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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1052755264   8 DPDIPYLIAGNYS-EHVTEQVEYILDHNPELEAIAFANNNMAKAGYRVCAARDLLVGYDIAITGFDDIDHAKTMEPPLTS 86
Cdd:COG1609   210 PPDPELVVEGDFSaESGYEAARRLLARGPRPTAIFCANDLMALGALRALREAGLRVPEDVSVVGFDDIPLARYLTPPLTT 289

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1052755264  87 VSHSSFQFSYQALQNALMLCQGKK--PQSCRMSAIFHQRSSCG 127
Cdd:COG1609   290 VRQPIEEMGRRAAELLLDRIEGPDapPERVLLPPELVVRESTA 332

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1052755264   8 DPDIPYLIAGNYS-EHVTEQVEYILDHNPELEAIAFANNNMAKAGYRVCAARDLLVGYDIAITGFDDIDHAKTMEPPLTS 86
Cdd:COG1609   210 PPDPELVVEGDFSaESGYEAARRLLARGPRPTAIFCANDLMALGALRALREAGLRVPEDVSVVGFDDIPLARYLTPPLTT 289

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1052755264  87 VSHSSFQFSYQALQNALMLCQGKK--PQSCRMSAIFHQRSSCG 127
Cdd:COG1609   290 VRQPIEEMGRRAAELLLDRIEGPDapPERVLLPPELVVRESTA 332

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).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1052755264   9 PDIPYLIAGNYSEHVTEQVEYILDHNPELEAIAFANNNMAKAGYRVCAARDLLVGYDIAITGFDDIDHAKTMEPPLTSVS 88
Cdd:pfam13377  41 DVEPTLYAGDDEAEAAAARERLRWLGALPTAVFVANDEVALGVLQALREAGLRVPEDLSVIGFDDSPLAALVSPPLTTVR 120

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1052755264  89 HSSFQFSYQALQNALMLCQGK--KPQSCRMSAIFHQRSSC 126
Cdd:pfam13377 121 VDAEELGRAAAELLLDLLNGEpaPPERVLLPPELVEREST 160

Cyclic di-GMP metabolism protein, combines GGDEF and EAL domains with a 6TM membrane domain [Signal transduction mechanisms];

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1052755264 137 LRHISmEQLRKCLPKDAITARLGGDEFVsFILTDILKHSDAI 178
Cdd:COG5001   309 LREVA-RRLRACLREGDTVARLGGDEFA-VLLPDLDDPEDAE 348

Diguanylate cyclase, GGDEF domain; This domain is found linked to a wide range of non-homologous domains in a variety of bacteria. It has been shown to be homologous to the adenylyl cyclase catalytic domain and has diguanylate cyclase activity. This observation correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate. In the WspR protein of Pseudomonas aeruginosa, the GGDEF domain acts as a diguanylate cyclase, PDB:3bre, when the whole molecule appears to form a tetramer consisting of two symmetrically-related dimers representing a biological unit. The active site is the GGD/EF motif, buried in the structure, and the cyclic dimeric guanosine monophosphate (c-di-GMP) bind to the inhibitory-motif RxxD on the surface. The enzyme thus catalyzes the cyclization of two guanosine triphosphate (GTP) molecules to one c-di-GMP molecule.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1052755264 137 LRHISmEQLRKCLPKDAITARLGGDEFVsFILTDIlKHSDAILYEEKVKR 186
Cdd:pfam00990  59 LQEVA-QRLSSSLRRSDLVARLGGDEFA-ILLPET-SLEGAQELAERIRR 105

cyclic di-GMP phosphodiesterase;

                          10        20
                  ....*....|....*....|
gi 1052755264 145 LRKCLPKDAITARLGGDEFV 164
Cdd:PRK10060  300 ILSCLEEDQTLARLGGDEFL 319

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1052755264   8 DPDIPYLIAGNYS-EHVTEQVEYILDHNPELEAIAFANNNMAKAGYRVCAARDLLVGYDIAITGFDDIDHAKTMEPPLTS 86
Cdd:COG1609   210 PPDPELVVEGDFSaESGYEAARRLLARGPRPTAIFCANDLMALGALRALREAGLRVPEDVSVVGFDDIPLARYLTPPLTT 289

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1052755264  87 VSHSSFQFSYQALQNALMLCQGKK--PQSCRMSAIFHQRSSCG 127
Cdd:COG1609   290 VRQPIEEMGRRAAELLLDRIEGPDapPERVLLPPELVVRESTA 332

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1052755264  25 EQVEYILDHNPELEAIAFANNNMAKAGYRVCAARDLLVGYDIAITGFDDIDHAKTMEPPLTSVSHSSFQFSYQALQnalM 104
Cdd:cd06292   170 AAAARLLDLGPPPTAIVCVSDLLALGAMRAARERGLRVGRDVSVVGFDDSPLAAFTHPPLTTVRQPIDEIGRAVVD---L 246

                  ...
gi 1052755264 105 LCQ 107
Cdd:cd06292   247 LLA 249

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1052755264  30 ILDHNPELEAIAFANNNMAKAGYRVCAARDLLVGYDIAITGFDDIDHAKTMEPPLTSVS 88
Cdd:cd01575   172 LLARHPDLDAIFCSNDDLALGALFECQRRGIRVPGDIAIAGFGDLDIAAALPPALTTVR 230

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1052755264  12 PYLIAGNYsehvtEQVEYILDHNPELEAIAFANNNMAKAGYRVCAARDLLVGYDIAITGFDDIDHAKTMEPPLTSVSHSS 91
Cdd:cd06270   158 DFTIEGGY-----AAAKQLLARGLPFTALFAYNDDMAIGALAALHEAGIKVPEDVSVIGFDDVPLARYLSPKLTTVHYPI 232

                          90       100
                  ....*....|....*....|
gi 1052755264  92 FQFSYQALQNALMLCQGKKP 111
Cdd:cd06270   233 EEMAQAAAELALNLAYGEPL 252

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1052755264  10 DIPY---LIA-GNYSEHVTEQ-VEYILDHNPELEAIAFANNNMAKAGYRVCAARDLLVGYDIAITGFDDIDHAKTMEPPL 84
Cdd:cd06280   146 GIPVdesLIFeGDSTIEGGYEaVKALLDLPPRPTAIFATNNLMAVGALRALRERGLEIPQDISVVGFDDSDWFEIVDPPL 225

                          90       100
                  ....*....|....*....|....*..
gi 1052755264  85 TSVSHSSFQFSYQALQNALMLCQGKKP 111
Cdd:cd06280   226 TVVAQPAYEIGRIAAQLLLERIEGQGE 252

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1052755264   2 LEDTPDDPDIPYLIAGNYSEHVT-EQVEYILDHNPELEAIAFANNNMAKAGYRVCAARDLLVGYDIAITGFDDIDHAKTM 80
Cdd:cd06290   141 LEDAGLEVDPRLIVEGDFTEESGyEAMKKLLKRGGPFTAIFAANDLMALGAMKALREAGIRVPDDVSVIGFDDLPFSKYT 220

                          90       100       110
                  ....*....|....*....|....*....|
gi 1052755264  81 EPPLTSVSHSSFQFSYQALQNALMLCQGKK 110
Cdd:cd06290   221 TPPLTTVRQPLYEMGKTAAEILLELIEGKG 250

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1052755264  25 EQVEYILDHNpELEAIAFANNNMAKAGYRVCAARDLLVGYDIAITGFDDIDHAKTMEPPLTSVSHSSFQFSYQALQNALM 104
Cdd:cd19976   167 KAAEELLKSK-NPTAIFAGNDLIAMGVYRAALELGLKIPEDLSVIGFDNIILSEYITPALTTIAQPIFEMGQEAAKLLLK 245

                          90       100
                  ....*....|....*....|...
gi 1052755264 105 LCQG--KKPQSCRMSAIFHQRSS 125
Cdd:cd19976   246 IIKNpaKKKEEIVLPPELIKRDS 268

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1052755264  39 AIAFANNNMAKAGYRVCAARDLLVGYDIAITGFDDIDHAKTMEPPLTSVSHSSFQFSYQALQNAL-MLCQGKKPQSCRMS 117
Cdd:cd01541   187 AIVCYNDEIALRLIQALREAGLRVPEDLSVVGFDDSYLASLSEPPLTSVVHPKEELGRKAAELLLrMIEEGRKPESVIFP 266

                  ....*...
gi 1052755264 118 AIFHQRSS 125
Cdd:cd01541   267 PELIERES 274

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1052755264   6 PDDPDipYLIAGNYS-EHVTEQVEYILDHNPELEAIAFANNNMAKAGYRVCAARDLLVGYDIAITGFDDIDHAKTMEPPL 84
Cdd:cd06284   147 PVDED--LIIEGDFSfEAGYAAARALLALPERPTAIFCASDELAIGAIKALRRAGLRVPEDVSVIGFDDIEFAEMFSPSL 224

                          90       100
                  ....*....|....*....|..
gi 1052755264  85 TSVSHSSFQFSYQAlqnALMLC 106
Cdd:cd06284   225 TTIRQPRYEIGETA---AELLL 243

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1052755264   4 DTPDDPdiPYLIAGNYSEHVTEQVEYILDHNPELEAIAFANNNMAKAGYRVCAARDLLVGYDIAITGFDDIDHAKTMEPP 83
Cdd:cd19977   146 GLPVDE--ELIKHVDRQDDVRKAISELLKLEKPPDAIFAANNLITLEVLKAIKELGLRIPDDIALIGFDDIPWADLFNPP 223

                          90
                  ....*....|
gi 1052755264  84 LTSVSHSSFQ 93
Cdd:cd19977   224 LTVIAQPTYE 233

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1052755264   6 PDDPDIpyLIAGNYS-EHVTEQVEYILDHNPELEAIAFANNNMAKAGYRVCAARDLLVGYDIAITGFDDIDHAKTMEPPL 84
Cdd:cd06296   149 AVDPDL--VREGDFTyEAGYRAARELLELPDPPTAVFAGNDEQALGVYRAARALGLRVPDDLSVIGFDDTPPARWTSPPL 226

                  ...
gi 1052755264  85 TSV 87
Cdd:cd06296   227 TTV 229

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1052755264  28 EYILDHNPELEAIAFANNNMAKAGYRVCAARDLLVGYDIAITGFDDIDHAKTMEPPLTSVSHSSFQFSYQAL 99
Cdd:cd06275   170 QRLLSQPPRPTAVFACNDMMALGALRAAQEQGLRVPQDISIIGYDDIELARYFSPALTTIHQPKDELGELAV 241

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1052755264  30 ILDHNPELEAIAFANNNMAKAGYRVCAARDLLVGYDIAITGFDDIDHAKTMEPPLTSV 87
Cdd:cd01544   172 LLKEGDLPTAFFVASDPMAIGALRALQEAGIKVPEDISIISFNDIEVAKYVTPPLTTV 229

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1052755264  30 ILDHNPELEAIAFANNNMAKAGYRVCAARDLLVGYDIAITGFDDIDHAKTMEPPLTSVSHSSFQFSYQALQ 100
Cdd:cd06293   173 LLAMPPRPTAVFAANDLLALGLLAGLRRAGLRVPDDVSVVGYDDLPFAAAANPPLTTVRQPSYELGRAAAD 243

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1052755264  20 SEHVTEQVEYILDHNPELEAIAFANNNMAKAGYRVCAARDLLVGYDIAITGFDDIDHAKTMEPPLTSV 87
Cdd:cd06295   168 EESGYAAMRALLDSGTAFDAIFAASDLIAMGAIRALRERGISVPGDVAVVGYDDIPLAAYFRPPLTTV 235

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1052755264  25 EQVEYILDHNPeLEAIAFANNNMAKAGYRVCAARDLLVGYDIAITGFDDIDHAKTMEPPLTSVSHSSFQFSYQALQNAL- 103
Cdd:cd01542   163 EAAKELLKENK-PDAIICATDNIALGAIKALRELGIKIPEDISVAGFGGYDLSEFVSPSLTTVKFDYEEAGEKAAELLLd 241

                          90
                  ....*....|....
gi 1052755264 104 MLCQGKKPQSCRMS 117
Cdd:cd01542   242 MIEGEKVPKKQKLP 255

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1052755264  40 IAFA-NNNMAKAGYRVcaardllvGYDIAITGFDDIDHAKTMEPPLTSVSHSSFQFSYQALQ 100
Cdd:cd19974   190 IAIQlIKALKEKGYRV--------PEDISVVGFDNIELAELSTPPLTTVEVDKEAMGRRAVE 243

Cyclic di-GMP metabolism protein, combines GGDEF and EAL domains with a 6TM membrane domain [Signal transduction mechanisms];

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1052755264 137 LRHISmEQLRKCLPKDAITARLGGDEFVsFILTDILKHSDAI 178
Cdd:COG5001   309 LREVA-RRLRACLREGDTVARLGGDEFA-VLLPDLDDPEDAE 348

Diguanylate-cyclase (DGC) or GGDEF domain; Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue pattern, and initially described as a domain of unknown function 1 (DUF1). This domain is widely present in bacteria, linked to a wide range of non-homologous domains in a variety of cell signaling proteins. The domain shows homology to the adenylyl cyclase catalytic domain. This correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate. Together with the EAL domain, GGDEF might be involved in regulating cell surface adhesion in bacteria.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1052755264 137 LRHISmEQLRKCLPKDAITARLGGDEFVsfILTDILKHSDAILYEEKVkrRASIKK 192
Cdd:cd01949    58 LKEVA-ERLRSSLRESDLVARLGGDEFA--ILLPGTDLEEAEALAERL--REAIEE 108

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1052755264  25 EQVEYILDHNPELEAIAFANNNMAKAGYRVCAARDLLVGYDIAITGFDDIDHAKTMEPPLTSVSHSSFQFSYQALQNALM 104
Cdd:cd01537   168 DKMDQWLSGPNKPTAVIANNDAMAMGAVEALKEHGLRVPSDISVFGYDALPEALKSGPLLTTILQDANNLGKTTFDLLLN 247

                          90
                  ....*....|....
gi 1052755264 105 LCQGKK--PQSCRM 116
Cdd:cd01537   248 LADNWKidNKVVRV 261

DNA-binding transcriptional repressor MalI; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1052755264  25 EQVEYILDHNPELEAIAFANNNMA--------KAGYRVC-AARDLLVGYDIAITGFDDIDHAKTMEPPLTSVSHSSFQFS 95
Cdd:PRK10014  232 EAITALLRHNPTISAVVCYNETIAmgawfgllRAGRQSGeSGVDRYFEQQVALAAFTDVPEAELDDPPLTWASTPAREIG 311

                  ....*...
gi 1052755264  96 YQALQNAL 103
Cdd:PRK10014  312 RTLADRMM 319

HTH-type transcriptional regulator GalR;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1052755264  30 ILDHNPELEAIAFANNNMAKAGYRVCAARDLLVGYDIAITGFDDIDHAKTMEPPLTSVSHSSFQFSYQALQNALMLCQGK 109
Cdd:PRK10727  231 LLGRGRNFTAVACYNDSMAAGAMGVLNDNGIDVPGEISLIGFDDVLVSRYVRPRLTTVRYPIVTMATQAAELALALADNR 310

                  ..
gi 1052755264 110 KP 111
Cdd:PRK10727  311 PL 312

diguanylate cyclase; Diguanylate cyclase, present in a variety of bacteria.

                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1052755264  137 LRHISmEQLRKCLPKDAITARLGGDEFVsFILTDI 171
Cdd:smart00267  61 LQEVA-QRLSSCLRPGDLLARLGGDEFA-LLLPET 93

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1052755264  30 ILDHNPELEAIAFA-NNNMA--------KAGYRVCAardllvgyDIAITGFDDIDHAKTMEPPLTSVS 88
Cdd:cd06277   177 LLDTGPKLPTAFFAeNDIIAlgcikalqEAGIRVPE--------DVSVIGFDDIPVSAMVDPPLTTIH 236