDQLLLLPTLFSKQGGYQAVPSII--ESAT 242
Cdd:PRK10423 157 NSLLGGDLATQYLIDKGYTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMQQLLalPLRP 236

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 243 TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKASAKLLLSRIQSPTKEWEEEL 322
Cdd:PRK10423 237 QAVFTGNDAMAVGVYQALYQAGLSVPQDIAVIGYDDIELARYMTPPLTTIHQPKDELGELAIDVLIHRMAQPTLQQQRLQ 316

                        330
                 ....*....|
gi 492535981 323 LPVKLEKRAS 332
Cdd:PRK10423 317 LTPELMERGS 326
Peripla_BP_3 pfam13377
Periplasmic binding protein-like domain; This domain is found in a variety of transcriptional ...
 176-333 6.26e-38

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: 132.85  E-value: 6.26e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  176 HLLSLGHENIALVYPENPP--ENIQLRIEGFKHALDFYQYSHDQLLLLPTLFSKQGGYQAVPSIIESATTAIFALNDELA 253
Cdd:pfam13377   1 HLAELGHRRIALIGPEGDRddPYSDLRERGFREAARELGLDVEPTLYAGDDEAEAAAARERLRWLGALPTAVFVANDEVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  254 FGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKASAKLLLSRIQSPTKEWEEELLPVKLEKRAST 333
Cdd:pfam13377  81 LGVLQALREAGLRVPEDLSVIGFDDSPLAALVSPPLTTVRVDAEELGRAAAELLLDLLNGEPAPPERVLLPPELVEREST 160
HTH_LACI smart00354
helix_turn _helix lactose operon repressor;
6-76 9.35e-28

helix_turn _helix lactose operon repressor;


Pssm-ID: 197675 [Multi-domain]  Cd Length: 70  Bit Score: 103.05  E-value: 9.35e-28
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 492535981     6 ITIKDVAKHSGVSIATVSLILNGNEaKFSPKTVEKVFASKKELGYQPDYLARQMITKETKTIGVLVPDITN 76
Cdd:smart00354   1 ATIKDVARLAGVSKATVSRVLNGKG-RVSEETREKVLAAMEELGYIPNRVARSLKGKKTKTIGLIVPDITN 70
fruct_sucro_rep TIGR02417
D-fructose-responsive transcription factor; Members of this family belong the lacI ...
 7-330 2.41e-26

D-fructose-responsive transcription factor; Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer. [Regulatory functions, DNA interactions]


Pssm-ID: 131470 [Multi-domain]  Cd Length: 327  Bit Score: 106.76  E-value: 2.41e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981    7 TIKDVAKHSGVSIATVSLILNG--NEAKFSPKTVEKVFASKKELGYQPDYLARQMITKETKTIGVLVPDITNPFF----N 80
Cdd:TIGR02417   1 TLSDIAKLAGVSKTTASYVINGkaKEYRISQETVERVMAVVREQGYQPNIHAASLRAGRSRTIGLVIPDLENYSYariaK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981   81 ILMRGIEEVLYQqhfVTILCnADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAINENLKKHGRPYIVLDQKKSHGFSD 160
Cdd:TIGR02417  81 ELEQQCREAGYQ---LLIAC-SDDNPDQEKVVIENLLARQVDALIVASCMPPEDAYYQKLQNEGLPVVALDRSLDDEHFC 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  161 SVRTDDFRGGYLAGVHLLSLGHENIALV--YPENPPEniQLRIEGFKHALDfyQYSHDQLLLLPTLFSKQGGYQAVPSII 238
Cdd:TIGR02417 157 SVISDDVDAAAELIERLLSQHADEFWYLgaQPELSVS--RDRLAGFRQALK--QATLEVEWVYGGNYSRESGYQMFAKLC 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  239 ESATT---AIFALNDELAFGLYRGLEEKgKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKASAKLLLSRIQSPT 315
Cdd:TIGR02417 233 ARLGRlpqALFTTSYTLLEGVLDYMLER-PLLDSQLHLATFGDNYLLDFLPLPINSVAQQHRQLAWHALELALAAIDGKK 311

                         330
                  ....*....|....*
gi 492535981  316 KEWEEELLPVKLEKR 330
Cdd:TIGR02417 312 PEPGQRYIPRTLQIR 326
 
Name Accession Description Interval E-value
PurR COG1609
DNA-binding transcriptional regulator, LacI/PurR family [Transcription];
3-337 3.08e-124

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


Pssm-ID: 441217 [Multi-domain]  Cd Length: 335  Bit Score: 359.90  E-value: 3.08e-124
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981   3 KKKITIKDVAKHSGVSIATVSLILNGNEaKFSPKTVEKVFASKKELGYQPDYLARQMITKETKTIGVLVPDITNPFFNIL 82
Cdd:COG1609    1 RKRVTIKDVARLAGVSVATVSRVLNGPP-RVSEETRERVLAAAEELGYRPNAAARSLRTGRTRTIGVVVPDLSNPFFAEL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  83 MRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAINEnLKKHGRPYIVLDQKKSHGFSDSV 162
Cdd:COG1609   80 LRGIEEAARERGYQLLLANSDEDPEREREALRLLLSRRVDGLILAGSRLDDARLER-LAEAGIPVVLIDRPLPDPGVPSV 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 163 RTDDFRGGYLAGVHLLSLGHENIALVypeNPPENI---QLRIEGFKHALDFYQYSHDQLLLLPTLFSKQGGYQAVPSIIE 239
Cdd:COG1609  159 GVDNRAGARLATEHLIELGHRRIAFI---GGPADSssaRERLAGYREALAEAGLPPDPELVVEGDFSAESGYEAARRLLA 235

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 240 SAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKASAKLLLSRIQSPTKE 317
Cdd:COG1609  236 RGPrpTAIFCANDLMALGALRALREAGLRVPEDVSVVGFDDIPLARYLTPPLTTVRQPIEEMGRRAAELLLDRIEGPDAP 315

                        330       340
                 ....*....|....*....|
gi 492535981 318 WEEELLPVKLEKRASTAPLK 337
Cdd:COG1609  316 PERVLLPPELVVRESTAPAP 335
PBP1_DegA_Like cd19976
ligand-binding domain of putative DNA transcription regulators highly similar to that of the ...
 66-332 1.15e-123

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: 355.79  E-value: 1.15e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAINENLKKHGR 145
Cdd:cd19976    1 TIGLIVPDISNPFFSELVRGIEDTLNELGYNIILCNTYNDFEREKKYIQELKERNVDGIIIASSNISDEAIIKLLKEEKI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVYPENPPENIQLRIEGFKHALDFYQYSHDQLLLLPTLF 225
Cdd:cd19976   81 PVVVLDRYIEDNDSDSVGVDDYRGGYEATKYLIELGHTRIGCIVGPPSTYNEHERIEGYKNALQDHNLPIDESWIYSGES 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 226 SKQGGYQAVPSIIESAT-TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKASA 304
Cdd:cd19976  161 SLEGGYKAAEELLKSKNpTAIFAGNDLIAMGVYRAALELGLKIPEDLSVIGFDNIILSEYITPALTTIAQPIFEMGQEAA 240

                        250       260
                 ....*....|....*....|....*...
gi 492535981 305 KLLLSRIQSPTKEWEEELLPVKLEKRAS 332
Cdd:cd19976  241 KLLLKIIKNPAKKKEEIVLPPELIKRDS 268
PBP1_LacI_sugar_binding-like cd06267
ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 ...
 66-327 1.06e-92

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: 277.09  E-value: 1.06e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAINEnLKKHGR 145
Cdd:cd06267    1 TIGLIVPDISNPFFAELLRGIEDAARERGYSLLLCNTDEDPEREREYLRLLLSRRVDGIILAPSSLDDELLEE-LLAAGI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVYPENPPENIQLRIEGFKHALDFYQYSHDQLLLLPTLF 225
Cdd:cd06267   80 PVVLIDRRLDGLGVDSVVVDNYAGAYLATEHLIELGHRRIAFIGGPLDLSTSRERLEGYRDALAEAGLPVDPELVVEGDF 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 226 SKQGGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKAS 303
Cdd:cd06267  160 SEESGYEAARELLALPPrpTAIFAANDLMAIGALRALRELGLRVPEDISVVGFDDIPLAALLTPPLTTVRQPAYEMGRAA 239

                        250       260
                 ....*....|....*....|....
gi 492535981 304 AKLLLSRIQSPTKEWEEELLPVKL 327
Cdd:cd06267  240 AELLLERIEGEEEPPRRIVLPTEL 263
PBP1_Qymf-like cd06291
ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing ...
 66-332 2.20e-80

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: 245.51  E-value: 2.20e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIatsaISTSAINENLKKHGR 145
Cdd:cd06291    1 TIGLIVPDISNPFFAELAKYIEKELFKKGYKMILCNSNEDEEKEKEYLEMLKRNKVDGIIL----GSHSLDIEEYKKLNI 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYIVLDQKKSHGFSdSVRTDDFRGGYLAGVHLLSLGHENIALVYPENPPENIQLRIEGFKHALDFYQYSHDQLLLLPTLF 225
Cdd:cd06291   77 PIVSIDRYLSEGIP-SVSSDNYQGGRLAAEHLIEKGCKKILHIGGPSNNSPANERYRGFEDALKEAGIEYEIIEIDENDF 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 226 SKQGGYQAVPSIIES--ATTAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKAS 303
Cdd:cd06291  156 SEEDAYELAKELLEKypDIDGIFASNDLLAIGVLKALQKLGIRVPEDVQIIGFDGIEISELLYPELTTIRQPIEEMAKEA 235

                        250       260
                 ....*....|....*....|....*....
gi 492535981 304 AKLLLSRIQSPTKEWEEELLPVKLEKRAS 332
Cdd:cd06291  236 VELLLKLIEGEEIEESRIVLPVELIERET 264
PBP1_LacI-like cd06285
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 66-333 1.31e-73

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: 228.65  E-value: 1.31e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAINEnLKKHGR 145
Cdd:cd06285    1 TIGVLVSDLSNPFYAELVEGIEDAARERGYTVLLADTGDDPERELAALDSLLSRRVDGLIITPARDDAPDLQE-LAARGV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVYPENPPENIQLRIEGFKHALDFYQYSHDQLLLLPTLF 225
Cdd:cd06285   80 PVVLVDRRIGDTALPSVTVDNELGGRLATRHLLELGHRRIAVVAGPLNASTGRDRLRGYRRALAEAGLPVPDERIVPGGF 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 226 SKQGGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKAS 303
Cdd:cd06285  160 TIEAGREAAYRLLSRPErpTAVFAANDLMAIGVLRAARDLGLRVPEDLSVVGFDDIPLAAFLPPPLTTVRQPKYEMGRRA 239

                        250       260       270
                 ....*....|....*....|....*....|
gi 492535981 304 AKLLLSRIQSPTKEWEEELLPVKLEKRAST 333
Cdd:cd06285  240 AELLLQLIEGGGRPPRSITLPPELVVREST 269
PBP1_LacI-like cd06284
ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus ...
 66-332 2.08e-70

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: 220.10  E-value: 2.08e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAINENlkkHGR 145
Cdd:cd06284    1 TILVLVPNISNPFYSEILRGIEDAAAEAGYDVLLGDTDSDPEREDDLLDMLRSRRVDGVILLSGRLDAELLSEL---SKR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYIVL------DQKKSHgfsdsVRTDDFRGGYLAGVHLLSLGHENIALVYpeNPPENI--QLRIEGFKHALDFYQYSHDQ 217
Cdd:cd06284   78 YPIVQcceyipDSGVPS-----VSIDNEAAAYDATEYLISLGHRRIAHIN--GPLDNVyaRERLEGYRRALAEAGLPVDE 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 218 LLLLPTLFSKQGGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQP 295
Cdd:cd06284  151 DLIIEGDFSFEAGYAAARALLALPErpTAIFCASDELAIGAIKALRRAGLRVPEDVSVIGFDDIEFAEMFSPSLTTIRQP 230

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 492535981 296 IVELGKASAKLLLSRIQSPTKEWEEELLPVKLEKRAS 332
Cdd:cd06284  231 RYEIGETAAELLLEKIEGEGVPPEHIILPHELIVRES 267
PBP1_LacI-like cd06290
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 66-332 5.90e-70

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: 219.02  E-value: 5.90e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAINENlkKHGR 145
Cdd:cd06290    1 TIGVLVPDIDSPFYSEILNGIEEVLAESGYTLIVSTSHWNADRELEILRLLLARKVDGIIVVGGFGDEELLKLL--AEGI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVY-PENPPENIQlRIEGFKHALDFYQYSHDQLLLLPTL 224
Cdd:cd06290   79 PVVLVDRELEGLNLPVVNVDNEQGGYNATNHLIDLGHRRIVHISgPEDHPDAQE-RYAGYRRALEDAGLEVDPRLIVEGD 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 225 FSKQGGYQAVPSIIE--SATTAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKA 302
Cdd:cd06290  158 FTEESGYEAMKKLLKrgGPFTAIFAANDLMALGAMKALREAGIRVPDDVSVIGFDDLPFSKYTTPPLTTVRQPLYEMGKT 237

                        250       260       270
                 ....*....|....*....|....*....|
gi 492535981 303 SAKLLLSRIQSPTKEWEEELLPVKLEKRAS 332
Cdd:cd06290  238 AAEILLELIEGKGRPPRRIILPTELVIRES 267
PBP1_PurR cd06275
ligand-binding domain of purine repressor, PurR, which functions as the master regulatory ...
 66-332 3.02e-69

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: 217.12  E-value: 3.02e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAiSTSAINENLKKHGR 145
Cdd:cd06275    1 TIGLLVTSSENPFFAEVVRGVEDACFRAGYSLILCNSDNDPEKQRAYLDMLAEKRVDGLLLMCSE-MTDDDAELLAALRS 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 -PYIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALV-YPENPPEnIQLRIEGFKHAL---------DFYQYS 214
Cdd:cd06275   80 iPVVVLDREIAGDNADAVLDDSFQGGYLATRHLIELGHRRIGCItGPLEHSV-SRERLAGFRRALaeagievppSWIVEG 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 215 HdqllllptlFSKQGGYQAVPSII--ESATTAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTI 292
Cdd:cd06275  159 D---------FEPEGGYEAMQRLLsqPPRPTAVFACNDMMALGALRAAQEQGLRVPQDISIIGYDDIELARYFSPALTTI 229

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 492535981 293 AQPIVELGKASAKLLLSRIQSPTKEWEEELLPVKLEKRAS 332
Cdd:cd06275  230 HQPKDELGELAVELLLDRIENKREEPQSIVLEPELIERES 269
PBP1_CcpA-like cd19975
ligand-binding domain of putative DNA transcription regulators highly similar to that of the ...
 66-332 9.24e-67

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: 210.88  E-value: 9.24e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAIsTSAINENLKKHGR 145
Cdd:cd19975    1 TIGVIIPDISNSFFAEILKGIEDEARENGYSVILCNTGSDEEREKKYLQLLKEKRVDGIIFASGTL-TEENKQLLKNMNI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVY--PENPPENIQlRIEGFKHALDFYQYSHDQLLLLPT 223
Cdd:cd19975   80 PVVLVSTESEDPDIPSVKIDDYQAAYDATNYLIKKGHRKIAMISgpLDDPNAGYP-RYEGYKKALKDAGLPIKENLIVEG 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 224 LFSKQGGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGK 301
Cdd:cd19975  159 DFSFKSGYQAMKRLLKNKKlpTAVFAASDEMALGVISAAYDHGIRVPEDISVIGFDNTEIAEMSIPPLTTVSQPFYEMGK 238

                        250       260       270
                 ....*....|....*....|....*....|.
gi 492535981 302 ASAKLLLSRIQSPTKEWEEELLPVKLEKRAS 332
Cdd:cd19975  239 KAVELLLDLIKNEKKEEKSIVLPHQIIERES 269
PBP1_LacI-like cd06280
ligand-binding domain of an uncharacterized transcription regulator from Staphylococcus ...
 66-327 5.90e-65

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: 206.34  E-value: 5.90e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAINeNLKKHGR 145
Cdd:cd06280    1 TIGLIVPDITNPFFTTIARGIEDAAEKHGYQVILANTDEDPEKEKRYLDSLLSKQVDGIILAPSAGPSRELK-RLLKHGI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVY-PENPPENIQlRIEGFKHALDFYQYSHDQLLLLPTL 224
Cdd:cd06280   80 PIVLIDREVEGLELDLVAGDNREGAYKAVKHLIELGHRRIGLITgPLEISTTRE-RLAGYREALAEAGIPVDESLIFEGD 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 225 FSKQGGYQAVPSII--ESATTAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKA 302
Cdd:cd06280  159 STIEGGYEAVKALLdlPPRPTAIFATNNLMAVGALRALRERGLEIPQDISVVGFDDSDWFEIVDPPLTVVAQPAYEIGRI 238

                        250       260
                 ....*....|....*....|....*
gi 492535981 303 SAKLLLSRIQSPTKEWEEELLPVKL 327
Cdd:cd06280  239 AAQLLLERIEGQGEEPRRIVLPTEL 263
PBP1_LacI-like cd06293
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 66-332 1.21e-64

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: 205.58  E-value: 1.21e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAInENLKKHGR 145
Cdd:cd06293    1 TIGLVVPDVSNPFFAEVARGVEDAARERGYAVVLCNSGRDPERERRYLEMLESQRVRGLIVTPSDDDLSHL-ARLRARGT 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVypeNPPENI---QLRIEGFKHALDFYQYSHDQLLLLP 222
Cdd:cd06293   80 AVVLLDRPAPGPAGCSVSVDDVQGGALAVDHLLELGHRRIAFV---SGPLRTrqvAERLAGARAAVAEAGLDPDEVVREL 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 223 TLFSK--QGGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVE 298
Cdd:cd06293  157 SAPDAnaELGRAAAAQLLAMPPrpTAVFAANDLLALGLLAGLRRAGLRVPDDVSVVGYDDLPFAAAANPPLTTVRQPSYE 236

                        250       260       270
                 ....*....|....*....|....*....|....
gi 492535981 299 LGKASAKLLLSRIQSPTKEWEEELLPVKLEKRAS 332
Cdd:cd06293  237 LGRAAADLLLDEIEGPGHPHEHVVFQPELVVRSS 270
PBP1_GalS-like cd06270
ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory ...
 66-331 6.61e-64

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: 203.52  E-value: 6.61e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKE---IEYLAEltrRGVDGFIIATSAISTSAINEnLKK 142
Cdd:cd06270    1 TIGLVVPDLSGPFFGSLLKGAERVARAHGKQLLITSGHHDAEEEreaIEFLLD---RRCDAIILHSRALSDEELIL-IAE 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 143 HGRPYIVLDqKKSHGFSD-SVRTDDFRGGYLAGVHLLSLGHENIALVYPENPPENIQLRIEGFKHALDFYQYSHDQLLLL 221
Cdd:cd06270   77 KIPPLVVIN-RYIPGLADrCVWLDNEQGGRLAAEHLLDLGHRRIACITGPLDIPDARERLAGYRDALAEAGIPLDPSLII 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 222 PTLFSKQGGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVEL 299
Cdd:cd06270  156 EGDFTIEGGYAAAKQLLARGLpfTALFAYNDDMAIGALAALHEAGIKVPEDVSVIGFDDVPLARYLSPKLTTVHYPIEEM 235

                        250       260       270
                 ....*....|....*....|....*....|..
gi 492535981 300 GKASAKLLLSRIQSPTKEWEEELLPvKLEKRA 331
Cdd:cd06270  236 AQAAAELALNLAYGEPLPISHEFTP-TLIERD 266
PBP1_EndR-like cd19977
periplasmic ligand-binding domain of putative repressor of the endoglucanase operon and its ...
 66-317 7.04e-64

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: 203.53  E-value: 7.04e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAInENLKKHGR 145
Cdd:cd19977    1 TIGLIVADILNPFFTSVVRGIEDEAYKNGYHVILCNTDEDPEKEKKYIEMLRAKQVDGIIIAPTGGNEDLI-EKLVKSGI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVYPENPPENIQLRIEGFKHALDFYQYSHDQLLLLpTLF 225
Cdd:cd19977   80 PVVFVDRYIPGLDVDTVVVDNFKGAYQATEHLIELGHKRIAFITYPLELSTRQERLEGYKAALADHGLPVDEELIK-HVD 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 226 SKQGGYQAVPSIIES--ATTAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKAS 303
Cdd:cd19977  159 RQDDVRKAISELLKLekPPDAIFAANNLITLEVLKAIKELGLRIPDDIALIGFDDIPWADLFNPPLTVIAQPTYEIGRKA 238

                        250
                 ....*....|....
gi 492535981 304 AKLLLSRIQSPTKE 317
Cdd:cd19977  239 AELLLDRIENKPKG 252
PBP1_MalI-like cd06289
ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia ...
 66-331 8.82e-64

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: 203.18  E-value: 8.82e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAINENLKKHGR 145
Cdd:cd06289    1 TVGLIVPDLSNPFFAELLAGIEEALEEAGYLVFLANTGEDPERQRRFLRRMLEQGVDGLILSPAAGTTAELLRRLKAWGI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALV--------YPEnppeniqlRIEGFKHALDFYQYSHDQ 217
Cdd:cd06289   81 PVVLALRDVPGSDLDYVGIDNRLGAQLATEHLIALGHRRIAFLgglsdsstRRE--------RLAGFRAALAEAGLPLDE 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 218 LLLLPTLFSKQGGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQP 295
Cdd:cd06289  153 SLIVPGPATREAGAEAARELLDAAPppTAVVCFNDLVALGAMLALRRRGLEPGRDIAVVGFDDVPEAALWTPPLTTVSVH 232

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 492535981 296 IVELGKASAKLLLSRIQSPTKEWEEELLPVKLEKRA 331
Cdd:cd06289  233 PREIGRRAARLLLRRIEGPDTPPERIIIEPRLVVRE 268
PRK10423 PRK10423
transcriptional repressor RbsR; Provisional
 8-332 3.14e-63

transcriptional repressor RbsR; Provisional


Pssm-ID: 182448 [Multi-domain]  Cd Length: 327  Bit Score: 203.78  E-value: 3.14e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981   8 IKDVAKHSGVSIATVSLILNGNeaKF-SPKTVEKVFASKKELGYQPDYLARQMITKETKTIGVLVPDITNPFFNILMRGI 86
Cdd:PRK10423   1 MKDVARLAGVSTSTVSHVINKD--RFvSEAITAKVEAAIKELNYAPSALARSLKLNQTRTIGMLITASTNPFYSELVRGV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  87 EEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFII-ATSAISTSAinENLKKH-GRPYIVLDQKKSHGFSDSVRT 164
Cdd:PRK10423  79 ERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLlCTETHQPSR--EIMQRYpSVPTVMMDWAPFDGDSDLIQD 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 165 DDFRGGYLAGVHLLSLGHENIALVYPENPPENIQLRIEGFKHALDFYQYSHDQLLLLPTLFSKQGGYQAVPSII--ESAT 242
Cdd:PRK10423 157 NSLLGGDLATQYLIDKGYTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMQQLLalPLRP 236

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 243 TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKASAKLLLSRIQSPTKEWEEEL 322
Cdd:PRK10423 237 QAVFTGNDAMAVGVYQALYQAGLSVPQDIAVIGYDDIELARYMTPPLTTIHQPKDELGELAIDVLIHRMAQPTLQQQRLQ 316

                        330
                 ....*....|
gi 492535981 323 LPVKLEKRAS 332
Cdd:PRK10423 317 LTPELMERGS 326
PRK10703 PRK10703
HTH-type transcriptional repressor PurR;
7-331 1.25e-62

HTH-type transcriptional repressor PurR;


Pssm-ID: 236739 [Multi-domain]  Cd Length: 341  Bit Score: 202.65  E-value: 1.25e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981   7 TIKDVAKHSGVSIATVSLILNgnEAKF-SPKTVEKVFASKKELGYQPDYLARQMITKETKTIGVLVPDITNPFFNILMRG 85
Cdd:PRK10703   3 TIKDVAKRAGVSTTTVSHVIN--KTRFvAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLATSSEAPYFAEIIEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  86 IEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATS-----AISTSAINENLkkhgrPYIVLDQKKSHG-FS 159
Cdd:PRK10703  81 VEKNCYQKGYTLILCNAWNNLEKQRAYLSMLAQKRVDGLLVMCSeypepLLAMLEEYRHI-----PMVVMDWGEAKAdFT 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 160 DSVRTDDFRGGYLAGVHLLSLGHENIALVYPENPPENIQLRIEGFKHALDFYQYSHDQLLLLPTLFSKQGGYQAVPSII- 238
Cdd:PRK10703 156 DAIIDNAFEGGYLAGRYLIERGHRDIGVIPGPLERNTGAGRLAGFMKAMEEANIKVPEEWIVQGDFEPESGYEAMQQILs 235

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 239 -ESATTAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKASAKLLLSRIQSPTKE 317
Cdd:PRK10703 236 qKHRPTAVFCGGDIMAMGAICAADEMGLRVPQDISVIGYDNVRNARYFTPALTTIHQPKDRLGETAFNMLLDRIVNKREE 315

                        330
                 ....*....|....*
gi 492535981 318 WEE-ELLPVKLEKRA 331
Cdd:PRK10703 316 PQTiEVHPRLVERRS 330
PBP1_sucrose_transcription_regulator cd06288
ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members ...
 66-332 3.69e-62

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: 198.93  E-value: 3.69e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDI-TNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSaiSTSAINENLKKHG 144
Cdd:cd06288    1 TIGLITDDIaTTPFAGDIIRGAQDAAEEHGYLLLLANTGGDPELEAEAIRELLSRRVDGIIYASM--HHREVTLPPELTD 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 145 RPYIVLDqkkshGFSD-----SVRTDDFRGGYLAGVHLLSLGHENIALVYPENPPENIQLRIEGFKHALDFYQYSHDQLL 219
Cdd:cd06288   79 IPLVLLN-----CFDDdpslpSVVPDDEQGGYLATRHLIEAGHRRIAFIGGPEDSLATRLRLAGYRAALAEAGIPYDPSL 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 220 LLPTLFSKQGGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIV 297
Cdd:cd06288  154 VVHGDWGRESGYEAAKRLLSAPDrpTAIFCGNDRMAMGVYQAAAELGLRVPEDLSVVGFDNQELAAYLRPPLTTVALPYY 233

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 492535981 298 ELGKASAKLLLSRIQSPTKEWEEELLPVKLEKRAS 332
Cdd:cd06288  234 EMGRRAAELLLDGIEGEPPEPGVIRVPCPLIERES 268
PBP1_AraR cd01541
ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a ...
 66-332 3.29e-55

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: 181.22  E-value: 3.29e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFII--ATSAISTSAIN--ENLK 141
Cdd:cd01541    1 TIGVITTYIDDYIFPSIIQGIESVLSENGYSLLLALTNNDVEKEREILESLLDQNVDGLIIepTKSALPNPNLDlyEELQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 142 KHGRPYIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVYPENppeNIQ--LRIEGFKHALDFYQ--YSHDQ 217
Cdd:cd01541   81 KKGIPVVFINSYYPELDAPSVSLDDEKGGYLATKHLIDLGHRRIAGIFKSD---DLQgvERYQGFIKALREAGlpIDDDR 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 218 LLLLPTL-FSKQGGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQ 294
Cdd:cd01541  158 ILWYSTEdLEDRFFAEELREFLRRLSrcTAIVCYNDEIALRLIQALREAGLRVPEDLSVVGFDDSYLASLSEPPLTSVVH 237

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 492535981 295 PIVELGKASAKLLLSRIQSPTKEwEEELLPVKLEKRAS 332
Cdd:cd01541  238 PKEELGRKAAELLLRMIEEGRKP-ESVIFPPELIERES 274
PBP1_TreR-like cd01542
ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a ...
 66-327 5.08e-53

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: 175.38  E-value: 5.08e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAIsTSAINENLKKHGR 145
Cdd:cd01542    1 LIGVIVPRLDSYSTSRVLEGIDEVLKENGYQPLIANTNLDEEREIEYLETLARQKVDGIILFATEI-TDEHRKALKKLKI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYIVLDQKkSHGFSdSVRTDDFRGGYLAGVHLLSLGHENIALV-YPENPPENIQLRIEGFKHALDFYQYSHDQLLLlpTL 224
Cdd:cd01542   80 PVVVLGQE-HEGFS-CVYHDDYGAGKLLGEYLLKKGHKNIAYIgVDEEDIAVGVARKQGYLDALKEHGIDEVEIVE--TD 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 225 FSKQGGYQAVPSIIE-SATTAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKAS 303
Cdd:cd01542  156 FSMESGYEAAKELLKeNKPDAIICATDNIALGAIKALRELGIKIPEDISVAGFGGYDLSEFVSPSLTTVKFDYEEAGEKA 235

                        250       260
                 ....*....|....*....|....
gi 492535981 304 AKLLLSRIQSPTKEwEEELLPVKL 327
Cdd:cd01542  236 AELLLDMIEGEKVP-KKQKLPYEL 258
PBP1_RegR_EndR_KdgR-like cd06283
ligand-binding domain of DNA transcription repressor RegR and other putative regulators such ...
 66-327 2.31e-52

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: 173.89  E-value: 2.31e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAINENLKKhGR 145
Cdd:cd06283    1 LIGVIVADITNPFSSLLLKGIEDVCREAGYQLLICNSNNDPEKERDYIESLLSQRVDGLILQPTGNNNDAYLELAQK-GL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PyIVLDQKKSHGFS-DSVRTDDFRGGYLAGVHLLSLGHENIALVypENPPENI---QLRIEGFKHALDFYQYSHDQLLLL 221
Cdd:cd06283   80 P-VVLVDRQIEPLNwDTVVTDNYDATYEATEHLKEQGYERIVFV--TEPIKGIstrRERLQGFLDALARYNIEGDVYVIE 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 222 PTLFSK-QGGYQAVPSIIESATTAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELG 300
Cdd:cd06283  157 IEDTEDlQQALAAFLSQHDGGKTAIFAANGVVLLRVLRALKALGIRIPDDVGLCGFDDWDWADLIGPGITTIRQPTYEIG 236

                        250       260
                 ....*....|....*....|....*..
gi 492535981 301 KASAKLLLSRIQSPTKEWEEELLPVKL 327
Cdd:cd06283  237 KAAAEILLERIEGDSGEPKEIELPSEL 263
PBP1_LacI-like cd06278
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 66-332 6.13e-52

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: 172.72  E-value: 6.13e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEiEYLAELTRRGVDGFIIATSAISTSAINEnLKKHGR 145
Cdd:cd06278    1 LVGVVVGDLSNPFYAELLEELSRALQARGLRPLLFNVDDEDDVD-DALRQLLQYRVDGVIVTSATLSSELAEE-CARRGI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALV-YPENPPENIQlRIEGFKHALdfyqysHDQLLLLPTL 224
Cdd:cd06278   79 PVVLFNRVVEDPGVDSVSCDNRAGGRLAADLLLAAGHRRIAFLgGPEGTSTSRE-RERGFRAAL------AELGLPPPAV 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 225 ----FSKQGGYQAVPSIIESAT--TAIFALNDELAFGLYRGL-EEKGKSIPDDYSIIGYDNIDMCE---YvkpKLTTIAQ 294
Cdd:cd06278  152 eagdYSYEGGYEAARRLLAAPDrpDAIFCANDLMALGALDAArQEGGLVVPEDISVVGFDDIPMAAwpsY---DLTTVRQ 228

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 492535981 295 PIVELGKASAKLLLSRIQSPTKEWEEELLPVKLEKRAS 332
Cdd:cd06278  229 PIEEMAEAAVDLLLERIENPETPPERRVLPGELVERGS 266
PBP1_CatR-like cd06296
ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in ...
 66-333 2.75e-51

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: 170.92  E-value: 2.75e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAIsTSAINENLKKHGR 145
Cdd:cd06296    1 LIDLVLPQLDSPYALEVLRGVERAAAAAGLDLVVTATRAGRAPVDDWVRRAVARGSAGVVLVTSDP-TSRQLRLLRSAGI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYIVLDQKKSHGFSD-SVRTDDFRGGYLAGVHLLSLGHENIALVypENPPENI--QLRIEGFKHALDFYQYSHDQLLLLP 222
Cdd:cd06296   80 PFVLIDPVGEPDPDLpSVGATNWAGGRLATEHLLDLGHRRIAVI--TGPPRSVsgRARLAGYRAALAEAGIAVDPDLVRE 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 223 TLFSKQGGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELG 300
Cdd:cd06296  158 GDFTYEAGYRAARELLELPDppTAVFAGNDEQALGVYRAARALGLRVPDDLSVIGFDDTPPARWTSPPLTTVHQPLREMG 237

                        250       260       270
                 ....*....|....*....|....*....|...
gi 492535981 301 KASAKLLLSRIQSPTKEWEEELLPVKLEKRAST 333
Cdd:cd06296  238 AVAVRLLLRLLEGGPPDARRIELATELVVRGST 270
PBP1_CcpB-like cd06286
ligand-binding domain of a novel transcription factor implicated in catabolite repression in ...
 66-330 4.67e-51

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: 170.42  E-value: 4.67e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAInENLKKHGR 145
Cdd:cd06286    1 TIGVVVPYIDHPYFSQLINGIAEAAFKKGYQVLLLQTNYDKEKELRALELLKTKQIDGLIITSRENDWEVI-EPYAKYGP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 pyIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVY--PENPPENIQLRIEGFKHALDFYQYSHDQLLLLPT 223
Cdd:cd06286   80 --IVLCEETDSPDIPSVYIDRYEAYLEALEYLKEKGHRKIGYCLgrPESSSASTQARLKAYQDVLGEHGLSLREEWIFTN 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 224 LFSKQGGYQAVPSIIESA--TTAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEyvKPKLTTIAQPIVELGK 301
Cdd:cd06286  158 CHTIEDGYKLAKKLLALKerPDAIFTNSDEVAAGIIAEAQKNGIRVPEDLAVIGFDNQPISE--LLNLTTIDQPLEEMGK 235

                        250       260
                 ....*....|....*....|....*....
gi 492535981 302 ASAKLLLSRIQSptKEWEEELLPVKLEKR 330
Cdd:cd06286  236 EAFELLLSQLES--KEPTKKELPSKLIER 262
PBP1_LacI-like cd06281
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 66-332 7.17e-51

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: 170.11  E-value: 7.17e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAINENLKKHGR 145
Cdd:cd06281    1 TVGCLVSDISNPLYARIVKAAEARLRAAGYTLLLASTGNDEERELELLSLFQRRRVDGLILTPGDEDDPELAAALARLDI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYIVLDQKKSHGFsDSVRTDDFRGGYLAGVHLLSLGHENIALVYPenPPEN--IQLRIEGFKHALDFYQYSHDQLLLLPT 223
Cdd:cd06281   81 PVVLIDRDLPGDI-DSVLVDHRSGVRQATEYLLSLGHRRIALLTG--GPDIrpGRERIAGFKAAFAAAGLPPDPDLVRLG 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 224 LFSKQGGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGK 301
Cdd:cd06281  158 SFSADSGFREAMALLRQPRppTAIIALGTQLLAGVLRAVRAAGLRIPGDLSVVSIGDSDLAELHDPPITAIRWDLDAVGR 237

                        250       260       270
                 ....*....|....*....|....*....|..
gi 492535981 302 ASAKLLLSRIQSPTK-EWEEELLPVKLEKRAS 332
Cdd:cd06281  238 AAAELLLDRIEGPPAgPPRRIVVPTELILRDS 269
PBP1_LacI cd01574
ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of ...
 66-332 3.79e-50

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: 168.14  E-value: 3.79e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEI-EYLAELTRRGVDGfIIATSAISTSAINENLKKHG 144
Cdd:cd01574    1 TIGVIATGLSLYGPASTLAGIERAARERGYSVSIATVDEDDPASVrEALDRLLSQRVDG-IIVIAPDEAVLEALRRLPPG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 145 RPYIVLDQKKSHGFSdSVRTDDFRGGYLAGVHLLSLGHENIALVypeNPPENI---QLRIEGFKHALDfyQYSHDQLLLL 221
Cdd:cd01574   80 LPVVIVGSGPSPGVP-TVSIDQEEGARLATRHLLELGHRRIAHI---AGPLDWvdaRARLRGWREALE--EAGLPPPPVV 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 222 PTLFSKQGGYQAVPSIIESAT-TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELG 300
Cdd:cd01574  154 EGDWSAASGYRAGRRLLDDGPvTAVFAANDQMALGALRALHERGLRVPEDVSVVGFDDIPEAAYFVPPLTTVRQDFAELG 233

                        250       260       270
                 ....*....|....*....|....*....|..
gi 492535981 301 KASAKLLLSRIQSPTKEWEEELLPVKLEKRAS 332
Cdd:cd01574  234 RRAVELLLALIEGPAPPPESVLLPPELVVRES 265
PBP1_MalR-like cd06294
ligand-binding domain of maltose transcription regulator MalR which is a member of the ...
 66-327 1.19e-48

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: 164.29  E-value: 1.19e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDIT-----NPFFNILMRGIEEVLYQQHFVTILCNADSDhQKEIEYLAELTRRG-VDGFIIaTSAISTSAINEN 139
Cdd:cd06294    1 TIGLVLPSSAeelfqNPFFSEVLRGISQVANENGYSLLLATGNTE-EELLEEVKRMVRGRrVDGFIL-LYSKEDDPLIEY 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 140 LKKHGRPYIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVYpENPPENIQL-RIEGFKHALDFYQYSHDQL 218
Cdd:cd06294   79 LKEEGFPFVVIGKPLDDNDVLYVDNDNVQAGYEATEYLIDKGHKRIAFIG-GDKNLVVSIdRLQGYKQALKEAGLPLDDD 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 219 LLLPTLFSKQGGYQAVPSIIES--ATTAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPI 296
Cdd:cd06294  158 YILLLDFSEEDGYDALQELLSKppPPTAIVATDDLLALGVLRYLQELGLRVPEDVSIISFNNSPLAELASPPLTSVDINP 237

                        250       260       270
                 ....*....|....*....|....*....|.
gi 492535981 297 VELGKASAKLLLSRIQSPTKEWEEELLPVKL 327
Cdd:cd06294  238 YELGREAAKLLINLLEGPESLPKNVIVPHEL 268
PBP1_LacI-like cd06273
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 66-332 2.41e-48

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: 163.45  E-value: 2.41e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIaTSAISTSAINENLKKHGR 145
Cdd:cd06273    1 TIGAIVPTLDNAIFARAIQALQQTLAEAGYTLLLATSEYDPARELEQVRALIERGVDGLIL-VGSDHDPELFELLEQRQV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVYPenPPEN---IQLRIEGFKHALDFYQYSHDQLLLLP 222
Cdd:cd06273   80 PYVLTWSYDEDSPHPSIGFDNRAAAARAAQHLLDLGHRRIAVISG--PTAGndrARARLAGIRDALAERGLELPEERVVE 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 223 TLFSKQGGYQAVPSIIESA--TTAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELG 300
Cdd:cd06273  158 APYSIEEGREALRRLLARPprPTAIICGNDVLALGALAECRRLGISVPEDLSITGFDDLELAAHLSPPLTTVRVPAREIG 237

                        250       260       270
                 ....*....|....*....|....*....|..
gi 492535981 301 KASAKLLLSRIQSPTKEWEEElLPVKLEKRAS 332
Cdd:cd06273  238 ELAARYLLALLEGGPPPKSVE-LETELIVRES 268
lacI PRK09526
lac repressor; Reviewed
 1-335 8.00e-47

lac repressor; Reviewed


Pssm-ID: 181929 [Multi-domain]  Cd Length: 342  Bit Score: 161.70  E-value: 8.00e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981   1 MGKKKITIKDVAKHSGVSIATVSLILNGNEaKFSPKTVEKVFASKKELGYQPDYLARQMITKETKTIGVLVPDITNPFFN 80
Cdd:PRK09526   1 MKSKPVTLYDVARYAGVSYQTVSRVLNQAS-HVSAKTREKVEAAMAELNYVPNRVAQQLAGKQSLTIGLATTSLALHAPS 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  81 ILMRGIEEVLYQQHF-VTILCNADSDHQKEIEYLAELTRRGVDGFII-----ATSAISTSAINENLkkhgrPYIVLDQKK 154
Cdd:PRK09526  80 QIAAAIKSRADQLGYsVVISMVERSGVEACQAAVNELLAQRVSGVIInvpleDADAEKIVADCADV-----PCLFLDVSP 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 155 ShgfSD--SVRTDDFRGGYLAGVHLLSLGHENIALVypeNPPEN---IQLRIEGFKHALDFYQyshdqllLLPTL----- 224
Cdd:PRK09526 155 Q---SPvnSVSFDPEDGTRLGVEHLVELGHQRIALL---AGPESsvsARLRLAGWLEYLTDYQ-------LQPIAvregd 221

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 225 FSKQGGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKA 302
Cdd:PRK09526 222 WSAMSGYQQTLQMLREGPvpSAILVANDQMALGVLRALHESGLRVPGQISVIGYDDTEDSSYFIPPLTTIKQDFRLLGKE 301

                        330       340       350
                 ....*....|....*....|....*....|...
gi 492535981 303 SAKLLLSRIQSPTkEWEEELLPVKLEKRASTAP 335
Cdd:PRK09526 302 AVDRLLALSQGQA-VKGSQLLPTSLVVRKSTAP 333
PBP1_LacI-like cd06282
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 66-311 8.67e-46

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: 156.67  E-value: 8.67e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAINENLKKHGR 145
Cdd:cd06282    1 TIGVLIPSLNNPVFAEAAQGIQRAARAAGYSLLIATTDYDPARELDAVETLLEQRVDGLILTVGDAQGSEALELLEEEGV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVY-PENPPENIQLRIEGFKHALDFYQYSHDQLLLLPtl 224
Cdd:cd06282   81 PYVLLFNQTENSSHPFVSVDNRLASYDVAEYLIALGHRRIAMVAgDFSASDRARLRYQGYRDALKEAGLKPIPIVEVD-- 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 225 FSKQGGYQAVPSII--ESATTAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKA 302
Cdd:cd06282  159 FPTNGLEEALTSLLsgPNPPTALFCSNDLLALSVISALRRLGIRVPDDVSVIGFDGIAIGELLTPTLATVVQPSRDMGRA 238


                 ....*....
gi 492535981 303 SAKLLLSRI 311
Cdd:cd06282  239 AADLLLAEI 247
PBP1_LacI-like cd19974
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 66-332 2.27e-45

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: 155.79  E-value: 2.27e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDI---TNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIAtSAISTSAINEnLKK 142
Cdd:cd19974    1 NIAVLIPERffgDNSFYGKIYQGIEKELSELGYNLVLEIISDEDEEELNLPSIISEEKVDGIIIL-GEISKEYLEK-LKE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 143 HGRPYIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVYPENPPENIQLRIEGFKHAL-DFYQYSHDQLLLL 221
Cdd:cd19974   79 LGIPVVLVDHYDEELNADSVLSDNYYGAYKLTSYLIEKGHKKIGFVGDINYTSSFMDRYLGYRKALlEAGLPPEKEEWLL 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 222 PTLFSKQGGYQAVPSIIESAT-TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELG 300
Cdd:cd19974  159 EDRDDGYGLTEEIELPLKLMLpTAFVCANDSIAIQLIKALKEKGYRVPEDISVVGFDNIELAELSTPPLTTVEVDKEAMG 238

                        250       260       270
                 ....*....|....*....|....*....|..
gi 492535981 301 KASAKLLLSRIQSPTKEWEEELLPVKLEKRAS 332
Cdd:cd19974  239 RRAVEQLLWRIENPDRPFEKILVSGKLIERDS 270
PBP1_LacI-like cd06279
ligand-binding domain of an uncharacterized transcription regulator from Corynebacterium ...
 66-332 3.94e-45

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: 155.44  E-value: 3.94e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPD-----ITNPFFNILMRGIEEVLyQQHFVTILCNADSDHQKeieyLAELTRRG-VDGFIIATSAISTSAInEN 139
Cdd:cd06279    1 AIGVLLPDdlsyaFSDPVAAQFLRGVAEVC-EEEGLGLLLLPATDEGS----AAAAVRNAaVDGFIVYGLSDDDPAV-AA 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 140 LKKHGRPYIVLDQKKSHGFSdSVRTDDFRGGYLAGVHLLSLGHENIALVYPENPPENIQLRIEGFKHALDFYQYSHDQL- 218
Cdd:cd06279   75 LRRRGLPLVVVDGPAPPGIP-SVGIDDRAAARAAARHLLDLGHRRIAILSLRLDRGRERGPVSAERLAAATNSVARERLa 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 219 ----------LLLPTL-------FSKQGGYQAVPSIIESA--TTAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNI 279
Cdd:cd06279  154 gyrdaleeagLDLDDVpvveapgNTEEAGRAAARALLALDprPTAILCMSDVLALGALRAARERGLRVPEDLSVTGFDDI 233

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 492535981 280 DMCEYVKPKLTTIAQPIVELGKASAKLLLSRIqsPTKEWEEELLPVKLEKRAS 332
Cdd:cd06279  234 PEAAAADPGLTTVRQPAVEKGRAAARLLLGLL--PGAPPRPVILPTELVVRAS 284
PBP1_CelR cd06295
ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly ...
 62-332 6.36e-45

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: 154.72  E-value: 6.36e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  62 KETKTIGVLVP-------DITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAeltRRGVDGFIIATSAISTS 134
Cdd:cd06295    1 QRSRTIAVVVPmdphgdqSITDPFFLELLGGISEALTDRGYDMLLSTQDEDANQLARLLD---SGRADGLIVLGQGLDHD 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 135 AINENLKKhGRPYIV----LDQKKSHgfsdSVRTDDFRGGYLAGVHLLSLGHENIALVYPENPPEnIQLRIEGFKHALDF 210
Cdd:cd06295   78 ALRELAQQ-GLPMVVwgapEDGQSYC----SVGSDNVKGGALATEHLIEIGRRRIAFLGDPPHPE-VADRLQGYRDALAE 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 211 YQYSHDQLLLLPTLFSKQGGYQAVPSIIESATT--AIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPK 288
Cdd:cd06295  152 AGLEADPSLLLSCDFTEESGYAAMRALLDSGTAfdAIFAASDLIAMGAIRALRERGISVPGDVAVVGYDDIPLAAYFRPP 231

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 492535981 289 LTTIAQPIVELGKASAKLLLSRIQSptKEWEEELLPVKLEKRAS 332
Cdd:cd06295  232 LTTVRQDLALAGRLLVEKLLALIAG--EPVTSSMLPVELVVRES 273
PBP1_AglR_RafR-like cd06292
Ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that ...
 66-333 9.82e-45

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: 154.35  E-value: 9.82e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDI----TNPFFNILMRGIEEVLYQQHFVTILCNAdSDHQKEIEYLAELTR-RGVDGFIIATSAISTSAINEnL 140
Cdd:cd06292    1 LIGYVVPELpggfSDPFFDEFLAALGHAAAARGYDVLLFTA-SGDEDEIDYYRDLVRsRRVDGFVLASTRHDDPRVRY-L 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 141 KKHGRPYIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVypeNPPENIQL---RIEGFKHALDFYQYSHDQ 217
Cdd:cd06292   79 HEAGVPFVAFGRANPDLDFPWVDVDGAAGMRQAVRHLIALGHRRIGLI---GGPEGSVPsddRLAGYRAALEEAGLPFDP 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 218 LLLLPTLFSKQGGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQP 295
Cdd:cd06292  156 GLVVEGENTEEGGYAAAARLLDLGPppTAIVCVSDLLALGAMRAARERGLRVGRDVSVVGFDDSPLAAFTHPPLTTVRQP 235

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 492535981 296 IVELGKASAKLLLSRIQSPTKEWEEELLPVKLEKRAST 333
Cdd:cd06292  236 IDEIGRAVVDLLLAAIEGNPSEPREILLQPELVVRESS 273
PRK10401 PRK10401
HTH-type transcriptional regulator GalS;
6-308 1.92e-44

HTH-type transcriptional regulator GalS;


Pssm-ID: 236681 [Multi-domain]  Cd Length: 346  Bit Score: 155.70  E-value: 1.92e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981   6 ITIKDVAKHSGVSIATVSLILNgNEAKFSPKTVEKVFASKKELGYQPDYLARQMITKETKTIGVLVPDITNPFFNILMRG 85
Cdd:PRK10401   2 ITIRDVARQAGVSVATVSRVLN-NSALVSADTREAVMKAVSELGYRPNANAQALATQVSDTIGVVVMDVSDAFFGALVKA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  86 IEEVLyQQHFVTILCNaDSDHQKEIEYLA--ELTRRGVDGFIIATSAISTSAINENLKKhgRPYIVLDQKKSHGFSDS-V 162
Cdd:PRK10401  81 VDLVA-QQHQKYVLIG-NSYHEAEKERHAieVLIRQRCNALIVHSKALSDDELAQFMDQ--IPGMVLINRVVPGYAHRcV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 163 RTDDFRGGYLAGVHLLSLGHENIALVYPENPPENIQLRIEGFKHAL--------DFYQYSHDqllllPTLfskQGGYQAV 234
Cdd:PRK10401 157 CLDNVSGARMATRMLLNNGHQRIGYLSSSHGIEDDAMRRAGWMSALkeqgiippESWIGTGT-----PDM---QGGEAAM 228

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 492535981 235 PSII--ESATTAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKASAKLLL 308
Cdd:PRK10401 229 VELLgrNLQLTAVFAYNDNMAAGALTALKDNGIAIPLHLSIIGFDDIPIARYTDPQLTTVRYPIASMAKLATELAL 304
PRK10014 PRK10014
DNA-binding transcriptional repressor MalI; Provisional
 1-331 2.17e-44

DNA-binding transcriptional repressor MalI; Provisional


Pssm-ID: 182193 [Multi-domain]  Cd Length: 342  Bit Score: 155.25  E-value: 2.17e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981   1 MGKKKITIKDVAKHSGVSIATVSLILNGnEAKFSPKTVEKVFASKKELGYQPDYLARQMITKETKTIGVLVPDITNPFFN 80
Cdd:PRK10014   2 ATAKKITIHDVALAAGVSVSTVSLVLSG-KGRISTATGERVNQAIEELGFVRNRQASALRGGQSGVIGLIVRDLSAPFYA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  81 ILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAINENLKKHGRPYIVLDQKKSHGFSD 160
Cdd:PRK10014  81 ELTAGLTEALEAQGRMVFLLQGGKDGEQLAQRFSTLLNQGVDGVVIAGAAGSSDDLREMAEEKGIPVVFASRASYLDDVD 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 161 SVRTDDFRGGYLAGVHLLSLGHENIALVYPENPPENIQLRIEGF-----KHALDFyqysHDQLLLLPTLFSKQGGyQAVP 235
Cdd:PRK10014 161 TVRPDNMQAAQLLTEHLIRNGHQRIAWLGGQSSSLTRAERVGGYcatllKFGLPF----HSEWVLECTSSQKQAA-EAIT 235

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 236 SIIES--ATTAIFALNDELAFGLYRGLEEKGKSI----PDDY-----SIIGYDNIDMCEYVKPKLTTIAQPIVELGKASA 304
Cdd:PRK10014 236 ALLRHnpTISAVVCYNETIAMGAWFGLLRAGRQSgesgVDRYfeqqvALAAFTDVPEAELDDPPLTWASTPAREIGRTLA 315

                        330       340
                 ....*....|....*....|....*..
gi 492535981 305 KLLLSRIQSPTKEWEEELLPVKLEKRA 331
Cdd:PRK10014 316 DRMMQRITHEETHSRNLIIPPRLIARK 342
PBP1_LacI-like cd06299
ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum ...
 66-332 1.00e-43

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: 151.28  E-value: 1.00e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGfIIATSAISTSAINENLKKHGR 145
Cdd:cd06299    1 TIGLLVPDIRNPFFAELASGIEDEARAHGYSVILGNSDEDPEREDESLEMLLSQRVDG-IIAVPTGENSEGLQALIAQGL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYIVLDQKKSH-GFSDSVRTDDFRGGYLAGVHLLSLGHENIALVYPENPPENIQLRIEGFKHALDFYQYSHDQLLLLPTL 224
Cdd:cd06299   80 PVVFVDREVEGlGGVPVVTSDNRPGAREAVEYLVSLGHRRIGYISGPLSTSTGRERLAAFRAALTAAGIPIDEELVAFGD 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 225 FSKQGGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKA 302
Cdd:cd06299  160 FRQDSGAAAAHRLLSRGDppTALIAGDSLMALGAIQALRELGLRIGDDVSLISFDDVPWFELLSPPLTVIAQPVERIGRR 239

                        250       260       270
                 ....*....|....*....|....*....|
gi 492535981 303 SAKLLLSRIQSPtKEWEEELLPVKLEKRAS 332
Cdd:cd06299  240 AVELLLALIENG-GRATSIRVPTELIPRES 268
PRK10727 PRK10727
HTH-type transcriptional regulator GalR;
7-309 7.97e-43

HTH-type transcriptional regulator GalR;


Pssm-ID: 182681 [Multi-domain]  Cd Length: 343  Bit Score: 151.06  E-value: 7.97e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981   7 TIKDVAKHSGVSIATVSLILNgNEAKFSPKTVEKVFASKKELGYQPDYLARQMITKETKTIGVLVPDITNPFFNILMRGI 86
Cdd:PRK10727   3 TIKDVARLAGVSVATVSRVIN-NSPKASEASRLAVHSAMESLSYHPNANARALAQQSTETVGLVVGDVSDPFFGAMVKAV 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  87 EEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAINENLKKhgRPYIVLDQKKSHGFSDS-VRTD 165
Cdd:PRK10727  82 EQVAYHTGNFLLIGNGYHNEQKERQAIEQLIRHRCAALVVHAKMIPDAELASLMKQ--IPGMVLINRILPGFENRcIALD 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 166 DFRGGYLAGVHLLSLGHENIALVYPENPPENIQLRIEGFKHALDFYQYSHDQLLLLPTLFSKQGGYQAVPSIIESAT--T 243
Cdd:PRK10727 160 DRYGAWLATRHLIQQGHTRIGYLCSNHSISDAEDRLQGYYDALAESGIPANDRLVTFGEPDESGGEQAMTELLGRGRnfT 239

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 492535981 244 AIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKASAKLLLS 309
Cdd:PRK10727 240 AVACYNDSMAAGAMGVLNDNGIDVPGEISLIGFDDVLVSRYVRPRLTTVRYPIVTMATQAAELALA 305
PBP1_AglR-like cd20010
Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) and ...
 66-327 4.48e-42

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: 146.93  E-value: 4.48e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVP----DITNPFFNILMRGIEEVLYQQH--FVTILCNADSDHQKEIEYLAEltRRGVDGFIIATSAISTSAInEN 139
Cdd:cd20010    1 AIGLVLPldpgDLGDPFFLEFLAGLSEALAERGldLLLAPAPSGEDELATYRRLVE--RGRVDGFILARTRVNDPRI-AY 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 140 LKKHGRPYIVldqkksHGFSDS------VRTDDFRGGYLAGVHLLSLGHENIALVypeNPPENI---QLRIEGFKHALDF 210
Cdd:cd20010   78 LLERGIPFVV------HGRSESgapyawVDIDNEGAFRRATRRLLALGHRRIALL---NGPEELnfaHQRRDGYRAALAE 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 211 YQYSHDQLLLLPTLFSKQGGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMC-EYVKP 287
Cdd:cd20010  149 AGLPVDPALVREGPLTEEGGYQAARRLLALPPppTAIVCGSDLLALGAYRALREAGLSPGKDVSVIGHDDLLPAlEYFSP 228

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 492535981 288 KLTTIAQPIVELGKASAKLLLSRIQSPTKEWEEELLPVKL 327
Cdd:cd20010  229 PLTTTRSSLRDAGRRLAEMLLALIDGEPAAELQELWPPEL 268
PBP1_GalR cd01544
ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory ...
 74-332 5.59e-42

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: 146.90  E-value: 5.59e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  74 ITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEylaeltrRGVDGfIIATSAISTSAINEnLKKHGRPYIVLDQK 153
Cdd:cd01544   14 LEDPYYLSIRLGIEKEAKKLGYEIKTIFRDDEDLESLL-------EKVDG-IIAIGKFSKEEIEK-LKKLNPNIVFVDSN 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 154 KSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALV----YPENPPENIQ-LRIEGFKHALDFYQYSHDQLLLLpTLFSKQ 228
Cdd:cd01544   85 PDPDGFDSVVPDFEQAVRQALDYLIELGHRRIGFIggkeYTSDDGEEIEdPRLRAFREYMKEKGLYNEEYIYI-GEFSVE 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 229 GGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKASAKL 306
Cdd:cd01544  164 SGYEAMKELLKEGDlpTAFFVASDPMAIGALRALQEAGIKVPEDISIISFNDIEVAKYVTPPLTTVHIPTEEMGRTAVRL 243

                        250       260
                 ....*....|....*....|....*.
gi 492535981 307 LLSRIQSPTKEWEEELLPVKLEKRAS 332
Cdd:cd01544  244 LLERINGGRTIPKKVLLPTKLIERES 269
PBP1_SalR cd01545
ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of ...
 66-332 1.00e-41

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: 146.16  E-value: 1.00e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQ--HFVTILCNADSDHQKEiEYLAELTRRGVDGFIIATSAISTSAINENLKKH 143
Cdd:cd01545    1 LIGLLYDNPSASYVSALQVGALRACREAgyHLVVEPCDSDDEDLAD-RLRRFLSRSRPDGVILTPPLSDDPALLDALDEL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 144 GRPYIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVypENPPENI--QLRIEGFKHALDFYQYSHDQLLLL 221
Cdd:cd01545   80 GIPYVRIAPGTDDDRSPSVRIDDRAAAREMTRHLIALGHRRIGFI--AGPPDHGasAERLEGFRDALAEAGLPLDPDLVV 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 222 PTLFSKQGGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVEL 299
Cdd:cd01545  158 QGDFTFESGLEAAEALLDLPDrpTAIFASNDEMAAGVLAAAHRLGLRVPDDLSVAGFDDSPIARLVWPPLTTVRQPIAEM 237

                        250       260       270
                 ....*....|....*....|....*....|...
gi 492535981 300 GKASAKLLLSRIQSPTKEWEEELLPVKLEKRAS 332
Cdd:cd01545  238 ARRAVELLIAAIRGAPAGPERETLPHELVIRES 270
PRK11041 PRK11041
DNA-binding transcriptional regulator CytR; Provisional
 32-337 1.33e-41

DNA-binding transcriptional regulator CytR; Provisional


Pssm-ID: 182923 [Multi-domain]  Cd Length: 309  Bit Score: 147.07  E-value: 1.33e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  32 KFSPKTVEKVFASKKELGYQPDYLARQMITKETKTIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILcnADSDHQKEIE 111
Cdd:PRK11041   3 KVSQATRQRVEQAVLEVGYSPQSLGRNLKRNESRTILVIVPDICDPFFSEIIRGIEVTAAEHGYLVLI--GDCAHQNQQE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 112 --YLAELTRRGVDGFIIATSAISTSAINE---NLkkhgrPYIVLdqkkSHGFSD-----SVRTDDFRGGYLAGVHLLSLG 181
Cdd:PRK11041  81 ktFVNLIITKQIDGMLLLGSRLPFDASKEeqrNL-----PPMVM----ANEFAPelelpTVHIDNLTAAFEAVNYLHELG 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 182 HENIALVY-PENPPEnIQLRIEGFKHALDFYQYSHDQLLLLPTLFSKQGGYQAVPSIIESAT--TAIFALNDELAFGLYR 258
Cdd:PRK11041 152 HKRIACIAgPEEMPL-CHYRLQGYVQALRRCGITVDPQYIARGDFTFEAGAKALKQLLDLPQppTAVFCHSDVMALGALS 230

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 492535981 259 GLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKASAKLLLSRIQSPTKEWEEELLPVKLEKRASTAPLK 337
Cdd:PRK11041 231 QAKRMGLRVPQDLSIIGFDDIDLAQYCDPPLTTVAQPRYEIGREAMLLLLEQLQGHHVSSGSRLLDCELIIRGSTAAPP 309
PBP1_GntR cd01575
ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of ...
 66-332 3.35e-38

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: 136.86  E-value: 3.35e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIaTSAISTSAINENLKKHGR 145
Cdd:cd01575    1 LVAVVVPSLSNSVFAETLQGLSDVLEPAGYQLLLGNTGYSPEREEELIRALLSRRPAGLIL-TGTEHTPATRKLLRAAGI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYI-VLDQKKSH-----GFSDsvrtddFRGGYLAGVHLLSLGHENIALVYPENPPENI-QLRIEGFKHALDFYQYSHDQL 218
Cdd:cd01575   80 PVVeTWDLPDDPidmavGFSN------FAAGRAMARHLIERGYRRIAFVGARLDGDSRaRQRLEGFRDALAEAGLPLPLV 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 219 LLLPTLFSKQGGYQAVPSIIESA--TTAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPI 296
Cdd:cd01575  154 LLVELPSSFALGREALAELLARHpdLDAIFCSNDDLALGALFECQRRGIRVPGDIAIAGFGDLDIAAALPPALTTVRVPR 233

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 492535981 297 VELGKASAKLLLSRIQSPTKEWEEELLPVKLEKRAS 332
Cdd:cd01575  234 YEIGRKAAELLLARLEGEEPEPRVVDLGFELVRRES 269
Peripla_BP_3 pfam13377
Periplasmic binding protein-like domain; This domain is found in a variety of transcriptional ...
 176-333 6.26e-38

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: 132.85  E-value: 6.26e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  176 HLLSLGHENIALVYPENPP--ENIQLRIEGFKHALDFYQYSHDQLLLLPTLFSKQGGYQAVPSIIESATTAIFALNDELA 253
Cdd:pfam13377   1 HLAELGHRRIALIGPEGDRddPYSDLRERGFREAARELGLDVEPTLYAGDDEAEAAAARERLRWLGALPTAVFVANDEVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  254 FGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKASAKLLLSRIQSPTKEWEEELLPVKLEKRAST 333
Cdd:pfam13377  81 LGVLQALREAGLRVPEDLSVIGFDDSPLAALVSPPLTTVRVDAEELGRAAAELLLDLLNGEPAPPERVLLPPELVEREST 160
PBP1_CcpA cd06298
ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major ...
 66-332 3.25e-37

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: 134.34  E-value: 3.25e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGfIIATSAISTSAINENLKKHGR 145
Cdd:cd06298    1 TVGVIIPDISNLYYAELARGIDDIATMYKYNIILSNSDNNVDKELDLLNTMLSKQVDG-IIFMGDELTEEIREEFKRSPV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVY-PENPPENIQLRIEGFKHALDFYQYSHDQLLLLPTL 224
Cdd:cd06298   80 PVVLAGTVDSDHEIPSVNIDYEQAAYDATKSLIDKGHKKIAFVSgPLKEYINNDKKLQGYKRALEEAGLEFNEPLIFEGD 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 225 FSKQGGYQAVPSIIES-ATTAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKAS 303
Cdd:cd06298  160 YDYDSGYELYEELLESgEPDAAIVVRDEIAVGLLNAAQDRGLKVPEDLEIIGFDNTRYATMSRPQLTSINQPLYDIGAVA 239

                        250       260
                 ....*....|....*....|....*....
gi 492535981 304 AKLLLSRIQSPTKEWEEELLPVKLEKRAS 332
Cdd:cd06298  240 MRLLTKLMNKEEVEETIVKLPHSIIWRQS 268
PBP1_LacI-like cd06277
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 77-332 1.84e-35

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: 380500 [Multi-domain]  Cd Length: 275  Bit Score: 130.05  E-value: 1.84e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  77 PFFNILMRGIEEVLYQQHFVTILCNADSDHQKEiEYLAELTRRGVDGFIIATSAISTSAINENLKKhGRPYIVLDQKKSH 156
Cdd:cd06277   19 PFFSELIDGIEREARKYGYNLLISSVDIGDDFD-EILKELTDDQSSGIILLGTELEEKQIKLFQDV-SIPVVVVDNYFED 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 157 GFSDSVRTDDFRGGYLAGVHLLSLGHENIALVYPENPPENIQLRIEGFKHAL---DFYQYSHDQLLLLPTLFSKQGGYQA 233
Cdd:cd06277   97 LNFDCVVIDNEDGAYEAVKYLVELGHTRIGYLASSYRIKNFEERRRGFRKAMrelGLSEDPEPEFVVSVGPEGAYKDMKA 176

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 234 VPSIIESATTAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKASAKLLLSRIQS 313
Cdd:cd06277  177 LLDTGPKLPTAFFAENDIIALGCIKALQEAGIRVPEDVSVIGFDDIPVSAMVDPPLTTIHVPKEQMGKLAVRRLIEKIKD 256

                        250
                 ....*....|....*....
gi 492535981 314 PTKEWEEELLPVKLEKRAS 332
Cdd:cd06277  257 PDGGTLKILVSTKLVERGS 275
PBP1_repressor_sugar_binding-like cd01537
Ligand-binding domain of the LacI-GalR family of transcription regulators and the ...
 67-327 6.05e-35

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: 128.52  E-value: 6.05e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  67 IGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAINENLKKHGRP 146
Cdd:cd01537    2 IGVTIYSYDDNFMSVIRKAIEQDAKQPGVQLLMNDSQNDQEKQNDQIDVLLAKRVKGLAINLVDPAAAGVAEKARGQNVP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 147 YIVLDQKKSHG-FSDSVRTDDFRGGYLAGVHLLSLGHENIALVypENPPENI--QLRIEGFKHALDFYQYSHDQLLLLPT 223
Cdd:cd01537   82 VVFFDKEPSRYdKAYYVITDSKEGGIIQGDLLAKHGHIQIVLL--KGPLGHPdaEARLAGVIKELNDKGIKTEQLQLDTG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 224 LFSKQGGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGK 301
Cdd:cd01537  160 DWDTASGKDKMDQWLSGPNkpTAVIANNDAMAMGAVEALKEHGLRVPSDISVFGYDALPEALKSGPLLTTILQDANNLGK 239

                        250       260
                 ....*....|....*....|....*.
gi 492535981 302 ASAKLLLSRIQSPTKEWEEELLPVKL 327
Cdd:cd01537  240 TTFDLLLNLADNWKIDNKVVRVPYVL 265
Peripla_BP_1 pfam00532
Periplasmic binding proteins and sugar binding domain of LacI family; This family includes the ...
 64-331 1.44e-31

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: 119.92  E-value: 1.44e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981   64 TKTIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAINENLKKH 143
Cdd:pfam00532   1 TLKLGALVPQLDEPFFQDLVKGITKAAKDHGFDVFLLAVGDGEDTLTNAIDLLLASGADGIIITTPAPSGDDITAKAEGY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  144 GRPYIVL-DQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVYPEN-PPENIQLRIEGFKHAL-DFYQYSHDQLLL 220
Cdd:pfam00532  81 GIPVIAAdDAFDNPDGVPCVMPDDTQAGYESTQYLIAEGHKRPIAVMAGPaSALTARERVQGFMAALaAAGREVKIYHVA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  221 LPTlFSKQGGYQAVPSIIESATT--AIFALNDELAFGLYRGLEEKGK-SIPDD-----YSIIGYDNIDMCE---YVKPKL 289
Cdd:pfam00532 161 TGD-NDIPDAALAANAMLVSHPTidAIVAMNDEAAMGAVRALLKQGRvKIPDIvgigiNSVVGFDGLSKAQdtgLYLSPL 239

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 492535981  290 TTIAQPIVELGKASAKLLLSRIQSPTKEWEEELLPVKLEKRA 331
Cdd:pfam00532 240 TVIQLPRQLLGIKASDMVYQWIPKFREHPRVLLIPRDFFKET 281
PBP1_hexuronate_repressor-like cd06272
ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon ...
 66-317 1.17e-30

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: 117.09  E-value: 1.17e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITnpFFNILMR---GIEEVLYQQHFVTIL--CNADSDHQKEIEYLaeLTRRGVDGFIIATSAISTSAINENL 140
Cdd:cd06272    1 TIGLYWPSVG--ERVALTRllsGINEAISKQGYNINLsiCPYKVGHLCTAKGL--FSENRFDGVIVFGISDSDIEYLNKN 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 141 KKhGRPyIVLDQKKSHGFSdSVRTDDFRGGYLAGVHLLSLGHENIALVYPENPPENIQLRIEGFKHALDFYQYSHDQLLL 220
Cdd:cd06272   77 KP-KIP-IVLYNRESPKYS-TVNVDNEKAGRLAVLLLIQKGHKSIAYIGNPNSNRNQTLRGKGFIETCEKHGIHLSDSII 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 221 LPTLFSKQGGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVE 298
Cdd:cd06272  154 DSRGLSIEGGDNAAKKLLKKKTlpKAIFCNSDDIALGVLRVLKENGISIPEDISIVSYDNIPQEARSDPPLTVVGVPIEK 233

                        250
                 ....*....|....*....
gi 492535981 299 LGKASAKLLLSRIQSPTKE 317
Cdd:cd06272  234 IAEESLRLILKLIEGRENE 252
PBP1_CcpA_TTHA0807 cd06297
ligand-binding domain of TTHA0807, a CcpA regulator, from Thermus thermophilus HB8 and its ...
 66-314 2.36e-30

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: 116.03  E-value: 2.36e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEiEYLAELTRRG-VDGfIIATSAISTSAINENLKKHG 144
Cdd:cd06297    1 TISLLVPEVMTPFYMRLLTGVERALDENRYDLAIFPLLSEYRLE-KYLRNSTLAYqCDG-LVMASLDLTELFEEVIVPTE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 145 RPYIVLDQKkSHGFsDSVRTDDFRGGYLAGVHLLSLGHENIALVYPENPPENIQL----RIEGFKHALDFYQYSHDQLLL 220
Cdd:cd06297   79 KPVVLIDAN-SMGY-DCVYVDNVKGGFMATEYLAGLGEREYVFFGIEEDTVFTETvfreREQGFLEALNKAGRPISSSRM 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 221 LPTLFSKQGGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEyvKPKLTTIAQPIVE 298
Cdd:cd06297  157 FRIDNSSKKAECLARELLKKADnpAAFFAAADLVALGLIRAAQSLGLRVGEDVAVIGFDGQPWAA--SPGLTTVRQPVEE 234

                        250
                 ....*....|....*.
gi 492535981 299 LGKASAKLLLSRIQSP 314
Cdd:cd06297  235 MGEAAAKLLLKRLNEY 250
HTH_LACI smart00354
helix_turn _helix lactose operon repressor;
6-76 9.35e-28

helix_turn _helix lactose operon repressor;


Pssm-ID: 197675 [Multi-domain]  Cd Length: 70  Bit Score: 103.05  E-value: 9.35e-28
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 492535981     6 ITIKDVAKHSGVSIATVSLILNGNEaKFSPKTVEKVFASKKELGYQPDYLARQMITKETKTIGVLVPDITN 76
Cdd:smart00354   1 ATIKDVARLAGVSKATVSRVLNGKG-RVSEETREKVLAAMEELGYIPNRVARSLKGKKTKTIGLIVPDITN 70
fruct_sucro_rep TIGR02417
D-fructose-responsive transcription factor; Members of this family belong the lacI ...
 7-330 2.41e-26

D-fructose-responsive transcription factor; Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer. [Regulatory functions, DNA interactions]


Pssm-ID: 131470 [Multi-domain]  Cd Length: 327  Bit Score: 106.76  E-value: 2.41e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981    7 TIKDVAKHSGVSIATVSLILNG--NEAKFSPKTVEKVFASKKELGYQPDYLARQMITKETKTIGVLVPDITNPFF----N 80
Cdd:TIGR02417   1 TLSDIAKLAGVSKTTASYVINGkaKEYRISQETVERVMAVVREQGYQPNIHAASLRAGRSRTIGLVIPDLENYSYariaK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981   81 ILMRGIEEVLYQqhfVTILCnADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAINENLKKHGRPYIVLDQKKSHGFSD 160
Cdd:TIGR02417  81 ELEQQCREAGYQ---LLIAC-SDDNPDQEKVVIENLLARQVDALIVASCMPPEDAYYQKLQNEGLPVVALDRSLDDEHFC 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  161 SVRTDDFRGGYLAGVHLLSLGHENIALV--YPENPPEniQLRIEGFKHALDfyQYSHDQLLLLPTLFSKQGGYQAVPSII 238
Cdd:TIGR02417 157 SVISDDVDAAAELIERLLSQHADEFWYLgaQPELSVS--RDRLAGFRQALK--QATLEVEWVYGGNYSRESGYQMFAKLC 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  239 ESATT---AIFALNDELAFGLYRGLEEKgKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKASAKLLLSRIQSPT 315
Cdd:TIGR02417 233 ARLGRlpqALFTTSYTLLEGVLDYMLER-PLLDSQLHLATFGDNYLLDFLPLPINSVAQQHRQLAWHALELALAAIDGKK 311

                         330
                  ....*....|....*
gi 492535981  316 KEWEEELLPVKLEKR 330
Cdd:TIGR02417 312 PEPGQRYIPRTLQIR 326
RbsB COG1879
ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH ...
 62-308 5.82e-26

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: 105.01  E-value: 5.82e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  62 KETKTIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIatSAISTSAIN---E 138
Cdd:COG1879   31 AKGKTIGFVVKTLGNPFFVAVRKGAEAAAKELGVELIVVDAEGDAAKQISQIEDLIAQGVDAIIV--SPVDPDALApalK 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 139 NLKKHGRPYIVLDQKKSHGFSDS-VRTDDFRGGYLAGVHLLSL--GHENIALVYPENPPENIQLRIEGFKHALDfyQYSH 215
Cdd:COG1879  109 KAKAAGIPVVTVDSDVDGSDRVAyVGSDNYAAGRLAAEYLAKAlgGKGKVAILTGSPGAPAANERTDGFKEALK--EYPG 186

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 216 DQLL-LLPTLFSKQGGYQAVPSIIES--ATTAIFALNDELAFGLYRGLEEKGKsiPDDYSIIGYD-NIDMCEYVK-PKLT 290
Cdd:COG1879  187 IKVVaEQYADWDREKALEVMEDLLQAhpDIDGIFAANDGMALGAAQALKAAGR--KGDVKVVGFDgSPEALQAIKdGTID 264

                        250
                 ....*....|....*....
gi 492535981 291 -TIAQPIVELGKASAKLLL 308
Cdd:COG1879  265 aTVAQDPYLQGYLAVDAAL 283
PRK14987 PRK14987
HTH-type transcriptional regulator GntR;
1-315 8.41e-25

HTH-type transcriptional regulator GntR;


Pssm-ID: 184949 [Multi-domain]  Cd Length: 331  Bit Score: 102.41  E-value: 8.41e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981   1 MGKKKITIKDVAKHSGVSIATVSLILNgNEAKFSPKTVEKVFASKKELGYQPDYLARQMITKETKTIGVLVPDITNPFFN 80
Cdd:PRK14987   1 MKKKRPVLQDVADRVGVTKMTVSRFLR-NPEQVSVALRGKIAAALDELGYIPNRAPDILSNATSRAIGVLLPSLTNQVFA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  81 ILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIaTSAISTSAINENLKKHGRPYIVLDQKKSHGFSD 160
Cdd:PRK14987  80 EVLRGIESVTDAHGYQTMLAHYGYKPEMEQERLESMLSWNIDGLIL-TERTHTPRTLKMIEVAGIPVVELMDSQSPCLDI 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 161 SVRTDDFRGGYLAGVHLLSLGHENIALVYPENPPENIqLRIEGFKHALdfyqySHDQLLLLPTLFSKQGGYQAVPSIIES 240
Cdd:PRK14987 159 AVGFDNFEAARQMTTAIIARGHRHIAYLGARLDERTI-IKQKGYEQAM-----LDAGLVPYSVMVEQSSSYSSGIELIRQ 232

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 241 AT------TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKASAKLLLSRIQSP 314
Cdd:PRK14987 233 ARreypqlDGVFCTNDDLAVGAAFECQRLGLKVPDDMAIAGFHGHDIGQVMEPRLASVLTPRERMGSIGAERLLARIRGE 312


                 .
gi 492535981 315 T 315
Cdd:PRK14987 313 S 313
PBP1_ABC_sugar_binding-like cd06319
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
 66-327 1.31e-24

periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380542 [Multi-domain]  Cd Length: 278  Bit Score: 100.90  E-value: 1.31e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIA-TSAISTSAINENLKKHG 144
Cdd:cd06319    1 KIGYSVYDLDNPFWQIMERGVQAAAEELGYEFVTYDQKNSANEQVTNANDLIAQGVDGIIISpTNSSAAPTVLDLANEAK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 145 RPYIVLDQKKSHGFSDS-VRTDDFRGGYLAGVHLLSLGHEN------IALVypENPPE--NIQLRIEGFKHALDFYQYSH 215
Cdd:cd06319   81 IPVVIADIGTGGGDYVSyIISDNYDGGYQAGEYLAEALKENgwgggsVGII--AIPQSrvNGQARTAGFEDALEEAGVEE 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 216 DQLLLLPTlFSKQGGYQAVPSIIESA--TTAIFALNDELAFGLYRGLEEKGKSipDDYSIIGYDNID-MCEYVKPK--LT 290
Cdd:cd06319  159 VALRQTPN-STVEETYSAAQDLLAANpdIKGIFAQNDQMAQGALQAIEEAGRT--GDILVVGFDGDPeALDLIKDGklDG 235

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 492535981 291 TIAQPIVELGKASAKLLLSRIQSPTKEWEEELLPVKL 327
Cdd:cd06319  236 TVAQQPFGMGARAVELAIQALNGDNTVEKEIYLPVLL 272
PRK11303 PRK11303
catabolite repressor/activator;
7-247 4.10e-23

catabolite repressor/activator;


Pssm-ID: 236897 [Multi-domain]  Cd Length: 328  Bit Score: 97.64  E-value: 4.10e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981   7 TIKDVAKHSGVSIATVSLILNGNEAKF--SPKTVEKVFASKKELGYQPDYLARQMITKETKTIGVLVPDITNPFF----N 80
Cdd:PRK11303   2 KLDEIARLAGVSRTTASYVINGKAKQYrvSDKTVEKVMAVVREHNYHPNAVAAGLRAGRTRSIGLIIPDLENTSYariaK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  81 ILMRGIEEVLYQqhfVTILCnadSDHQKEIEY-LAE-LTRRGVDGFIIATSAISTSAINENLKKHGRPYIVLDQKKSHGF 158
Cdd:PRK11303  82 YLERQARQRGYQ---LLIAC---SDDQPDNEMrCAEhLLQRQVDALIVSTSLPPEHPFYQRLQNDGLPIIALDRALDREH 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 159 SDSVRTDDFRGGYLAGVHLLSLGHENIALV--YPENPPEniQLRIEGFKHALDfyQYSHDQLLLLPTLFSKQGGYQAVPS 236
Cdd:PRK11303 156 FTSVVSDDQDDAEMLAESLLKFPAESILLLgaLPELSVS--FEREQGFRQALK--DDPREVHYLYANSFEREAGAQLFEK 231

                        250
                 ....*....|...
gi 492535981 237 IIESAT--TAIFA 247
Cdd:PRK11303 232 WLETHPmpDALFT 244
PBP1_ABC_sugar_binding-like cd01536
periplasmic sugar-binding domain of active transport systems that are members of the type 1 ...
 66-327 4.87e-23

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: 96.48  E-value: 4.87e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIAtsAISTSAINENLKK--- 142
Cdd:cd01536    1 KIGVVVKDLTNPFWVAVKKGAEAAAKELGVELVVLDAQGDVAKQISQIEDLIAQGVDAIIIA--PVDSEALVPAVKKana 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 143 HGRPYIVLDQK-KSHGFSDS-VRTDDFRGGYLAGVHLLS-LGHE-NIALVY--PENPPEniQLRIEGFKHALDfyQYSHD 216
Cdd:cd01536   79 AGIPVVAVDTDiDGGGDVVAfVGTDNYEAGKLAGEYLAEaLGGKgKVAILEgpPGSSTA--IDRTKGFKEALK--KYPDI 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 217 QLL-LLPTLFSKQGGYQAVPSIIES--ATTAIFALNDELAFGLYRGLEEKGKSipDDYSIIGYDNI-DMCEYVK-PKLT- 290
Cdd:cd01536  155 EIVaEQPANWDRAKALTVTENLLQAnpDIDAVFAANDDMALGAAEALKAAGRT--GDIKIVGVDGTpEALKAIKdGELDa 232

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 492535981 291 TIAQPIVELGKASAKLLLSRIQSPTKEwEEELLPVKL 327
Cdd:cd01536  233 TVAQDPYLQGYLAVEAAVKLLNGEKVP-KEILTPVTL 268
PBP1_AglR_RafR-like cd06271
ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and ...
 76-311 3.06e-20

ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators; Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) 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: 380495 [Multi-domain]  Cd Length: 264  Bit Score: 88.64  E-value: 3.06e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  76 NPFFNILMRGIEEVLYQ-QHFVTILCNADSDHQKEIEYLAEltRRGVDGFIIATSAISTSAInENLKKHGRPYIVL---D 151
Cdd:cd06271   14 NGTVSE*VSGITEEAGTtGYHLLVWPFEEAES*VPIRDLVE--TGSADGVILSEIEPNDPRV-QFLTKQNFPFVAHgrsD 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 152 QKKSHGFSDsvrTDDFRGGYLAGVHLLSLGHENIALVypeNPPENIQL---RIEGFKHALDFYQYSHDQLLLLPTLfskQ 228
Cdd:cd06271   91 *PIGHAWVD---IDNEAGAYEAVERLAGLGHRRIAFI---VPPARYSPhdrRLQGYVRA*RDAGLTGYPLDADTTL---E 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 229 GGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNI-DMCEYVKPKLTTIAQPIVELGKASAK 305
Cdd:cd06271  162 AGRAAAQRLLALSPrpTAIVTMNDSATIGLVAGLQAAGLKIGEDVSIIGKDSApFLGAMITPPLTTVHAPIAEAGRELAK 241


                 ....*.
gi 492535981 306 LLLSRI 311
Cdd:cd06271  242 ALLARI 247
PBP1_RafR-like cd20009
Ligand-binding domain of DNA transcription repressor specific for raffinose (RafR) and similar ...
 71-314 1.54e-18

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: 83.74  E-value: 1.54e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  71 VPDITNPFFNILMRGIEEVL----YqqHFVTILCNADSDHQKEIEYLAEltRRGVDGFIIATsaisTSAINEN---LKKH 143
Cdd:cd20009    8 TEDEIDGFTSQLISGISEALrgtpY--HLVVTPEFPGDDPLEPVRYIVE--NRLADGIIISH----TEPQDPRvryLLER 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 144 GRPYIvldqkkSHGfsdsvRTD--------DF---RGGYLAGVHLLSLGHENIALVypeNPPE---NIQLRIEGFKHALD 209
Cdd:cd20009   80 GFPFV------THG-----RTElstphayfDFdneAFAYEAVRRLAARGRRRIALV---APPReltYAQHRLRGFRRALA 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 210 FYQYSHDQLLLLPTLFSKQGGYQAVPSIIES--ATTAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKP 287
Cdd:cd20009  146 EAGLEVEPLLIVTLDSSAEAIRAAARRLLRQppRPDGIICASEIAALGALAGLEDAGLVVGRDVDVVAKETSPILDYFRP 225

                        250       260
                 ....*....|....*....|....*..
gi 492535981 288 KLTTIAQPIVELGKASAKLLLSRIQSP 314
Cdd:cd20009  226 PIDTLYEDIEEAGRFLAEALLRRIEGE 252
Peripla_BP_4 pfam13407
Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic ...
 67-312 5.49e-18

Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic binding proteins. This domain recognizes fructose (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 433182 [Multi-domain]  Cd Length: 259  Bit Score: 82.36  E-value: 5.49e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981   67 IGVLVPDITNPFFNILMRGIEEVLYQQHF-VTILCNADSDHQKEIEYLAELTRRGVDGFIIAtsAISTSAINENLKK--- 142
Cdd:pfam13407   1 IGVVPKSTGNPFFQAAEEGAEEAAKELGGeVIVVGPAEADAAEQVAQIEDAIAQGVDAIIVA--PVDPTALAPVLKKakd 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  143 HGRPYIVLDQ-KKSHGFSDSVRTDDFRGGYLAGVHLLSL--GHENIALVYPENPPENIQLRIEGFKHALdfyQYSHDQLL 219
Cdd:pfam13407  79 AGIPVVTFDSdAPSSPRLAYVGFDNEAAGEAAGELLAEAlgGKGKVAILSGSPGDPNANERIDGFKKVL---KEKYPGIK 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  220 LLPTLF----SKQGGYQAVPSIIESATT---AIFALNDELAFGLYRGLEEKGKSipDDYSIIGYDNID-MCEYVK-PKLT 290
Cdd:pfam13407 156 VVAEVEgtnwDPEKAQQQMEALLTAYPNpldGIISPNDGMAGGAAQALEAAGLA--GKVVVTGFDATPeALEAIKdGTID 233

                         250       260
                  ....*....|....*....|...
gi 492535981  291 -TIAQPIVELGKASAKLLLSRIQ 312
Cdd:pfam13407 234 aTVLQDPYGQGYAAVELAAALLK 256
PBP1_ABC_sugar_binding-like cd06322
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
 66-277 3.57e-17

periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380545 [Multi-domain]  Cd Length: 270  Bit Score: 80.01  E-value: 3.57e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIAT--SAISTSAINEnLKKH 143
Cdd:cd06322    1 TIGVSLLTLQHPFFVDIKDAMKKEAAELGVKVVVADANGDLAKQLSQIEDFIQQGVDAIILAPvdSGGIVPAIEA-ANEA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 144 GRPYIVLDQKKSHGFSDS-VRTDDFRGGYLAGVHLLSL---GHENIALV-YPENppENIQLRIEGFKHALDfyqySHDQL 218
Cdd:cd06322   80 GIPVFTVDVKADGAKVVThVGTDNYAGGKLAGEYALKAllgGGGKIAIIdYPEV--ESVVLRVNGFKEAIK----KYPNI 153

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 492535981 219 LLLPTL---FSKQGGYQAVPSIIESA--TTAIFALNDELAFGLYRGLEEKGKSipDDYSIIGYD 277
Cdd:cd06322  154 EIVAEQpgdGRREEALAATEDMLQANpdLDGIFAIGDPAALGALTAIESAGKE--DKIKVIGFD 215
HTH_LacI cd01392
Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; ...
 9-61 1.29e-16

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: 72.83  E-value: 1.29e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 492535981   9 KDVAKHSGVSIATVSLILNGNEaKFSPKTVEKVFASKKELGYQPDYLARQMIT 61
Cdd:cd01392    1 KDIARAAGVSVATVSRVLNGKP-RVSEETRERVLAAAEELGYRPNAAARSLRT 52
PBP1_FruR cd06274
ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its ...
 66-317 6.81e-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: 76.48  E-value: 6.81e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAiSTSAINENLKKHGR 145
Cdd:cd06274    1 TIGLIVPDLANRFFARLAEALERLARERGLQLLIACSDDDPEQERRLVENLIARQVDGLIVAPST-PPDDIYYLCQAAGL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 146 PYIVLDQKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALV--YPENPpeNIQLRIEGFKHALDFYQYSHDQLLLLPT 223
Cdd:cd06274   80 PVVFLDRPFSGSDAPSVVSDNRAGARALTEKLLAAGPGEIYFLggRPELP--STAERIRGFRAALAEAGITEGDDWILAE 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 224 LFSKQGGYQAVPSIIESATT---AIFAlNDELAF-GLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVEL 299
Cdd:cd06274  158 GYDRESGYQLMAELLARLGGlpqALFT-SSLTLLeGVLRFLRERLGAIPSDLVLGTFDDHPLLDFLPNPVDSVRQDHDEI 236

                        250
                 ....*....|....*...
gi 492535981 300 GKASAKLLLSRIQSPTKE 317
Cdd:cd06274  237 AEHAFELLDALIEGQPEP 254
LacI pfam00356
Bacterial regulatory proteins, lacI family;
7-53 6.19e-14

Bacterial regulatory proteins, lacI family;


Pssm-ID: 306791 [Multi-domain]  Cd Length: 46  Bit Score: 65.35  E-value: 6.19e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 492535981    7 TIKDVAKHSGVSIATVSLILNGNEaKFSPKTVEKVFASKKELGYQPD 53
Cdd:pfam00356   1 TIKDVARLAGVSKSTVSRVLNNPG-RVSEETRERVEAAMEELNYIPN 46
PBP1_ABC_sugar_binding-like cd06321
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
 66-327 9.24e-14

periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380544 [Multi-domain]  Cd Length: 270  Bit Score: 70.40  E-value: 9.24e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIE----EVLYQQHFVTIlcNADSDHQKEIEYLAELTRRGVDgfIIATSAISTSAINENL- 140
Cdd:cd06321    1 VIGVTVQDLGNPFFVAMVRGAEeaaaEINPGAKVTVV--DARYDLAKQFSQIDDFIAQGVD--LILLNAADSAGIEPAIk 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 141 --KKHGRPYIVLD--QKKSHGFsdsVRTDDFRGGYLAGVHLL-SLGHE-NIALVypENPP-ENIQLRIEGFKHALDFYQy 213
Cdd:cd06321   77 raKDAGIIVVAVDvaAEGADAT---VTTDNVQAGYLACEYLVeQLGGKgKVAII--DGPPvSAVIDRVNGCKEALAEYP- 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 214 shdQLLLLPTLFSKQ---GGYQAVPSIIES--ATTAIFALNDELAFGLYRGLEEKGKsipDDYSIIGYDNI-DMCEYVK- 286
Cdd:cd06321  151 ---GIKLVDDQNGKGsraGGLSVMTRMLTAhpDVDGVFAINDPGAIGALLAAQQAGR---DDIVITSVDGSpEAVAALKr 224

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 492535981 287 ---PKLTTIAQPIVELGKASAKLLLSRIQSPTKEWEEELLPVKL 327
Cdd:cd06321  225 egsPFIATAAQDPYDMARKAVELALKILNGQEPAPELVLIPSTL 268
PBP1_XylR cd01543
ligand-binding domain of DNA transcription repressor specific for xylose (XylR); ...
 113-333 2.15e-13

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: 69.15  E-value: 2.15e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 113 LAELTRRGVDGfIIATsaISTSAINENLKKHGRPYIVLD-QKKSHGFSdSVRTDDFRGGYLAGVHLLSLGHENIALV-YP 190
Cdd:cd01543   43 LDLLKGWKGDG-IIAR--LDDPELAEALRRLGIPVVNVSgSRPEPGFP-RVTTDNEAIGRMAAEHLLERGFRHFAFCgFR 118

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 191 ENPPEniQLRIEGFKHALDFYQYsHDQLLLLPTLFSKQGGYQAVPSIIE-----SATTAIFALNDELAFGLYRGLEEKGK 265
Cdd:cd01543  119 NAAWS--RERGEGFREALREAGY-ECHVYESPPSGSSRSWEEEREELADwlkslPKPVGIFACNDDRARQVLEACREAGI 195

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 266 SIPDDYSIIGYDNIDM-CEYVKPKLTTIAQPIVELGKASAKLLLSRIQSPTKEWEEELL-PVKLEKRAST 333
Cdd:cd01543  196 RVPEEVAVLGVDNDELiCELSSPPLSSIALDAEQIGYEAAELLDRLMRGERVPPEPILIpPLGVVTRQST 265
PBP1_ribose_binding cd06323
periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose ...
 66-301 6.17e-13

periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs; Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis D-ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group belong to the type 1 periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.


Pssm-ID: 380546 [Multi-domain]  Cd Length: 268  Bit Score: 67.71  E-value: 6.17e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFII---ATSAISTSAinENLKK 142
Cdd:cd06323    1 TIGLSVSTLNNPFFVSLKDGAQAEAKELGVELVVLDAQNDPAKQLSQVEDLIVRKVDALLInptDSDAVSPAV--EEANE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 143 HGRPYIVLDQKKSHGFSDS-VRTDDFRGGYLAGVHLLSLGHENIALVYPENPP------EniqlRIEGFKHALDFYQySH 215
Cdd:cd06323   79 AGIPVITVDRSVTGGKVVShIASDNVAGGEMAAEYIAKKLGGKGKVVELQGIPgtsaarE----RGKGFHNAIAKYP-KI 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 216 DQLLLLPTLFSKQGGYQAVPSIIESATT--AIFALNDELAFGLYRGLEEKGKSipdDYSIIGYDNI-DMCEYVKPK--LT 290
Cdd:cd06323  154 NVVASQTADFDRTKGLNVMENLLQAHPDidAVFAHNDEMALGAIQALKAAGRK---DVIVVGFDGTpDAVKAVKDGklAA 230

                        250
                 ....*....|.
gi 492535981 291 TIAQPIVELGK 301
Cdd:cd06323  231 TVAQQPEEMGA 241
PBP1_ABC_sugar_binding-like cd19971
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
 66-327 1.25e-12

monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380626 [Multi-domain]  Cd Length: 267  Bit Score: 66.84  E-value: 1.25e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIatSAISTSAIN---ENLKK 142
Cdd:cd19971    1 KFGFSYMTMNNPFFIAINDGIKKAVEANGDELITRDPQLDQNKQNEQIEDMINQGVDAIFL--NPVDSEGIRpalEAAKE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 143 HGRPYIVLD-QKKSHGFSDS-VRTDDFRGGYLAGVHLLSLGHE--NIALV-YPENppENIQLRIEGFKHAL-DFYQYshd 216
Cdd:cd19971   79 AGIPVINVDtPVKDTDLVDStIASDNYNAGKLCGEDMVKKLPEgaKIAVLdHPTA--ESCVDRIDGFLDAIkKNPKF--- 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 217 qllllpTLFSKQGGYQAVP-------SIIESAT--TAIFALNDELAFGLYRGLEEKGKsiPDDYSIIGYD-NIDMCEYVK 286
Cdd:cd19971  154 ------EVVAQQDGKGQLEvampimeDILQAHPdlDAVFALNDPSALGALAALKAAGK--LGDILVYGVDgSPDAKAAIK 225

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 492535981 287 P-KLT-TIAQPIVELGKASAKLLLSRIQSPTKEwEEELLPVKL 327
Cdd:cd19971  226 DgKMTaTAAQSPIEIGKKAVETAYKILNGEKVE-KEIVVPTFL 267
PRK10339 PRK10339
DNA-binding transcriptional repressor EbgR; Provisional
 7-333 4.23e-12

DNA-binding transcriptional repressor EbgR; Provisional


Pssm-ID: 182389 [Multi-domain]  Cd Length: 327  Bit Score: 65.94  E-value: 4.23e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981   7 TIKDVAKHSGVSIATVSLILNgNEAKFSPK--TVEKVFASKKELGYQPDYlARQMITKETKTIGVLV-------PDITNP 77
Cdd:PRK10339   3 TLKDIAIEAGVSLATVSRVLN-DDPTLNVKeeTKHRILEIAEKLEYKTSS-ARKLQTGAVNQHHILAiysyqqeLEINDP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  78 FFNILMRGIEEvlyQQHFVTILCNADSDHQKEIEYLAeltrrgVDGFIIATSaiSTSAINENLKKHGRPYIVLDQKKSHG 157
Cdd:PRK10339  81 YYLAIRHGIET---QCEKLGIELTNCYEHSGLPDIKN------VTGILIVGK--PTPALRAAASALTDNICFIDFHEPGS 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 158 FSDSVRTDDFRGGYLAGVHLLSLGHENIALVYPENPPENIQLRIEGFkhaLDFYQ----------YSHDqllllptlFSK 227
Cdd:PRK10339 150 GYDAVDIDLARISKEIIDFYINQGVNRIGFIGGEDEPGKADIREVAF---AEYGRlkqvvreediWRGG--------FSS 218

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 228 QGGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNIDMCEYVKPKLTTIAQPIVELGKASAK 305
Cdd:PRK10339 219 SSGYELAKQMLAREDypKALFVASDSIAIGVLRAIHERGLNIPQDISLISVNDIPTARFTFPPLSTVRIHSEMMGSQGVN 298

                        330       340
                 ....*....|....*....|....*...
gi 492535981 306 LLLSRIQSPTKEWEEELLPVKLEKRAST 333
Cdd:PRK10339 299 LLYEKARDGRALPLLVFVPSKLKLRGTT 326
PBP1_tmGBP cd06314
periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and ...
 66-308 8.38e-12

periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs; Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs from other bacteria. They are members of the type 1 periplasmic binding protein superfamily which consists of two domains connected by a three-stranded hinge. TmGBP is specific for glucose and its binding pocket is buried at the interface of the two domains. TmGBP also exhibits high thermostability and the highest structural similarity to E. coli glucose binding protein (ecGBP).


Pssm-ID: 380537 [Multi-domain]  Cd Length: 271  Bit Score: 64.53  E-value: 8.38e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHF-VTILCNADSDHQKEIEYLAELTRRGVDGfiIATSAISTSAINENLKK-- 142
Cdd:cd06314    1 TFALVPKGLNNPFWDLAEAGAEKAAKELGVnVEFVGPQKSDAAEQVQLIEDLIARGVDG--IAISPNDPEAVTPVINKaa 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 143 -HGRPYIVLDqkkshgfSDSVR--------TDDFRGGYLAGVHLL-SLGHE-NIALVYPENPPENIQLRIEGFKHALDFY 211
Cdd:cd06314   79 dKGIPVITFD-------SDAPDskrlayigTDNYEAGREAGELMKkALPGGgKVAIITGGLGADNLNERIQGFKDALKGS 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 212 qyshDQLLLLPTLFSKQGGYQAVpSIIESAT------TAIFALNDELAFGLYRGLEEKGKsiPDDYSIIGYDNIDMC-EY 284
Cdd:cd06314  152 ----PGIEIVDPLSDNDDIAKAV-QNVEDILkanpdlDAIFGVGAYNGPAIAAALKDAGK--VGKVKIVGFDTLPETlQG 224

                        250       260
                 ....*....|....*....|....*.
gi 492535981 285 VKPKL--TTIAQPIVELGKASAKLLL 308
Cdd:cd06314  225 IKDGViaATVGQRPYEMGYLSVKLLY 250
PBP1_TmRBP-like cd19967
D-ribose ABC transporter substrate-binding protein such as Thermoanaerobacter tengcongensis ...
 66-320 3.95e-11

D-ribose ABC transporter substrate-binding protein such as Thermoanaerobacter tengcongensis ribose binding protein (ttRBP); Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type 1 periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.


Pssm-ID: 380622 [Multi-domain]  Cd Length: 272  Bit Score: 62.72  E-value: 3.95e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGfIIATSAISTSAIN--ENLKKH 143
Cdd:cd19967    1 LVAVIVSTPNNPFFVVEAEGAKEKAKELGYEVTVFDHQNDTAKEAELFDTAIASGAKA-IILDPADADASIAavKKAKDA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 144 GRPYIVLDQK-KSHGFSDS-VRTDDFRGGYLAGVHLLSLGHEN---IALVYPENPpENIQLRIEGFKHALDFY------- 211
Cdd:cd19967   80 GIPVFLIDREiNAEGVAVAqIVSDNYQGAVLLAQYFVKLMGEKglyVELLGKESD-TNAQLRSQGFHSVIDQYpelkmva 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 212 QYSHDqllllptlFSKQGGYQAVPSIIESAT--TAIFALNDELAFGLYRGLEEKGKsiPDDYSIIGYDNI-DMCEYVKP- 287
Cdd:cd19967  159 QQSAD--------WDRTEAFEKMESILQANPdiKGVICGNDEMALGAIAALKAAGR--AGDVIIVGFDGSnDVRDAIKEg 228

                        250       260       270
                 ....*....|....*....|....*....|....
gi 492535981 288 KLT-TIAQPIVELGKASAKLLLSRIQSPTKEWEE 320
Cdd:cd19967  229 KISaTVLQPAKLIARLAVEQADQYLKGGSTGKEE 262
PRK10653 PRK10653
ribose ABC transporter substrate-binding protein RbsB;
66-328 7.85e-11

ribose ABC transporter substrate-binding protein RbsB;


Pssm-ID: 182620 [Multi-domain]  Cd Length: 295  Bit Score: 62.03  E-value: 7.85e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFII---ATSAISTSAINENLKK 142
Cdd:PRK10653  28 TIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLInptDSDAVGNAVKMANQAN 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 143 hgRPYIVLDQKKSHGFSDS-VRTDDFRGGYLAGvhllslghENIALVYPENPpENIQL-----------RIEGFKHALDF 210
Cdd:PRK10653 108 --IPVITLDRGATKGEVVShIASDNVAGGKMAG--------DFIAKKLGEGA-KVIQLegiagtsaareRGEGFKQAVAA 176

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 211 YQYshDQLLLLPTLFSKQGGYQAVPSIIES--ATTAIFALNDELAFGLYRGLEEKGKsipDDYSIIGYDNIDmcEYVKP- 287
Cdd:PRK10653 177 HKF--NVLASQPADFDRTKGLNVMQNLLTAhpDVQAVFAQNDEMALGALRALQTAGK---SDVMVVGFDGTP--DGIKAv 249

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 492535981 288 ---KL-TTIAQ-P--IVELGKASAKLLLSriqsptKEWEEELLPVKLE 328
Cdd:PRK10653 250 nrgKLaATIAQqPdqIGAIGVETADKVLK------GEKVEAKIPVDLK 291
PBP1_sensor_kinase-like cd06308
periplasmic binding domain of two-component sensor kinase signaling systems; Periplasmic ...
 66-277 5.56e-10

periplasmic binding domain of two-component sensor kinase signaling systems; Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail.


Pssm-ID: 380531 [Multi-domain]  Cd Length: 268  Bit Score: 59.10  E-value: 5.56e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVT-ILCNADSDHQKEIEYLAELTRRGVDGFIIA--TSAISTSAINEnLKK 142
Cdd:cd06308    1 VIGFSQCSLNDPWRAAMNEEIKAEAAKYPNVElIVTDAQGDAAKQIADIEDLIAQGVDLLIVSpnEADALTPVVKK-AYD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 143 HGRPYIVLDQK-KSHGFSDSVRTDDFRGGYLAGVHLLSL--GHENIALV--YPENPPEniQLRIEGFKHALDFYqYSHDQ 217
Cdd:cd06308   80 AGIPVIVLDRKvSGDDYTAFIGADNVEIGRQAGEYIAELlnGKGNVVEIqgLPGSSPA--IDRHKGFLEAIAKY-PGIKI 156

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 492535981 218 LLLLPTLFSKQGGYQAVPSIIE--SATTAIFALNDELAFGLYRGLEEKGksIPDDYSIIGYD 277
Cdd:cd06308  157 VASQDGDWLRDKAIKVMEDLLQahPDIDAVYAHNDEMALGAYQALKKAG--REKEIKIIGVD 216
PBP1_galactofuranose_YtfQ-like cd06309
periplasmic binding domain of ABC-type galactofuranose YtfQ-like transport systems; ...
 66-286 6.47e-10

periplasmic binding domain of ABC-type galactofuranose YtfQ-like transport systems; Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally.


Pssm-ID: 380532 [Multi-domain]  Cd Length: 285  Bit Score: 59.15  E-value: 6.47e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIatSAISTSAINENL---KK 142
Cdd:cd06309    1 TVGFSQAGSESPWRVANTKSIKEAAKKRGYELVYTDANQDQEKQINDIRDLIAQGVDAILI--SPIDATGWDPVLkeaKD 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 143 HGRPYIVLDQKKSHGFSD----SVRTDDFRGGYLAG---VHLLSLGHENIALVypENPPEN--IQLRIEGFKHALDFYQ- 212
Cdd:cd06309   79 AGIPVILVDRTIDGEDGSlyvtFIGSDFVEEGRRAAewlVKNYKGGKGNVVEL--QGTAGSsvAIDRSKGFREVIKKHPn 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 213 ----YSHDqllllpTLFSKQGGYQAVPSIIESAT---TAIFALNDELAFGLYRGLEEKGKSIPDDYSIIGYDNI-DMCEY 284
Cdd:cd06309  157 ikivASQS------GNFTREKGQKVMENLLQAGPgdiDVIYAHNDDMALGAIQALKEAGLKPGKDVLVVGIDGQkDALEA 230


                 ..
gi 492535981 285 VK 286
Cdd:cd06309  231 IK 232
PBP1_ABC_D-talitol-like cd06318
periplasmic D-talitol-binding protein of an ABC transport system and similar proteins; ...
 66-265 1.13e-08

periplasmic D-talitol-binding protein of an ABC transport system and similar proteins; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380541 [Multi-domain]  Cd Length: 282  Bit Score: 55.49  E-value: 1.13e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIAT--SAISTSAINeNLKKH 143
Cdd:cd06318    1 KIGFSQRTLASPYYAALVAAAKAEAKKLGVELVVTDAQNDLTKQISDVEDLITRGVDVLILNPvdPEGLTPAVK-AAKAA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 144 GRPYIVLDQ--KKSHGFSDSVRTDDFRGGYLAGVHLLS-LGHENIALVYPENPPENI--QLRIEGFKHALDFYQ---YSH 215
Cdd:cd06318   80 GIPVITVDSalDPSANVATQVGRDNKQNGVLVGKEAAKaLGGDPGKIIELSGDKGNEvsRDRRDGFLAGVNEYQlrkYGK 159

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 492535981 216 DQLLLLPTLFSK---QGGYQAVPSIIESATTA--IFALNDELAFGLYRGLEEKGK 265
Cdd:cd06318  160 SNIKVVAQPYGNwirSGAVAAMEDLLQAHPDInvVYAENDDMALGAMKALKAAGM 214
Periplasmic_Binding_Protein_type1 cd01391
Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This ...
 67-317 2.77e-08

Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins, the ligands are monosaccharides, including lactose, ribose, fructose, xylose, arabinose, galactose/glucose and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has six beta strands while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold.


Pssm-ID: 380477 [Multi-domain]  Cd Length: 280  Bit Score: 54.20  E-value: 2.77e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  67 IGVLV---PDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATSAISTSAINENLKKH 143
Cdd:cd01391    2 IGVVTsslHQIREQFGIQRVEAIFHTADKLGASVEIRDSCWHGSVALEQSIEFIRDNIAGVIGPGSSSVAIVIQNLAQLF 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 144 GRPYIVLD-------QKKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVypENPPENI-QLRIEGFKHALdfyqySH 215
Cdd:cd01391   82 DIPQLALDatsqdlsDKTLYKYFLSVVFSDTLGARLGLDIVKRKNWTYVAAI--HGEGLNSgELRMAGFKELA-----KQ 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 216 DQLLLLPT----LFSKQGGYQAVPSIIES--ATTAIFALNDELAFGLYRGLEEKGKSipDDYSIIGYDNI-DMCEYVK-- 286
Cdd:cd01391  155 EGICIVASdkadWNAGEKGFDRALRKLREglKARVIVCANDMTARGVLSAMRRLGLV--GDVSVIGSDGWaDRDEVGYev 232

                        250       260       270
                 ....*....|....*....|....*....|...
gi 492535981 287 --PKLTTIAQPIVELGKASAKLLLSRIQSPTKE 317
Cdd:cd01391  233 eaNGLTTIKQQKMGFGITAIKAMADGSQNMHEE 265
PBP1_rhizopine_binding-like cd06301
periplasmic binding proteins specific to rhizopines; Periplasmic binding proteins specific to ...
 65-306 2.80e-08

periplasmic binding proteins specific to rhizopines; Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily.


Pssm-ID: 380524 [Multi-domain]  Cd Length: 272  Bit Score: 54.16  E-value: 2.80e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  65 KTIGVLVPDITNPFFNILMRGIEEVLYQQHFVT-ILCNADSDHQKEIEYLAELTRRGVDGFII-ATSAISTSAINENLKK 142
Cdd:cd06301    1 IKIGVSMQNFSDEFLTYLRDAIEAYAKEYPGVKlVIVDAQSDAAKQLSQVENFIAQGVDAIIVnPVDTDASAPAVDAAAD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 143 HGRPYIVLDQK-KSHGFSDS-VRTDDFRGGYLAGVHLLSL--GHENIALV--YPENPPEniQLRIEGFKHALDfyQYSHD 216
Cdd:cd06301   81 AGIPLVYVNREpDSKPKGVAfVGSDDIESGELQMEYLAKLlgGKGNIAILdgVLGHEAQ--ILRTEGNKDVLA--KYPGM 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 217 QLLLLPT-LFSKQGGYQAVPSIIESATT--AIFALNDELAFGLYRGLEEKGKSipDDYSIIGYDNI-DMCEYVKPKL--T 290
Cdd:cd06301  157 KIVAEQTaNWSREKAMDIVENWLQSGDKidAIVANNDEMAIGAILALEAAGKK--DDILVAGIDATpDALKAMKAGRldA 234

                        250
                 ....*....|....*.
gi 492535981 291 TIAQPIVELGKASAKL 306
Cdd:cd06301  235 TVFQDAAGQGETAVDV 250
PBP1_ABC_sugar_binding-like cd19970
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
 66-280 3.39e-07

monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380625 [Multi-domain]  Cd Length: 275  Bit Score: 50.71  E-value: 3.39e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNA---DSDHQKEIEYLAELTRRGVDGFIIATSaiSTSAINENLKK 142
Cdd:cd19970    1 KVALVMKSLANEFFIEMEKGARKHAKEANGYELLVKGikqETDIEQQIAIVENLIAQKVDAIVIAPA--DSKALVPVLKK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 143 ---HGRPYIVLDQKKSHGFSDS-------VRTDDFRGGYLAGVHLLSL--GHENIALVypENPP--ENIQLRIEGFKHAL 208
Cdd:cd19970   79 avdAGIAVINIDNRLDADALKEgginvpfVGPDNRQGAYLAGDYLAKKlgKGGKVAII--EGIPgaDNAQQRKAGFLKAF 156

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 492535981 209 DFYQYshdQLLLLPTLFSKQ-GGYQAVPSIIES--ATTAIFALNDELAFGLYRGLEEKGKSipDDYSIIGYDNID 280
Cdd:cd19970  157 EEAGM---KIVASQSANWEIdEANTVAANLLTAhpDIRGILCANDNMALGAIKAVDAAGKA--GKVLVVGFDNIP 226
PBP1_ABC_sugar_binding-like cd06324
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
 66-277 4.63e-07

periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380547 [Multi-domain]  Cd Length: 317  Bit Score: 50.68  E-value: 4.63e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDI-TNPFFNI---LMR------GIE-EVLYqqhfvtilcnADSDHQKEIEYLAELTRR--GVDgFIIATSAIS 132
Cdd:cd06324    1 RVVFINPGKeDEPFWQNvtrFMQaaakdlGIElEVLY----------ANRNRFKMLELAEELLARppKPD-YLILVNEKG 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 133 TSA-INENLKKHGRPYIVL------DQKKSHG-----FSD---SVRTDDFRGGYLAGVHLLSLGHenialvyPENPPENI 197
Cdd:cd06324   70 VAPeLLELAEQAKIPVFLInndltdEERALLGkprekFKYwlgSIVPDNEQAGYLLAKALIKAAR-------KKSDDGKI 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 198 QL--------------RIEGFKHALDfyqySHDQLLLLPTLF---SKQGGYQAVPSIIE--SATTAIFALNDELAFGLYR 258
Cdd:cd06324  143 RVlaisgdkstpasilREQGLRDALA----EHPDVTLLQIVYanwSEDEAYQKTEKLLQryPDIDIVWAANDAMALGAID 218

                        250
                 ....*....|....*....
gi 492535981 259 GLEEKGKSIPDDYSIIGYD 277
Cdd:cd06324  219 ALEEAGLKPGKDVLVGGID 237
PBP1_ABC_sugar_binding-like cd20006
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 101-278 5.05e-06

monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380661 [Multi-domain]  Cd Length: 274  Bit Score: 47.21  E-value: 5.05e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 101 NADSDHQKEIEYLAELTRRGVDGFIIAtsAISTSAIN---ENLKKHGRPYIVLDQK-KSHGFSDSVRTDDFRGGYLAGVH 176
Cdd:cd20006   40 ESEEDIDGQIELIEEAIAQKPDAIVLA--ASDYDRLVeavERAKKAGIPVITIDSPvNSKKADSFVATDNYEAGKKAGEK 117

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 177 LLSLGHEN--IALVYPENPPENIQLRIEGFKHALDfyqySHDQLLLLPTLFSK---QGGYQAVPSIIES--ATTAIFALN 249
Cdd:cd20006  118 LASLLGEKgkVAIVSFVKGSSTAIEREEGFKQALA----EYPNIKIVETEYCDsdeEKAYEITKELLSKypDINGIVALN 193

                        170       180
                 ....*....|....*....|....*....
gi 492535981 250 DELAFGLYRGLEEKGKSipDDYSIIGYDN 278
Cdd:cd20006  194 EQSTLGAARALKELGLG--GKVKVVGFDS 220
PBP1_ABC_IbpA-like cd19968
periplasmic sugar-binding protein IbpA of an ABC transporter and similar proteins; The ...
 66-316 6.69e-06

periplasmic sugar-binding protein IbpA of an ABC transporter and similar proteins; The periplasmic binding protein (PBP) IbpA mediates the uptake of myo-inositol by an ABC transporter that consists of the PBP IbpA, the transmembrane permease IatP, and the ABC IatA. IbpA shares homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge.


Pssm-ID: 380623 [Multi-domain]  Cd Length: 271  Bit Score: 47.00  E-value: 6.69e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIA--TSAISTSAINENLKKh 143
Cdd:cd19968    1 KIGFSFPNLSFPFFVYMHEQAVDEAAKLGVKLVVLDAQNSSSKQASDLENAIAQGVDGIIVSpiDVKALVPAIEAAIKA- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 144 GRPYIVLDQK-KSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVYPENPP---ENIQlRIEGFKHALDfyQYSHDQLL 219
Cdd:cd19968   80 GIPVVTVDRRaEGAAPVPHVGADNVAGGREVAKFVVDKLPNGAKVIELTGTPgssPAID-RTKGFHEELA--AGPKIKVV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 220 LLPTL-FSKQGGYQAVPSIIESATT---AIFALNDELAFGLYRGLEEKG---KSIPddysIIGYDNI-DMCEYVKPK--L 289
Cdd:cd19968  157 FEQTGnFERDEGLTVMENILTSLPGppdAIICANDDMALGAIEAMRAAGldlKKVK----VIGFDAVpDALQAIKDGelY 232

                        250       260
                 ....*....|....*....|....*..
gi 492535981 290 TTIAQPIVELGKASAKLLLSRIQSPTK 316
Cdd:cd19968  233 ATVEQPPGGQARTALRILVDYLKDKKA 259
PBP1_ABC_sugar_binding-like cd19972
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
 66-327 7.94e-06

monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380627 [Multi-domain]  Cd Length: 269  Bit Score: 46.66  E-value: 7.94e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFI-IATSAISTSAINENLKKHG 144
Cdd:cd19972    1 TIGLAVANLQADFFNQIKQSVEAEAKKKGYKVITVDAKGDSATQVNQIQDLITQNIDALIyIPAGATAAAVPVKAARAAG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 145 RPYIVLDQKKSHGFSDS-VRTDDFRGGYLAGVHLLSL--GHENIALVYPE--NPPEniQLRIEGFKHAL----------- 208
Cdd:cd19972   81 IPVIAVDRNPEDAPGDTfIATDSVAAAKELGEWVIKQtgGKGEIAILHGQlgTTPE--VDRTKGFQEALaeapgikvvae 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 209 ---DFYQ---YSHDQLLLlptlfskqggyQAVPSIiesatTAIFALNDELAFGLYRGLEEKGksIPDDYSIIGYD-NIDM 281
Cdd:cd19972  159 qtaDWDQdegFKVAQDML-----------QANPNI-----TVFFGQSDAMALGAAQAVKVAG--LDHKIWVVGFDgDVAG 220

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 492535981 282 CEYVKPKLT--TIAQPIVELGKASAKLLLSrIQSPTKEWEEELLPVKL 327
Cdd:cd19972  221 LKAVKDGVLdaTMTQQTQKMGRLAVDSAID-LLNGKAVPKEQLQDAVL 267
PBP1_ABC_ThpA_XypA cd06313
periplasmic sugar-binding proteins (ThpA and XypA) of ABC-type transport systems; This group ...
 66-286 2.26e-05

periplasmic sugar-binding proteins (ThpA and XypA) of ABC-type transport systems; This group includes periplasmic D-threitol-binding protein ThpA and xylitol/L-sorbitol-binding protein XypA, which are part of sugar ABC-type transport systems. Both ThpA and XypA share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge.


Pssm-ID: 380536 [Multi-domain]  Cd Length: 277  Bit Score: 45.34  E-value: 2.26e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFIIATsaISTSAIN---ENLKK 142
Cdd:cd06313    1 KIGFTVYGLSSEFITNLVEAMKAVAKELNVDLVVLDGNGDVSTQINQVDTLIAQGVDAIIVVP--VDADALApavEKAKE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 143 HGRPYIVLDQKKSHGFSDS-VRTDDFRGGYLAGVHLLSL--GHENIALVypENPPEN---IQlRIEGFKHALdfYQYSHD 216
Cdd:cd06313   79 AGIPLVGVNALIENEDLTAyVGSDDVVAGELEGQAVADRlgGKGNVVIL--EGPIGQsaqID-RGKGIENVL--KKYPDI 153

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 492535981 217 QLLLLPTL-FSKQGGYQAVPSIIESATT---AIFALNDELAFGLYRGLEEKGKsipDDYSIIGYDNI-DMCEYVK 286
Cdd:cd06313  154 KVLAEQTAnWSRDEAMSLMENWLQAYGDeidGIIAQNDDMALGALQAVKAAGR---DDIPVVGIDGIeDALQAVK 225
PBP1_ABC_sugar_binding-like cd20004
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 103-266 5.84e-05

monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380659 [Multi-domain]  Cd Length: 273  Bit Score: 44.15  E-value: 5.84e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 103 DSDHQKEIEYLAELTRRGVDGFIIATSaiSTSAIN---ENLKKHGRPYIVLDqkkshgfSDS--------VRTDDFRGGY 171
Cdd:cd20004   40 EDDVEAQIQIIEYFIDQGVDGIVLAPL--DRKALVapvERARAQGIPVVIID-------SDLggdavisfVATDNYAAGR 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 172 LAGVHLLSL--GHENIALVYPEnppENIQ---LRIEGFKHAL----DFYQYSHDQLlllptlfskqGGYQaVPSIIESAT 242
Cdd:cd20004  111 LAAKRMAKLlnGKGKVALLRLA---KGSAsttDRERGFLEALkklaPGLKVVDDQY----------AGGT-VGEARSSAE 176

                        170       180       190
                 ....*....|....*....|....*....|...
gi 492535981 243 T---------AIFALNDELAFGLYRGLEEKGKS 266
Cdd:cd20004  177 NllnqypdvdGIFTPNESTTIGALRALRRLGLA 209
PBP1_LacI-like cd06287
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
 221-332 9.71e-05

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: 43.18  E-value: 9.71e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 221 LPTLFSKQGGYQAVPSIIES--ATTAIFALNDELAFGLYRGLEEKGKSIPDDYSIIG-YDNIDMCEyVKPKLTTIAQPIV 297
Cdd:cd06287  156 VPESEGERAGYEAAAALLAAhpDIDAVCVPVDAFAVGAMRAARDSGRSVPEDLMVVTrYDGIRART-ADPPLTAVDLHLD 234

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 492535981 298 ELGKASAKLLLSRIQSPTKEWEEELLPvKLEKRAS 332
Cdd:cd06287  235 RVARTAIDLLFASLSGEERSVEVGPAP-ELVVRAS 268
PBP1_ABC_sugar_binding-like cd20008
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 66-278 1.02e-04

monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380663 [Multi-domain]  Cd Length: 277  Bit Score: 43.37  E-value: 1.02e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLyQQHFVTILCNA---DSDHQKEIEYLAELTRRGVDGFIIA-TSAISTSAINENLK 141
Cdd:cd20008    1 KIAVIVKDTDSEYWQTVLKGAEKAA-KELGVEVTFLGpatEADIAGQVNLVENAISRKPDAIVLApNDTAALVPAVEAAD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 142 KhGRPYIVLD-QKKSHGFSDSVRTDDFRGGYLAG---VHLLSLGHEN---IALVYPENPPENIQLRIEGFKHALDFYqys 214
Cdd:cd20008   80 A-GIPVVLVDsGANTDDYDAFLATDNVAAGALAAdelAELLKASGGGkgkVAIISFQAGSQTLVDREEGFRDYIKEK--- 155

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 492535981 215 HDQLLLLPTLFS---KQGGYQAVPSIIES--ATTAIFALNDELAFGLYRGLEEKGKSipDDYSIIGYDN 278
Cdd:cd20008  156 YPDIEIVDVQYSdgdIAKALNQTTDLLTAnpDLVGIFGANNPSAVGVAQALAEAGKA--GKIVLVGFDS 222
PBP1_ABC_sugar_binding-like cd20007
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 69-277 1.05e-04

monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380662 [Multi-domain]  Cd Length: 271  Bit Score: 43.38  E-value: 1.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  69 VLVPDIT-NPFFNILMRGIE--------EVLYQqhfvtilcNADS-DHQKEIEYLAELTRRGVDGFIIA-TSAISTSAIN 137
Cdd:cd20007    3 ALVPGVTgDPFYITMQCGAEaaakelgvELDVQ--------GPPTfDPTLQTPIVNAVIAKKPDALLIApTDPQALIAPL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 138 ENLKKHGRPYIVLDQ--KKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALVYPENPPEN--IQLRIEGFKHALDfyqy 213
Cdd:cd20007   75 KRAADAGIKVVTVDTtlGDPSFVLSQIASDNVAGGALAAEALAELIGGKGKVLVINSTPGVstTDARVKGFAEEMK---- 150

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 492535981 214 SHDQLLLLPTLFSkqGGYQAVPSIIESAT-------TAIFALNDELAFGLYRGLEEKGKSipDDYSIIGYD 277
Cdd:cd20007  151 KYPGIKVLGVQYS--ENDPAKAASIVAAAlqanpdlAGIFGTNTFSAEGAAAALRNAGKT--GKVKVVGFD 217
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
3-55 4.46e-04

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 37.88  E-value: 4.46e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 492535981     3 KKKITIKDVAKHSGVSIATVSLILNGnEAKFSPKTVEKVFaskKELGYQPDYL 55
Cdd:smart00530   8 EKGLTQEELAEKLGVSRSTLSRIENG-KRKPSLETLKKLA---KALGVSLDEL 56
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
1-41 8.46e-04

DNA-binding transcriptional regulator, XRE family [Transcription];


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 37.43  E-value: 8.46e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 492535981   1 MGKKKITIKDVAKHSGVSIATVSLILNGNEAKFSPKTVEKV 41
Cdd:COG3655   10 LAERGMTKKELAEATGISRATLSRLKNGKAKAVRLDTLEKI 50
PBP1_GGBP cd01539
periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and ...
 66-338 8.53e-04

periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species; Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. GGBP is a member of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic GGBP is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.


Pssm-ID: 380481 [Multi-domain]  Cd Length: 302  Bit Score: 40.65  E-value: 8.53e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTIL-CNADSDHQKEIEYLAELTRRGVDGFIIA---TSAISTsaINENLK 141
Cdd:cd01539    2 KIGVFIYNYDDTFISSVRKALEKAAKAGGKIELEiYDAQNDQSTQNDQIDTMIAKGVDLLVVNlvdRTAAQT--IIDKAK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 142 KHGRPYI------VLDQKKSHGFSDSVRTDDFRGGYLAG--VHLLSLGHENIAL--------VYPENPPENI--QLRIEG 203
Cdd:cd01539   80 AANIPVIffnrepSREDLKSYDKAYYVGTDAEESGIMQGeiIADYWKANPEIDKngdgkiqyVMLKGEPGHQdaIARTKY 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 204 FKHALDFYQYSHDQLLLLPTLFSKQGGYQAVPSIIESATT---AIFALNDELAFGLYRGLEEKG-------KSIPddysI 273
Cdd:cd01539  160 SVKTLNDAGIKTEQLAEDTANWDRAQAKDKMDAWLSKYGDkieLVIANNDDMALGAIEALKAAGyntgdgdKYIP----V 235

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 492535981 274 IGYDNID-MCEYVKP-KLT-TIAQPIVELGKASAKLLLSRIQspTKEWEEELLPVKLEKRASTAPLKK 338
Cdd:cd01539  236 FGVDATPeALEAIKEgKMLgTVLNDAKAQAKAIYELAKNLAN--GKEPLETGYKFLVEGKYVRIPYKK 301
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 6-63 1.24e-03

Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense mechanisms];


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 37.48  E-value: 1.24e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 492535981   6 ITIKDVAKHSGVSIATVSLILNGnEAKFSPKT---VEKVFASKKE--LGYQPDY---LARQMITKE 63
Cdd:COG3093   23 LSQTELAKALGVSRQRISEILNG-KRAITADTalrLARAFGTSAEfwLNLQAAYdlwLARQKAGEE 87
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 3-55 1.36e-03

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 36.38  E-value: 1.36e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 492535981   3 KKKITIKDVAKHSGVSIATVSLILNGnEAKFSPKTVEKVFaskKELGYQPDYL 55
Cdd:cd00093   10 EKGLTQEELAEKLGVSRSTISRIENG-KRNPSLETLEKLA---KALGVSLDEL 58
PBP1_ABC_sugar_binding-like cd06311
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
 66-275 1.57e-03

periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380534 [Multi-domain]  Cd Length: 270  Bit Score: 39.66  E-value: 1.57e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  66 TIGVLVPDITNPFFNILMRGIEEVLYQQHFVTILCNADSDHQKEIEYLAELTRRGVDGFII--ATSAISTSAINENLKKh 143
Cdd:cd06311    1 TIGISIPSADHGWTAGVAYYAEKQAKELADLEYKLVTSSNANEQVSQLEDLIAQKVDAIVIlpQDSEELTVAAQKAKDA- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 144 GRPYIVLDQKKSHGFSDS-VRTDDFRGGYLAGVHLL-SLGHENIALVYpENPPENI--QLRIEGFKHALDfYQYSHDQLL 219
Cdd:cd06311   80 GIPVVNFDRGLNVLIYDLyVAGDNPGMGVVSAEYIGkKLGGKGNVVVL-EVPSSGSvnEERVAGFKEVIK-GNPGIKILA 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 492535981 220 LLPTLFSKQGGYQAVPSIIES--ATTAIFALNDELAFGLYRGLEEKGKSipDDYSIIG 275
Cdd:cd06311  158 MQAGDWTREDGLKVAQDILTKnkKIDAVWAADDDMAIGVLQAIKEAGRT--DIKVMTG 213
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
3-55 1.63e-03

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 36.90  E-value: 1.63e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 492535981   3 KKKITIKDVAKHSGVSIATVSLILNGnEAKFSPKTVEKVfasKKELGYQPDYL 55
Cdd:COG1396   18 ARGLTQEELAERLGVSRSTISRIERG-RRNPSLETLLKL---AKALGVSLDEL 66
PBP1_ABC_sugar_binding-like cd06312
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
 72-266 2.00e-03

periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380535 [Multi-domain]  Cd Length: 272  Bit Score: 39.14  E-value: 2.00e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981  72 PDITNPFFNILMRGIE--------EVLYQQhfvtilcNADSDHQKEIEYLAELTRRGVDGfiIATSAISTSAINENLK-- 141
Cdd:cd06312    8 GSPSDPFWSVVKKGAKdaakdlgvTVQYLG-------PQNNDIADQARLIEQAIAAKPDG--IIVTIPDPDALEPALKra 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492535981 142 -KHGRPYIVLDQ-----KKSHGFSDSVRTDDFRGGYLAGVHLLSLGHENIALV--YPENPpeNIQLRIEGFKHALDfyqy 213
Cdd:cd06312   79 vAAGIPVIAINSgddrsKERLGALTYVGQDEYLAGQAAGERALEAGPKNALCVnhEPGNP--GLEARCKGFADAFK---- 152

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 492535981 214 shDQLLLLPTLFSKqGGYQAVPSIIESA------TTAIFALNDELAFGLYRGLEEKGKS 266
Cdd:cd06312  153 --GAGILVELLDVG-GDPTEAQEAIKAYlqadpdTDAVLTLGPVGADPALKAVKEAGLK 208
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 1-41 2.66e-03

Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433211 [Multi-domain]  Cd Length: 63  Bit Score: 35.59  E-value: 2.66e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 492535981    1 MGKKKITIKDVAKHSGVSIATVSLILNGNEAKFSPKTVEKV 41
Cdd:pfam13443   6 MADRGISKSDLARATGISRATLSRLRKGKPKRVSLDTLDKI 46
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 3-55 6.25e-03

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 34.44  E-value: 6.25e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 492535981    3 KKKITIKDVAKHSGVSIATVSLILNGnEAKFSPKTVEKVFaskKELGYQPDYL 55
Cdd:pfam01381   7 ELGLSQEELAEKLGVSRSTISKIENG-KREPSLETLKKLA---EALGVSLDEL 55
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH