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Conserved domains on  [gi|16131621|ref|NP_418209|]
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DNA-binding transcriptional dual regulator RbsR [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

ribose operon transcriptional repressor RbsR( domain architecture ID 11484714)

ribose operon transcriptional repressor RbsR binds to a region of perfect dyad symmetry spanning the rbs operon transcriptional start site

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PRK10423 PRK10423
transcriptional repressor RbsR; Provisional
4-330 0e+00

transcriptional repressor RbsR; Provisional


:

Pssm-ID: 182448 [Multi-domain]  Cd Length: 327  Bit Score: 742.67  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621    4 MKDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSALARSLKLNQTHTIGMLITASTNPFYSELVRGVER 83
Cdd:PRK10423   1 MKDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSALARSLKLNQTRTIGMLITASTNPFYSELVRGVER 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   84 SCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYPTVPTVMMDWAPFDGDSDLIQDNSLL 163
Cdd:PRK10423  81 SCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYPSVPTVMMDWAPFDGDSDLIQDNSLL 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  164 GGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMRQLLSHPLRPQAVF 243
Cdd:PRK10423 161 GGDLATQYLIDKGYTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMQQLLALPLRPQAVF 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  244 TGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGELAIDVLIHRITQPTLQQQRLQLTPI 323
Cdd:PRK10423 241 TGNDAMAVGVYQALYQAGLSVPQDIAVIGYDDIELARYMTPPLTTIHQPKDELGELAIDVLIHRMAQPTLQQQRLQLTPE 320

                 ....*..
gi 16131621  324 LMERGSA 330
Cdd:PRK10423 321 LMERGSV 327
 
Name Accession Description Interval E-value
PRK10423 PRK10423
transcriptional repressor RbsR; Provisional
4-330 0e+00

transcriptional repressor RbsR; Provisional


Pssm-ID: 182448 [Multi-domain]  Cd Length: 327  Bit Score: 742.67  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621    4 MKDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSALARSLKLNQTHTIGMLITASTNPFYSELVRGVER 83
Cdd:PRK10423   1 MKDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSALARSLKLNQTRTIGMLITASTNPFYSELVRGVER 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   84 SCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYPTVPTVMMDWAPFDGDSDLIQDNSLL 163
Cdd:PRK10423  81 SCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYPSVPTVMMDWAPFDGDSDLIQDNSLL 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  164 GGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMRQLLSHPLRPQAVF 243
Cdd:PRK10423 161 GGDLATQYLIDKGYTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMQQLLALPLRPQAVF 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  244 TGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGELAIDVLIHRITQPTLQQQRLQLTPI 323
Cdd:PRK10423 241 TGNDAMAVGVYQALYQAGLSVPQDIAVIGYDDIELARYMTPPLTTIHQPKDELGELAIDVLIHRMAQPTLQQQRLQLTPE 320

                 ....*..
gi 16131621  324 LMERGSA 330
Cdd:PRK10423 321 LMERGSV 327
PurR COG1609
DNA-binding transcriptional regulator, LacI/PurR family [Transcription];
1-330 9.40e-146

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


Pssm-ID: 441217 [Multi-domain]  Cd Length: 335  Bit Score: 414.21  E-value: 9.40e-146
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   1 MATMKDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSALARSLKLNQTHTIGMLITASTNPFYSELVRG 80
Cdd:COG1609   3 RVTIKDVARLAGVSVATVSRVLNGPPRVSEETRERVLAAAEELGYRPNAAARSLRTGRTRTIGVVVPDLSNPFFAELLRG 82
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  81 VERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYPtVPTVMMDWAPFDGDSDLIQDN 160
Cdd:COG1609  83 IEEAARERGYQLLLANSDEDPEREREALRLLLSRRVDGLILAGSRLDDARLERLAEAG-IPVVLIDRPLPDPGVPSVGVD 161
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 161 SLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMRQLLSHPLRPQ 240
Cdd:COG1609 162 NRAGARLATEHLIELGHRRIAFIGGPADSSSARERLAGYREALAEAGLPPDPELVVEGDFSAESGYEAARRLLARGPRPT 241
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 241 AVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGELAIDVLIHRITQPTLQQQRLQL 320
Cdd:COG1609 242 AIFCANDLMALGALRALREAGLRVPEDVSVVGFDDIPLARYLTPPLTTVRQPIEEMGRRAAELLLDRIEGPDAPPERVLL 321
                       330
                ....*....|
gi 16131621 321 TPILMERGSA 330
Cdd:COG1609 322 PPELVVREST 331
PBP1_PurR cd06275
ligand-binding domain of purine repressor, PurR, which functions as the master regulatory ...
61-329 4.99e-141

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: 399.71  E-value: 4.99e-141
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYPTV 140
Cdd:cd06275   1 TIGLLVTSSENPFFAEVVRGVEDACFRAGYSLILCNSDNDPEKQRAYLDMLAEKRVDGLLLMCSEMTDDDAELLAALRSI 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 141 PTVMMDWAPFDGDSDLIQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDF 220
Cdd:cd06275  81 PVVVLDREIAGDNADAVLDDSFQGGYLATRHLIELGHRRIGCITGPLEHSVSRERLAGFRRALAEAGIEVPPSWIVEGDF 160
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 221 EFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGELA 300
Cdd:cd06275 161 EPEGGYEAMQRLLSQPPRPTAVFACNDMMALGALRAAQEQGLRVPQDISIIGYDDIELARYFSPALTTIHQPKDELGELA 240
                       250       260
                ....*....|....*....|....*....
gi 16131621 301 IDVLIHRITQPTLQQQRLQLTPILMERGS 329
Cdd:cd06275 241 VELLLDRIENKREEPQSIVLEPELIERES 269
Peripla_BP_3 pfam13377
Periplasmic binding protein-like domain; This domain is found in a variety of transcriptional ...
171-329 1.92e-42

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: 144.40  E-value: 1.92e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   171 YLIDKGHTRIACIT--GPLDKTPARLRLEGYRAAMKRAGLnIPDGYEVTGDFEFNGGFDAMRqLLSHPLRPQAVFTGNDA 248
Cdd:pfam13377   1 HLAELGHRRIALIGpeGDRDDPYSDLRERGFREAARELGL-DVEPTLYAGDDEAEAAAARER-LRWLGALPTAVFVANDE 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   249 MAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGELAIDVLIHRITQPTLQQQRLQLTPILMERG 328
Cdd:pfam13377  79 VALGVLQALREAGLRVPEDLSVIGFDDSPLAALVSPPLTTVRVDAEELGRAAAELLLDLLNGEPAPPERVLLPPELVERE 158

                  .
gi 16131621   329 S 329
Cdd:pfam13377 159 S 159
HTH_LACI smart00354
helix_turn _helix lactose operon repressor;
2-71 8.20e-34

helix_turn _helix lactose operon repressor;


Pssm-ID: 197675 [Multi-domain]  Cd Length: 70  Bit Score: 118.84  E-value: 8.20e-34
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621      2 ATMKDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSALARSLKLNQTHTIGMLITASTN 71
Cdd:smart00354   1 ATIKDVARLAGVSKATVSRVLNGKGRVSEETREKVLAAMEELGYIPNRVARSLKGKKTKTIGLIVPDITN 70
 
Name Accession Description Interval E-value
PRK10423 PRK10423
transcriptional repressor RbsR; Provisional
4-330 0e+00

transcriptional repressor RbsR; Provisional


Pssm-ID: 182448 [Multi-domain]  Cd Length: 327  Bit Score: 742.67  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621    4 MKDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSALARSLKLNQTHTIGMLITASTNPFYSELVRGVER 83
Cdd:PRK10423   1 MKDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSALARSLKLNQTRTIGMLITASTNPFYSELVRGVER 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   84 SCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYPTVPTVMMDWAPFDGDSDLIQDNSLL 163
Cdd:PRK10423  81 SCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYPSVPTVMMDWAPFDGDSDLIQDNSLL 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  164 GGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMRQLLSHPLRPQAVF 243
Cdd:PRK10423 161 GGDLATQYLIDKGYTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMQQLLALPLRPQAVF 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  244 TGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGELAIDVLIHRITQPTLQQQRLQLTPI 323
Cdd:PRK10423 241 TGNDAMAVGVYQALYQAGLSVPQDIAVIGYDDIELARYMTPPLTTIHQPKDELGELAIDVLIHRMAQPTLQQQRLQLTPE 320

                 ....*..
gi 16131621  324 LMERGSA 330
Cdd:PRK10423 321 LMERGSV 327
PRK10703 PRK10703
HTH-type transcriptional repressor PurR;
1-329 8.65e-153

HTH-type transcriptional repressor PurR;


Pssm-ID: 236739 [Multi-domain]  Cd Length: 341  Bit Score: 432.23  E-value: 8.65e-153
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621    1 MATMKDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSALARSLKLNQTHTIGMLITASTNPFYSELVRG 80
Cdd:PRK10703   1 MATIKDVAKRAGVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLATSSEAPYFAEIIEA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   81 VERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYPTVPTVMMDWAPFDGD-SDLIQD 159
Cdd:PRK10703  81 VEKNCYQKGYTLILCNAWNNLEKQRAYLSMLAQKRVDGLLVMCSEYPEPLLAMLEEYRHIPMVVMDWGEAKADfTDAIID 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  160 NSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMRQLLSHPLRP 239
Cdd:PRK10703 161 NAFEGGYLAGRYLIERGHRDIGVIPGPLERNTGAGRLAGFMKAMEEANIKVPEEWIVQGDFEPESGYEAMQQILSQKHRP 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  240 QAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGELAIDVLIHRITQPTLQQQRLQ 319
Cdd:PRK10703 241 TAVFCGGDIMAMGAICAADEMGLRVPQDISVIGYDNVRNARYFTPALTTIHQPKDRLGETAFNMLLDRIVNKREEPQTIE 320
                        330
                 ....*....|
gi 16131621  320 LTPILMERGS 329
Cdd:PRK10703 321 VHPRLVERRS 330
PurR COG1609
DNA-binding transcriptional regulator, LacI/PurR family [Transcription];
1-330 9.40e-146

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


Pssm-ID: 441217 [Multi-domain]  Cd Length: 335  Bit Score: 414.21  E-value: 9.40e-146
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   1 MATMKDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSALARSLKLNQTHTIGMLITASTNPFYSELVRG 80
Cdd:COG1609   3 RVTIKDVARLAGVSVATVSRVLNGPPRVSEETRERVLAAAEELGYRPNAAARSLRTGRTRTIGVVVPDLSNPFFAELLRG 82
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  81 VERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYPtVPTVMMDWAPFDGDSDLIQDN 160
Cdd:COG1609  83 IEEAARERGYQLLLANSDEDPEREREALRLLLSRRVDGLILAGSRLDDARLERLAEAG-IPVVLIDRPLPDPGVPSVGVD 161
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 161 SLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMRQLLSHPLRPQ 240
Cdd:COG1609 162 NRAGARLATEHLIELGHRRIAFIGGPADSSSARERLAGYREALAEAGLPPDPELVVEGDFSAESGYEAARRLLARGPRPT 241
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 241 AVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGELAIDVLIHRITQPTLQQQRLQL 320
Cdd:COG1609 242 AIFCANDLMALGALRALREAGLRVPEDVSVVGFDDIPLARYLTPPLTTVRQPIEEMGRRAAELLLDRIEGPDAPPERVLL 321
                       330
                ....*....|
gi 16131621 321 TPILMERGSA 330
Cdd:COG1609 322 PPELVVREST 331
PBP1_PurR cd06275
ligand-binding domain of purine repressor, PurR, which functions as the master regulatory ...
61-329 4.99e-141

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: 399.71  E-value: 4.99e-141
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYPTV 140
Cdd:cd06275   1 TIGLLVTSSENPFFAEVVRGVEDACFRAGYSLILCNSDNDPEKQRAYLDMLAEKRVDGLLLMCSEMTDDDAELLAALRSI 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 141 PTVMMDWAPFDGDSDLIQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDF 220
Cdd:cd06275  81 PVVVLDREIAGDNADAVLDDSFQGGYLATRHLIELGHRRIGCITGPLEHSVSRERLAGFRRALAEAGIEVPPSWIVEGDF 160
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 221 EFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGELA 300
Cdd:cd06275 161 EPEGGYEAMQRLLSQPPRPTAVFACNDMMALGALRAAQEQGLRVPQDISIIGYDDIELARYFSPALTTIHQPKDELGELA 240
                       250       260
                ....*....|....*....|....*....
gi 16131621 301 IDVLIHRITQPTLQQQRLQLTPILMERGS 329
Cdd:cd06275 241 VELLLDRIENKREEPQSIVLEPELIERES 269
PBP1_LacI_sugar_binding-like cd06267
ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 ...
61-325 2.84e-106

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: 310.99  E-value: 2.84e-106
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYPtV 140
Cdd:cd06267   1 TIGLIVPDISNPFFAELLRGIEDAARERGYSLLLCNTDEDPEREREYLRLLLSRRVDGIILAPSSLDDELLEELLAAG-I 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 141 PTVMMDWAPFDGDSDLIQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDF 220
Cdd:cd06267  80 PVVLIDRRLDGLGVDSVVVDNYAGAYLATEHLIELGHRRIAFIGGPLDLSTSRERLEGYRDALAEAGLPVDPELVVEGDF 159
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 221 EFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGELA 300
Cdd:cd06267 160 SEESGYEAARELLALPPRPTAIFAANDLMAIGALRALRELGLRVPEDISVVGFDDIPLAALLTPPLTTVRQPAYEMGRAA 239
                       250       260
                ....*....|....*....|....*
gi 16131621 301 IDVLIHRITQPTLQQQRLQLTPILM 325
Cdd:cd06267 240 AELLLERIEGEEEPPRRIVLPTELV 264
PBP1_LacI-like cd06285
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
61-330 1.88e-92

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: 276.41  E-value: 1.88e-92
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQP-SREIMQRypT 139
Cdd:cd06285   1 TIGVLVSDLSNPFYAELVEGIEDAARERGYTVLLADTGDDPERELAALDSLLSRRVDGLIITPARDDAPdLQELAAR--G 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 140 VPTVMMDWAPFDGDSDLIQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGD 219
Cdd:cd06285  79 VPVVLVDRRIGDTALPSVTVDNELGGRLATRHLLELGHRRIAVVAGPLNASTGRDRLRGYRRALAEAGLPVPDERIVPGG 158
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 220 FEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGEL 299
Cdd:cd06285 159 FTIEAGREAAYRLLSRPERPTAVFAANDLMAIGVLRAARDLGLRVPEDLSVVGFDDIPLAAFLPPPLTTVRQPKYEMGRR 238
                       250       260       270
                ....*....|....*....|....*....|.
gi 16131621 300 AIDVLIHRITQPTLQQQRLQLTPILMERGSA 330
Cdd:cd06285 239 AAELLLQLIEGGGRPPRSITLPPELVVREST 269
PBP1_LacI-like cd06284
ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus ...
61-329 3.39e-90

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: 270.56  E-value: 3.39e-90
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLctETHQPSREIMQRYPTV 140
Cdd:cd06284   1 TILVLVPNISNPFYSEILRGIEDAAAEAGYDVLLGDTDSDPEREDDLLDMLRSRRVDGVILL--SGRLDAELLSELSKRY 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 141 PTVMM-DWAPfdgDSDL----IQDNSllGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYE 215
Cdd:cd06284  79 PIVQCcEYIP---DSGVpsvsIDNEA--AAYDATEYLISLGHRRIAHINGPLDNVYARERLEGYRRALAEAGLPVDEDLI 153
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 216 VTGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDE 295
Cdd:cd06284 154 IEGDFSFEAGYAAARALLALPERPTAIFCASDELAIGAIKALRRAGLRVPEDVSVIGFDDIEFAEMFSPSLTTIRQPRYE 233
                       250       260       270
                ....*....|....*....|....*....|....
gi 16131621 296 LGELAIDVLIHRITQPTLQQQRLQLTPILMERGS 329
Cdd:cd06284 234 IGETAAELLLEKIEGEGVPPEHIILPHELIVRES 267
PBP1_DegA_Like cd19976
ligand-binding domain of putative DNA transcription regulators highly similar to that of the ...
61-329 1.34e-86

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: 261.41  E-value: 1.34e-86
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLlCTETHQPS--REIMQRYP 138
Cdd:cd19976   1 TIGLIVPDISNPFFSELVRGIEDTLNELGYNIILCNTYNDFEREKKYIQELKERNVDGIII-ASSNISDEaiIKLLKEEK 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 139 TvPTVMMDWAPFDGDSDLIQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTG 218
Cdd:cd19976  80 I-PVVVLDRYIEDNDSDSVGVDDYRGGYEATKYLIELGHTRIGCIVGPPSTYNEHERIEGYKNALQDHNLPIDESWIYSG 158
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 219 DFEFNGGFDAMRQLLSHPlRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGE 298
Cdd:cd19976 159 ESSLEGGYKAAEELLKSK-NPTAIFAGNDLIAMGVYRAALELGLKIPEDLSVIGFDNIILSEYITPALTTIAQPIFEMGQ 237
                       250       260       270
                ....*....|....*....|....*....|.
gi 16131621 299 LAIDVLIHRITQPTLQQQRLQLTPILMERGS 329
Cdd:cd19976 238 EAAKLLLKIIKNPAKKKEEIVLPPELIKRDS 268
PBP1_Qymf-like cd06291
ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing ...
61-329 5.42e-84

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: 254.37  E-value: 5.42e-84
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLcteTHQPSREIMQRYpTV 140
Cdd:cd06291   1 TIGLIVPDISNPFFAELAKYIEKELFKKGYKMILCNSNEDEEKEKEYLEMLKRNKVDGIILG---SHSLDIEEYKKL-NI 76
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 141 PTVMMDWApFDGDSDLIQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDF 220
Cdd:cd06291  77 PIVSIDRY-LSEGIPSVSSDNYQGGRLAAEHLIEKGCKKILHIGGPSNNSPANERYRGFEDALKEAGIEYEIIEIDENDF 155
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 221 EFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGELA 300
Cdd:cd06291 156 SEEDAYELAKELLEKYPDIDGIFASNDLLAIGVLKALQKLGIRVPEDVQIIGFDGIEISELLYPELTTIRQPIEEMAKEA 235
                       250       260
                ....*....|....*....|....*....
gi 16131621 301 IDVLIHRITQPTLQQQRLQLTPILMERGS 329
Cdd:cd06291 236 VELLLKLIEGEEIEESRIVLPVELIERET 264
PBP1_sucrose_transcription_regulator cd06288
ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members ...
61-329 1.34e-83

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: 253.62  E-value: 1.34e-83
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLI-TASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQpsREIMQRYPT 139
Cdd:cd06288   1 TIGLITdDIATTPFAGDIIRGAQDAAEEHGYLLLLANTGGDPELEAEAIRELLSRRVDGIIYASMHHRE--VTLPPELTD 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 140 VPTVMMD-WAPFDGDSDLIQDNSLlGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTG 218
Cdd:cd06288  79 IPLVLLNcFDDDPSLPSVVPDDEQ-GGYLATRHLIEAGHRRIAFIGGPEDSLATRLRLAGYRAALAEAGIPYDPSLVVHG 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 219 DFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGE 298
Cdd:cd06288 158 DWGRESGYEAAKRLLSAPDRPTAIFCGNDRMAMGVYQAAAELGLRVPEDLSVVGFDNQELAAYLRPPLTTVALPYYEMGR 237
                       250       260       270
                ....*....|....*....|....*....|.
gi 16131621 299 LAIDVLIHRITQPTLQQQRLQLTPILMERGS 329
Cdd:cd06288 238 RAAELLLDGIEGEPPEPGVIRVPCPLIERES 268
PBP1_LacI-like cd06293
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
61-329 7.05e-80

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: 244.10  E-value: 7.05e-80
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPS-REIMQRypT 139
Cdd:cd06293   1 TIGLVVPDVSNPFFAEVARGVEDAARERGYAVVLCNSGRDPERERRYLEMLESQRVRGLIVTPSDDDLSHlARLRAR--G 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 140 VPTVMMD--WAPFDGDSDLIQDnsLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVT 217
Cdd:cd06293  79 TAVVLLDrpAPGPAGCSVSVDD--VQGGALAVDHLLELGHRRIAFVSGPLRTRQVAERLAGARAAVAEAGLDPDEVVREL 156
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 218 GDFEFN--GGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDE 295
Cdd:cd06293 157 SAPDANaeLGRAAAAQLLAMPPRPTAVFAANDLLALGLLAGLRRAGLRVPDDVSVVGYDDLPFAAAANPPLTTVRQPSYE 236
                       250       260       270
                ....*....|....*....|....*....|....
gi 16131621 296 LGELAIDVLIHRITQPTLQQQRLQLTPILMERGS 329
Cdd:cd06293 237 LGRAAADLLLDEIEGPGHPHEHVVFQPELVVRSS 270
PBP1_GalS-like cd06270
ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory ...
61-327 4.30e-77

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: 237.03  E-value: 4.30e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETH-QPSREIMQRYPt 139
Cdd:cd06270   1 TIGLVVPDLSGPFFGSLLKGAERVARAHGKQLLITSGHHDAEEEREAIEFLLDRRCDAIILHSRALSdEELILIAEKIP- 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 140 vPTVMMDWApFDGDSD----LiqDNSLlGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYE 215
Cdd:cd06270  80 -PLVVINRY-IPGLADrcvwL--DNEQ-GGRLAAEHLLDLGHRRIACITGPLDIPDARERLAGYRDALAEAGIPLDPSLI 154
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 216 VTGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDE 295
Cdd:cd06270 155 IEGDFTIEGGYAAAKQLLARGLPFTALFAYNDDMAIGALAALHEAGIKVPEDVSVIGFDDVPLARYLSPKLTTVHYPIEE 234
                       250       260       270
                ....*....|....*....|....*....|..
gi 16131621 296 LGELAIDVLIHRITQPTLQQQRlQLTPILMER 327
Cdd:cd06270 235 MAQAAAELALNLAYGEPLPISH-EFTPTLIER 265
PBP1_LacI-like cd06290
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
61-329 5.56e-76

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: 234.05  E-value: 5.56e-76
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTE-THQPSREIMqryPT 139
Cdd:cd06290   1 TIGVLVPDIDSPFYSEILNGIEEVLAESGYTLIVSTSHWNADRELEILRLLLARKVDGIIVVGGFgDEELLKLLA---EG 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 140 VPTVMMDWAPFDGDSDLIQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGD 219
Cdd:cd06290  78 IPVVLVDRELEGLNLPVVNVDNEQGGYNATNHLIDLGHRRIVHISGPEDHPDAQERYAGYRRALEDAGLEVDPRLIVEGD 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 220 FEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGEL 299
Cdd:cd06290 158 FTEESGYEAMKKLLKRGGPFTAIFAANDLMALGAMKALREAGIRVPDDVSVIGFDDLPFSKYTTPPLTTVRQPLYEMGKT 237
                       250       260       270
                ....*....|....*....|....*....|
gi 16131621 300 AIDVLIHRITQPTLQQQRLQLTPILMERGS 329
Cdd:cd06290 238 AAEILLELIEGKGRPPRRIILPTELVIRES 267
PBP1_EndR-like cd19977
periplasmic ligand-binding domain of putative repressor of the endoglucanase operon and its ...
61-325 6.93e-75

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: 231.26  E-value: 6.93e-75
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPS-REIMQRypT 139
Cdd:cd19977   1 TIGLIVADILNPFFTSVVRGIEDEAYKNGYHVILCNTDEDPEKEKKYIEMLRAKQVDGIIIAPTGGNEDLiEKLVKS--G 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 140 VPTVMMDWAPFDGDSDLIQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYeVTGD 219
Cdd:cd19977  79 IPVVFVDRYIPGLDVDTVVVDNFKGAYQATEHLIELGHKRIAFITYPLELSTRQERLEGYKAALADHGLPVDEEL-IKHV 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 220 FEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGEL 299
Cdd:cd19977 158 DRQDDVRKAISELLKLEKPPDAIFAANNLITLEVLKAIKELGLRIPDDIALIGFDDIPWADLFNPPLTVIAQPTYEIGRK 237
                       250       260
                ....*....|....*....|....*..
gi 16131621 300 AIDVLIHRITQ-PTLQQQRLQLTPILM 325
Cdd:cd19977 238 AAELLLDRIENkPKGPPRQIVLPTELI 264
PBP1_LacI-like cd06280
ligand-binding domain of an uncharacterized transcription regulator from Staphylococcus ...
61-327 8.94e-75

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: 230.99  E-value: 8.94e-75
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLlcTETHQPSREIMQRYPT- 139
Cdd:cd06280   1 TIGLIVPDITNPFFTTIARGIEDAAEKHGYQVILANTDEDPEKEKRYLDSLLSKQVDGIIL--APSAGPSRELKRLLKHg 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 140 VPTVMMDWAPFDGDSDLIQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGD 219
Cdd:cd06280  79 IPIVLIDREVEGLELDLVAGDNREGAYKAVKHLIELGHRRIGLITGPLEISTTRERLAGYREALAEAGIPVDESLIFEGD 158
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 220 FEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGEL 299
Cdd:cd06280 159 STIEGGYEAVKALLDLPPRPTAIFATNNLMAVGALRALRERGLEIPQDISVVGFDDSDWFEIVDPPLTVVAQPAYEIGRI 238
                       250       260
                ....*....|....*....|....*...
gi 16131621 300 AIDVLIHRITQPTLQQQRLQLTPILMER 327
Cdd:cd06280 239 AAQLLLERIEGQGEEPRRIVLPTELIIR 266
PBP1_CcpA-like cd19975
ligand-binding domain of putative DNA transcription regulators highly similar to that of the ...
61-329 9.85e-74

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: 228.59  E-value: 9.85e-74
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLcteTHQPSREIMQ--RYP 138
Cdd:cd19975   1 TIGVIIPDISNSFFAEILKGIEDEARENGYSVILCNTGSDEEREKKYLQLLKEKRVDGIIFA---SGTLTEENKQllKNM 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 139 TVPTVMmdwapFDGDSDLIQ------DNSLLGGDlATQYLIDKGHTRIACITGPL-DKTPARLRLEGYRAAMKRAGLNIP 211
Cdd:cd19975  78 NIPVVL-----VSTESEDPDipsvkiDDYQAAYD-ATNYLIKKGHRKIAMISGPLdDPNAGYPRYEGYKKALKDAGLPIK 151
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 212 DGYEVTGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQ 291
Cdd:cd19975 152 ENLIVEGDFSFKSGYQAMKRLLKNKKLPTAVFAASDEMALGVISAAYDHGIRVPEDISVIGFDNTEIAEMSIPPLTTVSQ 231
                       250       260       270
                ....*....|....*....|....*....|....*...
gi 16131621 292 PKDELGELAIDVLIHRITQPTLQQQRLQLTPILMERGS 329
Cdd:cd19975 232 PFYEMGKKAVELLLDLIKNEKKEEKSIVLPHQIIERES 269
PBP1_AraR cd01541
ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a ...
61-329 5.66e-73

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: 226.67  E-value: 5.66e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPS------REIM 134
Cdd:cd01541   1 TIGVITTYIDDYIFPSIIQGIESVLSENGYSLLLALTNNDVEKEREILESLLDQNVDGLIIEPTKSALPNpnldlyEELQ 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 135 QRypTVPTVMMDWAPFDGDSDLIQDNSLLGGDLATQYLIDKGHTRIACITgPLDKTPARLRLEGYRAAMKRAGLNIPDGY 214
Cdd:cd01541  81 KK--GIPVVFINSYYPELDAPSVSLDDEKGGYLATKHLIDLGHRRIAGIF-KSDDLQGVERYQGFIKALREAGLPIDDDR 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 215 EV---TGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQ 291
Cdd:cd01541 158 ILwysTEDLEDRFFAEELREFLRRLSRCTAIVCYNDEIALRLIQALREAGLRVPEDLSVVGFDDSYLASLSEPPLTSVVH 237
                       250       260       270
                ....*....|....*....|....*....|....*...
gi 16131621 292 PKDELGELAIDVLIHRITQPTLQQQRLqLTPILMERGS 329
Cdd:cd01541 238 PKEELGRKAAELLLRMIEEGRKPESVI-FPPELIERES 274
PBP1_LacI cd01574
ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of ...
61-329 2.10e-71

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: 222.46  E-value: 2.10e-71
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNT-EGDEQRMNRNLETLMQKRVDGLLLLctETHQPSREIMQRYP- 138
Cdd:cd01574   1 TIGVIATGLSLYGPASTLAGIERAARERGYSVSIATVdEDDPASVREALDRLLSQRVDGIIVI--APDEAVLEALRRLPp 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 139 TVPTVMMDWAPFDGDSDLIQDNSLlGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDgyEVTG 218
Cdd:cd01574  79 GLPVVIVGSGPSPGVPTVSIDQEE-GARLATRHLLELGHRRIAHIAGPLDWVDARARLRGWREALEEAGLPPPP--VVEG 155
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 219 DFEFNGGFDAMRQLLSHPlRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGE 298
Cdd:cd01574 156 DWSAASGYRAGRRLLDDG-PVTAVFAANDQMALGALRALHERGLRVPEDVSVVGFDDIPEAAYFVPPLTTVRQDFAELGR 234
                       250       260       270
                ....*....|....*....|....*....|.
gi 16131621 299 LAIDVLIHRITQPTLQQQRLQLTPILMERGS 329
Cdd:cd01574 235 RAVELLLALIEGPAPPPESVLLPPELVVRES 265
PBP1_repressor_sugar_binding-like cd01537
Ligand-binding domain of the LacI-GalR family of transcription regulators and the ...
62-324 3.94e-71

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: 221.74  E-value: 3.94e-71
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  62 IGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYPTVP 141
Cdd:cd01537   2 IGVTIYSYDDNFMSVIRKAIEQDAKQPGVQLLMNDSQNDQEKQNDQIDVLLAKRVKGLAINLVDPAAAGVAEKARGQNVP 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 142 TVMMDWAPFDGD-SDLIQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDF 220
Cdd:cd01537  82 VVFFDKEPSRYDkAYYVITDSKEGGIIQGDLLAKHGHIQIVLLKGPLGHPDAEARLAGVIKELNDKGIKTEQLQLDTGDW 161
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 221 EFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGELA 300
Cdd:cd01537 162 DTASGKDKMDQWLSGPNKPTAVIANNDAMAMGAVEALKEHGLRVPSDISVFGYDALPEALKSGPLLTTILQDANNLGKTT 241
                       250       260
                ....*....|....*....|....
gi 16131621 301 IDVLIHRITQPTLQQQRLQLTPIL 324
Cdd:cd01537 242 FDLLLNLADNWKIDNKVVRVPYVL 265
PBP1_MalI-like cd06289
ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia ...
61-327 5.60e-71

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: 221.29  E-value: 5.60e-71
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLL-CTEThqpSREIMQRYPT 139
Cdd:cd06289   1 TVGLIVPDLSNPFFAELLAGIEEALEEAGYLVFLANTGEDPERQRRFLRRMLEQGVDGLILSpAAGT---TAELLRRLKA 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 140 --VPTVMMDWAPFDGDSDLIQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVT 217
Cdd:cd06289  78 wgIPVVLALRDVPGSDLDYVGIDNRLGAQLATEHLIALGHRRIAFLGGLSDSSTRRERLAGFRAALAEAGLPLDESLIVP 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 218 GDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELG 297
Cdd:cd06289 158 GPATREAGAEAARELLDAAPPPTAVVCFNDLVALGAMLALRRRGLEPGRDIAVVGFDDVPEAALWTPPLTTVSVHPREIG 237
                       250       260       270
                ....*....|....*....|....*....|
gi 16131621 298 ELAIDVLIHRITQPTLQQQRLQLTPILMER 327
Cdd:cd06289 238 RRAARLLLRRIEGPDTPPERIIIEPRLVVR 267
lacI PRK09526
lac repressor; Reviewed
2-330 6.26e-71

lac repressor; Reviewed


Pssm-ID: 181929 [Multi-domain]  Cd Length: 342  Bit Score: 223.72  E-value: 6.26e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621    2 ATMKDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSALARSLKLNQTHTIGmLITASTN---PfySELV 78
Cdd:PRK09526   6 VTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVPNRVAQQLAGKQSLTIG-LATTSLAlhaP--SQIA 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   79 RGVERSCFERGYSLVLCNTE-GDEQRMNRNLETLMQKRVDGLLL---LCTETHQPsreIMQRYPTVPTVMMDWAPfdgDS 154
Cdd:PRK09526  83 AAIKSRADQLGYSVVISMVErSGVEACQAAVNELLAQRVSGVIInvpLEDADAEK---IVADCADVPCLFLDVSP---QS 156
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  155 DL--IQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEvtGDFEFNGGFDAMRQL 232
Cdd:PRK09526 157 PVnsVSFDPEDGTRLGVEHLVELGHQRIALLAGPESSVSARLRLAGWLEYLTDYQLQPIAVRE--GDWSAMSGYQQTLQM 234
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  233 LSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGELAIDVLIHRITQPT 312
Cdd:PRK09526 235 LREGPVPSAILVANDQMALGVLRALHESGLRVPGQISVIGYDDTEDSSYFIPPLTTIKQDFRLLGKEAVDRLLALSQGQA 314
                        330
                 ....*....|....*...
gi 16131621  313 lQQQRLQLTPILMERGSA 330
Cdd:PRK09526 315 -VKGSQLLPTSLVVRKST 331
PBP1_LacI-like cd06299
ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum ...
61-329 8.70e-71

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: 221.00  E-value: 8.70e-71
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRyPTV 140
Cdd:cd06299   1 TIGLLVPDIRNPFFAELASGIEDEARAHGYSVILGNSDEDPEREDESLEMLLSQRVDGIIAVPTGENSEGLQALIA-QGL 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 141 PTVMMDWA-PFDGDSDLIQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGD 219
Cdd:cd06299  80 PVVFVDREvEGLGGVPVVTSDNRPGAREAVEYLVSLGHRRIGYISGPLSTSTGRERLAAFRAALTAAGIPIDEELVAFGD 159
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 220 FEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGEL 299
Cdd:cd06299 160 FRQDSGAAAAHRLLSRGDPPTALIAGDSLMALGAIQALRELGLRIGDDVSLISFDDVPWFELLSPPLTVIAQPVERIGRR 239
                       250       260       270
                ....*....|....*....|....*....|
gi 16131621 300 AIDVLIHRITQPTlQQQRLQLTPILMERGS 329
Cdd:cd06299 240 AVELLLALIENGG-RATSIRVPTELIPRES 268
PBP1_SalR cd01545
ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of ...
61-329 1.14e-69

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: 218.19  E-value: 1.14e-69
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVL--CNTeGDEQRMNRNLETLMQKRVDGLLL---LCTetHQPSREIMQ 135
Cdd:cd01545   1 LIGLLYDNPSASYVSALQVGALRACREAGYHLVVepCDS-DDEDLADRLRRFLSRSRPDGVILtppLSD--DPALLDALD 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 136 RYpTVPTVMMdwAPF--DGDSDLIQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDG 213
Cdd:cd01545  78 EL-GIPYVRI--APGtdDDRSPSVRIDDRAAAREMTRHLIALGHRRIGFIAGPPDHGASAERLEGFRDALAEAGLPLDPD 154
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 214 YEVTGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPK 293
Cdd:cd01545 155 LVVQGDFTFESGLEAAEALLDLPDRPTAIFASNDEMAAGVLAAAHRLGLRVPDDLSVAGFDDSPIARLVWPPLTTVRQPI 234
                       250       260       270
                ....*....|....*....|....*....|....*.
gi 16131621 294 DELGELAIDVLIHRITQPTLQQQRLQLTPILMERGS 329
Cdd:cd01545 235 AEMARRAVELLIAAIRGAPAGPERETLPHELVIRES 270
PBP1_AglR_RafR-like cd06292
Ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that ...
61-330 4.77e-69

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: 216.75  E-value: 4.77e-69
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITAS----TNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPsreimqR 136
Cdd:cd06292   1 LIGYVVPELpggfSDPFFDEFLAALGHAAAARGYDVLLFTASGDEDEIDYYRDLVRSRRVDGFVLASTRHDDP------R 74
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 137 YP-----TVPTVMMDWAPFDGDSDLIQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIP 211
Cdd:cd06292  75 VRylheaGVPFVAFGRANPDLDFPWVDVDGAAGMRQAVRHLIALGHRRIGLIGGPEGSVPSDDRLAGYRAALEEAGLPFD 154
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 212 DGYEVTGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQ 291
Cdd:cd06292 155 PGLVVEGENTEEGGYAAAARLLDLGPPPTAIVCVSDLLALGAMRAARERGLRVGRDVSVVGFDDSPLAAFTHPPLTTVRQ 234
                       250       260       270       280
                ....*....|....*....|....*....|....*....|
gi 16131621 292 PKDELGELAIDVLIHRI-TQPTLQQQRLqLTPILMERGSA 330
Cdd:cd06292 235 PIDEIGRAVVDLLLAAIeGNPSEPREIL-LQPELVVRESS 273
PRK11041 PRK11041
DNA-binding transcriptional regulator CytR; Provisional
28-330 9.84e-68

DNA-binding transcriptional regulator CytR; Provisional


Pssm-ID: 182923 [Multi-domain]  Cd Length: 309  Bit Score: 214.48  E-value: 9.84e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   28 VSEAITAKVEAAIKELNYAPSALARSLKLNQTHTIGMLITASTNPFYSELVRGVERSCFERGYsLVLCnteGDEQRMNRN 107
Cdd:PRK11041   4 VSQATRQRVEQAVLEVGYSPQSLGRNLKRNESRTILVIVPDICDPFFSEIIRGIEVTAAEHGY-LVLI---GDCAHQNQQ 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  108 LET----LMQKRVDGLLLLctETHQP---SREIMQRYPtvPTVMM-DWAPfdgDSDL--IQDNSLLGGDLATQYLIDKGH 177
Cdd:PRK11041  80 EKTfvnlIITKQIDGMLLL--GSRLPfdaSKEEQRNLP--PMVMAnEFAP---ELELptVHIDNLTAAFEAVNYLHELGH 152
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  178 TRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGvyqAL 257
Cdd:PRK11041 153 KRIACIAGPEEMPLCHYRLQGYVQALRRCGITVDPQYIARGDFTFEAGAKALKQLLDLPQPPTAVFCHSDVMALG---AL 229
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  258 YQAE---LQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGELAIDVLIHRitqptLQQQRLQLTPILME-----RGS 329
Cdd:PRK11041 230 SQAKrmgLRVPQDLSIIGFDDIDLAQYCDPPLTTVAQPRYEIGREAMLLLLEQ-----LQGHHVSSGSRLLDceliiRGS 304

                 .
gi 16131621  330 A 330
Cdd:PRK11041 305 T 305
PBP1_LacI-like cd06278
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
61-329 8.44e-65

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: 205.46  E-value: 8.44e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQrMNRNLETLMQKRVDGLLLLcteTHQPSREIMQRYPT- 139
Cdd:cd06278   1 LVGVVVGDLSNPFYAELLEELSRALQARGLRPLLFNVDDEDD-VDDALRQLLQYRVDGVIVT---SATLSSELAEECARr 76
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 140 -VPTVMMDWAPFDGDSDLIQ-DNSLlGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDgyEVT 217
Cdd:cd06278  77 gIPVVLFNRVVEDPGVDSVScDNRA-GGRLAADLLLAAGHRRIAFLGGPEGTSTSRERERGFRAALAELGLPPPA--VEA 153
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 218 GDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQAL-YQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDEL 296
Cdd:cd06278 154 GDYSYEGGYEAARRLLAAPDRPDAIFCANDLMALGALDAArQEGGLVVPEDISVVGFDDIPMAAWPSYDLTTVRQPIEEM 233
                       250       260       270
                ....*....|....*....|....*....|...
gi 16131621 297 GELAIDVLIHRITQPTLQQQRLQLTPILMERGS 329
Cdd:cd06278 234 AEAAVDLLLERIENPETPPERRVLPGELVERGS 266
PBP1_LacI-like cd06273
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
61-329 9.12e-65

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: 205.44  E-value: 9.12e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYPtV 140
Cdd:cd06273   1 TIGAIVPTLDNAIFARAIQALQQTLAEAGYTLLLATSEYDPARELEQVRALIERGVDGLILVGSDHDPELFELLEQRQ-V 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 141 PTVMMdWApFDGDSDLIQ---DNSLlGGDLATQYLIDKGHTRIACITGPLDKTP-ARLRLEGYRAAMKRAGLNIPDGYEV 216
Cdd:cd06273  80 PYVLT-WS-YDEDSPHPSigfDNRA-AAARAAQHLLDLGHRRIAVISGPTAGNDrARARLAGIRDALAERGLELPEERVV 156
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 217 TGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDEL 296
Cdd:cd06273 157 EAPYSIEEGREALRRLLARPPRPTAIICGNDVLALGALAECRRLGISVPEDLSITGFDDLELAAHLSPPLTTVRVPAREI 236
                       250       260       270
                ....*....|....*....|....*....|....
gi 16131621 297 GELAIDVLIHRI-TQPTLQQQRLQLTpiLMERGS 329
Cdd:cd06273 237 GELAARYLLALLeGGPPPKSVELETE--LIVRES 268
PBP1_LacI-like cd06281
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
61-329 1.62e-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: 380504 [Multi-domain]  Cd Length: 270  Bit Score: 204.78  E-value: 1.62e-64
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLL-LCTETHQPSREIMQRYPt 139
Cdd:cd06281   1 TVGCLVSDISNPLYARIVKAAEARLRAAGYTLLLASTGNDEERELELLSLFQRRRVDGLILtPGDEDDPELAAALARLD- 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 140 VPTVMMDWAPfDGDSDLIQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGD 219
Cdd:cd06281  80 IPVVLIDRDL-PGDIDSVLVDHRSGVRQATEYLLSLGHRRIALLTGGPDIRPGRERIAGFKAAFAAAGLPPDPDLVRLGS 158
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 220 FEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGEL 299
Cdd:cd06281 159 FSADSGFREAMALLRQPRPPTAIIALGTQLLAGVLRAVRAAGLRIPGDLSVVSIGDSDLAELHDPPITAIRWDLDAVGRA 238
                       250       260       270
                ....*....|....*....|....*....|.
gi 16131621 300 AIDVLIHRITQPTLQQ-QRLQLTPILMERGS 329
Cdd:cd06281 239 AAELLLDRIEGPPAGPpRRIVVPTELILRDS 269
PBP1_GalR cd01544
ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory ...
61-329 1.18e-63

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: 202.75  E-value: 1.18e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITAS-----TNPFYSELVRGVERSCFERGYSLVLCNTEGDEQrmnrnleTLMQKRVDGLLLLCTETHQPSREIMQ 135
Cdd:cd01544   1 TIGIIQWYSeeeelEDPYYLSIRLGIEKEAKKLGYEIKTIFRDDEDL-------ESLLEKVDGIIAIGKFSKEEIEKLKK 73
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 136 RYPTVptVMMDWAPFDGDSDLIQDNSLLGGDLATQYLIDKGHTRIACITG----PLDKTPAR-LRLEGYRAAMKRAGLNI 210
Cdd:cd01544  74 LNPNI--VFVDSNPDPDGFDSVVPDFEQAVRQALDYLIELGHRRIGFIGGkeytSDDGEEIEdPRLRAFREYMKEKGLYN 151
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 211 PDgYEVTGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIH 290
Cdd:cd01544 152 EE-YIYIGEFSVESGYEAMKELLKEGDLPTAFFVASDPMAIGALRALQEAGIKVPEDISIISFNDIEVAKYVTPPLTTVH 230
                       250       260       270
                ....*....|....*....|....*....|....*....
gi 16131621 291 QPKDELGELAIDVLIHRITQPTLQQQRLQLTPILMERGS 329
Cdd:cd01544 231 IPTEEMGRTAVRLLLERINGGRTIPKKVLLPTKLIERES 269
PBP1_CatR-like cd06296
ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in ...
61-329 7.61e-63

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: 200.58  E-value: 7.61e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLcNTEGDEQRMNRN-LETLMQKRVDGLLLLCTETHQPSREIMQRyPT 139
Cdd:cd06296   1 LIDLVLPQLDSPYALEVLRGVERAAAAAGLDLVV-TATRAGRAPVDDwVRRAVARGSAGVVLVTSDPTSRQLRLLRS-AG 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 140 VPTVMMDwAPFDGDSDL--IQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVT 217
Cdd:cd06296  79 IPFVLID-PVGEPDPDLpsVGATNWAGGRLATEHLLDLGHRRIAVITGPPRSVSGRARLAGYRAALAEAGIAVDPDLVRE 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 218 GDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELG 297
Cdd:cd06296 158 GDFTYEAGYRAARELLELPDPPTAVFAGNDEQALGVYRAARALGLRVPDDLSVIGFDDTPPARWTSPPLTTVHQPLREMG 237
                       250       260       270
                ....*....|....*....|....*....|..
gi 16131621 298 ELAIDVLIHRITQPTLQQQRLQLTPILMERGS 329
Cdd:cd06296 238 AVAVRLLLRLLEGGPPDARRIELATELVVRGS 269
PBP1_LacI-like cd06282
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
61-329 1.72e-57

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: 186.72  E-value: 1.72e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLL-LCTETHQPSREIMQRYpT 139
Cdd:cd06282   1 TIGVLIPSLNNPVFAEAAQGIQRAARAAGYSLLIATTDYDPARELDAVETLLEQRVDGLILtVGDAQGSEALELLEEE-G 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 140 VPTVMM-DWAPFDGDSDLIQDNSLLGGDLAtQYLIDKGHTRIACITGPLDKTP-ARLRLEGYRAAMKRAGLNIPDGYEVt 217
Cdd:cd06282  80 VPYVLLfNQTENSSHPFVSVDNRLASYDVA-EYLIALGHRRIAMVAGDFSASDrARLRYQGYRDALKEAGLKPIPIVEV- 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 218 gDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELG 297
Cdd:cd06282 158 -DFPTNGLEEALTSLLSGPNPPTALFCSNDLLALSVISALRRLGIRVPDDVSVIGFDGIAIGELLTPTLATVVQPSRDMG 236
                       250       260       270
                ....*....|....*....|....*....|...
gi 16131621 298 ELAIDVLIHRI-TQPTLQQQRLQLTpiLMERGS 329
Cdd:cd06282 237 RAAADLLLAEIeGESPPTSIRLPHH--LREGGS 267
PBP1_MalR-like cd06294
ligand-binding domain of maltose transcription regulator MalR which is a member of the ...
61-317 8.93e-57

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: 185.09  E-value: 8.93e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITAST-----NPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNrNLETLMQ-KRVDGLLLLCTETHQPSREIM 134
Cdd:cd06294   1 TIGLVLPSSAeelfqNPFFSEVLRGISQVANENGYSLLLATGNTEEELLE-EVKRMVRgRRVDGFILLYSKEDDPLIEYL 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 135 QRYPtVPTVMMDWAPFDGDSDLIQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGY 214
Cdd:cd06294  80 KEEG-FPFVVIGKPLDDNDVLYVDNDNVQAGYEATEYLIDKGHKRIAFIGGDKNLVVSIDRLQGYKQALKEAGLPLDDDY 158
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 215 EVTGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKD 294
Cdd:cd06294 159 ILLLDFSEEDGYDALQELLSKPPPPTAIVATDDLLALGVLRYLQELGLRVPEDVSIISFNNSPLAELASPPLTSVDINPY 238
                       250       260
                ....*....|....*....|...
gi 16131621 295 ELGELAIDVLIHRITQPTLQQQR 317
Cdd:cd06294 239 ELGREAAKLLINLLEGPESLPKN 261
PBP1_CelR cd06295
ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly ...
57-305 6.48e-56

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: 182.84  E-value: 6.48e-56
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  57 NQTHTIGMLI-------TASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRmnrNLETLMQKRVDGLLLL-CTETHQ 128
Cdd:cd06295   1 QRSRTIAVVVpmdphgdQSITDPFFLELLGGISEALTDRGYDMLLSTQDEDANQ---LARLLDSGRADGLIVLgQGLDHD 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 129 PSREIMQRypTVPTVMmdWAPFDGDSDLI---QDNsLLGGDLATQYLIDKGHTRIACITGPLDKTPArLRLEGYRAAMKR 205
Cdd:cd06295  78 ALRELAQQ--GLPMVV--WGAPEDGQSYCsvgSDN-VKGGALATEHLIEIGRRRIAFLGDPPHPEVA-DRLQGYRDALAE 151
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 206 AGLNIPDGYEVTGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPP 285
Cdd:cd06295 152 AGLEADPSLLLSCDFTEESGYAAMRALLDSGTAFDAIFAASDLIAMGAIRALRERGISVPGDVAVVGYDDIPLAAYFRPP 231
                       250       260
                ....*....|....*....|
gi 16131621 286 LTTIHQPKDELGELAIDVLI 305
Cdd:cd06295 232 LTTVRQDLALAGRLLVEKLL 251
PBP1_GntR cd01575
ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of ...
61-329 1.39e-55

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: 181.92  E-value: 1.39e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRyPTV 140
Cdd:cd01575   1 LVAVVVPSLSNSVFAETLQGLSDVLEPAGYQLLLGNTGYSPEREEELIRALLSRRPAGLILTGTEHTPATRKLLRA-AGI 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 141 PTV-MMDWA--PFDgdsdlIQ---DNSLLGGDLAtQYLIDKGHTRIACITGPLDKTP-ARLRLEGYRAAMKRAGLNIPDG 213
Cdd:cd01575  80 PVVeTWDLPddPID-----MAvgfSNFAAGRAMA-RHLIERGYRRIAFVGARLDGDSrARQRLEGFRDALAEAGLPLPLV 153
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 214 YEVTGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPK 293
Cdd:cd01575 154 LLVELPSSFALGREALAELLARHPDLDAIFCSNDDLALGALFECQRRGIRVPGDIAIAGFGDLDIAAALPPALTTVRVPR 233
                       250       260       270
                ....*....|....*....|....*....|....*.
gi 16131621 294 DELGELAIDVLIHRITQPTLQQQRLQLTPILMERGS 329
Cdd:cd01575 234 YEIGRKAAELLLARLEGEEPEPRVVDLGFELVRRES 269
PBP1_LacI-like cd19974
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
61-329 1.04e-53

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: 176.97  E-value: 1.04e-53
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLIT---ASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCtETHQPSREIMQRY 137
Cdd:cd19974   1 NIAVLIPerfFGDNSFYGKIYQGIEKELSELGYNLVLEIISDEDEEELNLPSIISEEKVDGIIILG-EISKEYLEKLKEL 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 138 PtVPTVMMDWAPFDGDSDLIQDNSLLGGDLATQYLIDKGHTRIACItGPLDKTPA-RLRLEGYRAAMKRAGLNIPDGYEV 216
Cdd:cd19974  80 G-IPVVLVDHYDEELNADSVLSDNYYGAYKLTSYLIEKGHKKIGFV-GDINYTSSfMDRYLGYRKALLEAGLPPEKEEWL 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 217 TGDFEFNGGfdaMRQLLSHPL---RPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPK 293
Cdd:cd19974 158 LEDRDDGYG---LTEEIELPLklmLPTAFVCANDSIAIQLIKALKEKGYRVPEDISVVGFDNIELAELSTPPLTTVEVDK 234
                       250       260       270
                ....*....|....*....|....*....|....*.
gi 16131621 294 DELGELAIDVLIHRITQPTLQQQRLQLTPILMERGS 329
Cdd:cd19974 235 EAMGRRAVEQLLWRIENPDRPFEKILVSGKLIERDS 270
PBP1_CcpB-like cd06286
ligand-binding domain of a novel transcription factor implicated in catabolite repression in ...
61-327 1.38e-53

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: 176.58  E-value: 1.38e-53
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLcteTHQPSREIMQRY--- 137
Cdd:cd06286   1 TIGVVVPYIDHPYFSQLINGIAEAAFKKGYQVLLLQTNYDKEKELRALELLKTKQIDGLIIT---SRENDWEVIEPYaky 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 138 -----------PTVPTVMMDwapfdgdsdliQDNSLLggdLATQYLIDKGHTRIACITG--PLDKTPARLRLEGYRAAMK 204
Cdd:cd06286  78 gpivlceetdsPDIPSVYID-----------RYEAYL---EALEYLKEKGHRKIGYCLGrpESSSASTQARLKAYQDVLG 143
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 205 RAGLNIPDGYEVTGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMtp 284
Cdd:cd06286 144 EHGLSLREEWIFTNCHTIEDGYKLAKKLLALKERPDAIFTNSDEVAAGIIAEAQKNGIRVPEDLAVIGFDNQPISELL-- 221
                       250       260       270       280
                ....*....|....*....|....*....|....*....|...
gi 16131621 285 PLTTIHQPKDELGELAIDVLIHRITQPTLQQQrlQLTPILMER 327
Cdd:cd06286 222 NLTTIDQPLEEMGKEAFELLLSQLESKEPTKK--ELPSKLIER 262
PBP1_TreR-like cd01542
ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a ...
61-318 2.77e-52

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: 173.06  E-value: 2.77e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYPtV 140
Cdd:cd01542   1 LIGVIVPRLDSYSTSRVLEGIDEVLKENGYQPLIANTNLDEEREIEYLETLARQKVDGIILFATEITDEHRKALKKLK-I 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 141 PTVMM--DwapFDGDSDLIQDNSLLGGDLaTQYLIDKGHTRIACITGPL-DKTPARLRLEGYRAAMKRAGlnIPDGYEVT 217
Cdd:cd01542  80 PVVVLgqE---HEGFSCVYHDDYGAGKLL-GEYLLKKGHKNIAYIGVDEeDIAVGVARKQGYLDALKEHG--IDEVEIVE 153
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 218 GDFEFNGGFDAMRQLLSHPlRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELG 297
Cdd:cd01542 154 TDFSMESGYEAAKELLKEN-KPDAIICATDNIALGAIKALRELGIKIPEDISVAGFGGYDLSEFVSPSLTTVKFDYEEAG 232
                       250       260
                ....*....|....*....|.
gi 16131621 298 ELAIDVLIHRITQPTLQQQRL 318
Cdd:cd01542 233 EKAAELLLDMIEGEKVPKKQK 253
PBP1_AglR-like cd20010
Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) and ...
61-319 2.49e-51

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: 170.81  E-value: 2.49e-51
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLI----TASTNPFYSELVRGVERSCFERGYSLVL--CNTEGDEqrmnrnLETLMQ----KRVDGLLLLCTETHQPS 130
Cdd:cd20010   1 AIGLVLpldpGDLGDPFFLEFLAGLSEALAERGLDLLLapAPSGEDE------LATYRRlverGRVDGFILARTRVNDPR 74
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 131 REIMQRYpTVPTVMM---------DWAPFDGDSdliqdnsllGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRA 201
Cdd:cd20010  75 IAYLLER-GIPFVVHgrsesgapyAWVDIDNEG---------AFRRATRRLLALGHRRIALLNGPEELNFAHQRRDGYRA 144
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 202 AMKRAGLNIPDGYEVTGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDI-ELAS 280
Cdd:cd20010 145 ALAEAGLPVDPALVREGPLTEEGGYQAARRLLALPPPPTAIVCGSDLLALGAYRALREAGLSPGKDVSVIGHDDLlPALE 224
                       250       260       270       280
                ....*....|....*....|....*....|....*....|.
gi 16131621 281 FMTPPLTTIHQPKDELGELAIDVLIHRI--TQPTLQQQRLQ 319
Cdd:cd20010 225 YFSPPLTTTRSSLRDAGRRLAEMLLALIdgEPAAELQELWP 265
PBP1_RegR_EndR_KdgR-like cd06283
ligand-binding domain of DNA transcription repressor RegR and other putative regulators such ...
61-327 9.62e-51

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: 169.27  E-value: 9.62e-51
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLL-LCTETHQPSREIMQRypT 139
Cdd:cd06283   1 LIGVIVADITNPFSSLLLKGIEDVCREAGYQLLICNSNNDPEKERDYIESLLSQRVDGLILqPTGNNNDAYLELAQK--G 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 140 VPTVMMDWAPFDGDSDLIQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPAR-LRLEGYRAAMKRAGLNIpDGYEVTG 218
Cdd:cd06283  79 LPVVLVDRQIEPLNWDTVVTDNYDATYEATEHLKEQGYERIVFVTEPIKGISTRrERLQGFLDALARYNIEG-DVYVIEI 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 219 DFEfNGGFDAMRQLLS-HPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELG 297
Cdd:cd06283 158 EDT-EDLQQALAAFLSqHDGGKTAIFAANGVVLLRVLRALKALGIRIPDDVGLCGFDDWDWADLIGPGITTIRQPTYEIG 236
                       250       260       270
                ....*....|....*....|....*....|
gi 16131621 298 ELAIDVLIHRITQPTLQQQRLQLTPILMER 327
Cdd:cd06283 237 KAAAEILLERIEGDSGEPKEIELPSELIIR 266
PRK10727 PRK10727
HTH-type transcriptional regulator GalR;
1-292 4.87e-50

HTH-type transcriptional regulator GalR;


Pssm-ID: 182681 [Multi-domain]  Cd Length: 343  Bit Score: 169.94  E-value: 4.87e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621    1 MATMKDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSALARSLKLNQTHTIGMLITASTNPFYSELVRG 80
Cdd:PRK10727   1 MATIKDVARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLSYHPNANARALAQQSTETVGLVVGDVSDPFFGAMVKA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   81 VERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLlctetHQ---PSREIMQRYPTVP-TVMMDWAPFDGDSDL 156
Cdd:PRK10727  81 VEQVAYHTGNFLLIGNGYHNEQKERQAIEQLIRHRCAALVV-----HAkmiPDAELASLMKQIPgMVLINRILPGFENRC 155
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  157 IQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMRQLLSHP 236
Cdd:PRK10727 156 IALDDRYGAWLATRHLIQQGHTRIGYLCSNHSISDAEDRLQGYYDALAESGIPANDRLVTFGEPDESGGEQAMTELLGRG 235
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 16131621  237 LRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQP 292
Cdd:PRK10727 236 RNFTAVACYNDSMAAGAMGVLNDNGIDVPGEISLIGFDDVLVSRYVRPRLTTVRYP 291
PBP1_LacI-like cd06277
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
61-329 4.23e-49

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: 165.49  E-value: 4.23e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTnPFYSELVRGVERSCFERGYSLVLCNTEGDEQRmNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYPtV 140
Cdd:cd06277   9 DNGDGVVNET-PFFSELIDGIEREARKYGYNLLISSVDIGDDF-DEILKELTDDQSSGIILLGTELEEKQIKLFQDVS-I 85
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 141 PTVMMDWAPFDGDSDLIQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDF 220
Cdd:cd06277  86 PVVVVDNYFEDLNFDCVVIDNEDGAYEAVKYLVELGHTRIGYLASSYRIKNFEERRRGFRKAMRELGLSEDPEPEFVVSV 165
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 221 EFNGGFDAMRQLLS-HPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGEL 299
Cdd:cd06277 166 GPEGAYKDMKALLDtGPKLPTAFFAENDIIALGCIKALQEAGIRVPEDVSVIGFDDIPVSAMVDPPLTTIHVPKEQMGKL 245
                       250       260       270
                ....*....|....*....|....*....|
gi 16131621 300 AIDVLIHRITQPTLQQQRLQLTPILMERGS 329
Cdd:cd06277 246 AVRRLIEKIKDPDGGTLKILVSTKLVERGS 275
PBP1_LacI-like cd06279
ligand-binding domain of an uncharacterized transcription regulator from Corynebacterium ...
61-329 3.93e-46

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: 157.76  E-value: 3.93e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLIT-----ASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLmqkrVDGLLLLCTETHQPSREIMQ 135
Cdd:cd06279   1 AIGVLLPddlsyAFSDPVAAQFLRGVAEVCEEEGLGLLLLPATDEGSAAAAVRNAA----VDGFIVYGLSDDDPAVAALR 76
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 136 RYPtVPTVMMDWAPFDGDSD-LIQDNSllGGDLATQYLIDKGHTRIACITGPLDKTP-----------------ARLRLE 197
Cdd:cd06279  77 RRG-LPLVVVDGPAPPGIPSvGIDDRA--AARAAARHLLDLGHRRIAILSLRLDRGRergpvsaerlaaatnsvARERLA 153
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 198 GYRAAMKRAGLNIPDGY-EVTGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDI 276
Cdd:cd06279 154 GYRDALEEAGLDLDDVPvVEAPGNTEEAGRAAARALLALDPRPTAILCMSDVLALGALRAARERGLRVPEDLSVTGFDDI 233
                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|...
gi 16131621 277 ELASFMTPPLTTIHQPKDELGELAIDVLIHRITQPTLQQQRLQLTpiLMERGS 329
Cdd:cd06279 234 PEAAAADPGLTTVRQPAVEKGRAAARLLLGLLPGAPPRPVILPTE--LVVRAS 284
PRK10014 PRK10014
DNA-binding transcriptional repressor MalI; Provisional
2-328 6.81e-45

DNA-binding transcriptional repressor MalI; Provisional


Pssm-ID: 182193 [Multi-domain]  Cd Length: 342  Bit Score: 156.41  E-value: 6.81e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621    2 ATMKDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSALARSLKLNQTHTIGMLITASTNPFYSELVRGV 81
Cdd:PRK10014   7 ITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVRNRQASALRGGQSGVIGLIVRDLSAPFYAELTAGL 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   82 ERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLL-CTETHQPSREiMQRYPTVPTVMMDWAPFDGDSDLIQDN 160
Cdd:PRK10014  87 TEALEAQGRMVFLLQGGKDGEQLAQRFSTLLNQGVDGVVIAgAAGSSDDLRE-MAEEKGIPVVFASRASYLDDVDTVRPD 165
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  161 SLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMRQLLSHPLRPQ 240
Cdd:PRK10014 166 NMQAAQLLTEHLIRNGHQRIAWLGGQSSSLTRAERVGGYCATLLKFGLPFHSEWVLECTSSQKQAAEAITALLRHNPTIS 245
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  241 AVFTGNDAMAVGVYQALYQAELQV---------PQDIAVIGYDDIELASFMTPPLTTIHQPKDELGELAIDVLIHRITQP 311
Cdd:PRK10014 246 AVVCYNETIAMGAWFGLLRAGRQSgesgvdryfEQQVALAAFTDVPEAELDDPPLTWASTPAREIGRTLADRMMQRITHE 325
                        330
                 ....*....|....*..
gi 16131621  312 TLQQQRLQLTPILMERG 328
Cdd:PRK10014 326 ETHSRNLIIPPRLIARK 342
Peripla_BP_3 pfam13377
Periplasmic binding protein-like domain; This domain is found in a variety of transcriptional ...
171-329 1.92e-42

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: 144.40  E-value: 1.92e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   171 YLIDKGHTRIACIT--GPLDKTPARLRLEGYRAAMKRAGLnIPDGYEVTGDFEFNGGFDAMRqLLSHPLRPQAVFTGNDA 248
Cdd:pfam13377   1 HLAELGHRRIALIGpeGDRDDPYSDLRERGFREAARELGL-DVEPTLYAGDDEAEAAAARER-LRWLGALPTAVFVANDE 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   249 MAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGELAIDVLIHRITQPTLQQQRLQLTPILMERG 328
Cdd:pfam13377  79 VALGVLQALREAGLRVPEDLSVIGFDDSPLAALVSPPLTTVRVDAEELGRAAAELLLDLLNGEPAPPERVLLPPELVERE 158

                  .
gi 16131621   329 S 329
Cdd:pfam13377 159 S 159
PRK10401 PRK10401
HTH-type transcriptional regulator GalS;
1-300 2.92e-40

HTH-type transcriptional regulator GalS;


Pssm-ID: 236681 [Multi-domain]  Cd Length: 346  Bit Score: 144.15  E-value: 2.92e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621    1 MATMKDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSALARSLKLNQTHTIGMLITASTNPFYSELVRG 80
Cdd:PRK10401   1 MITIRDVARQAGVSVATVSRVLNNSALVSADTREAVMKAVSELGYRPNANAQALATQVSDTIGVVVMDVSDAFFGALVKA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   81 VERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLL----LCTEthqpsrEIMQRYPTVP-TVMMDWAPFDGDSD 155
Cdd:PRK10401  81 VDLVAQQHQKYVLIGNSYHEAEKERHAIEVLIRQRCNALIVhskaLSDD------ELAQFMDQIPgMVLINRVVPGYAHR 154
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  156 LIQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMRQLLSH 235
Cdd:PRK10401 155 CVCLDNVSGARMATRMLLNNGHQRIGYLSSSHGIEDDAMRRAGWMSALKEQGIIPPESWIGTGTPDMQGGEAAMVELLGR 234
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16131621  236 PLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGELA 300
Cdd:PRK10401 235 NLQLTAVFAYNDNMAAGALTALKDNGIAIPLHLSIIGFDDIPIARYTDPQLTTVRYPIASMAKLA 299
PBP1_CcpA cd06298
ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major ...
61-304 1.37e-38

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: 137.81  E-value: 1.37e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYPT- 139
Cdd:cd06298   1 TVGVIIPDISNLYYAELARGIDDIATMYKYNIILSNSDNNVDKELDLLNTMLSKQVDGIIFMGDELTEEIREEFKRSPVp 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 140 ------------VPTVMMDW--APFDgdsdliqdnsllggdlATQYLIDKGHTRIACITGPLDKTPAR-LRLEGYRAAMK 204
Cdd:cd06298  81 vvlagtvdsdheIPSVNIDYeqAAYD----------------ATKSLIDKGHKKIAFVSGPLKEYINNdKKLQGYKRALE 144
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 205 RAGLNIPDGYEVTGDFEFNGGFDAMRQLLSHPLrPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTP 284
Cdd:cd06298 145 EAGLEFNEPLIFEGDYDYDSGYELYEELLESGE-PDAAIVVRDEIAVGLLNAAQDRGLKVPEDLEIIGFDNTRYATMSRP 223
                       250       260
                ....*....|....*....|
gi 16131621 285 PLTTIHQPKDELGELAIDVL 304
Cdd:cd06298 224 QLTSINQPLYDIGAVAMRLL 243
PBP1_CcpA_TTHA0807 cd06297
ligand-binding domain of TTHA0807, a CcpA regulator, from Thermus thermophilus HB8 and its ...
61-329 1.39e-36

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: 132.59  E-value: 1.39e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEgDEQRMNRNLE-TLMQKRVDGLLLLC---TETHQPSREIMQR 136
Cdd:cd06297   1 TISLLVPEVMTPFYMRLLTGVERALDENRYDLAIFPLL-SEYRLEKYLRnSTLAYQCDGLVMASldlTELFEEVIVPTEK 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 137 yptvPTVMmdwapFDGDS---DLIQDNSLLGGDLATQYLIDKGHTRIACITGPLD----KTPARLRLEGYRAAMKRAGLN 209
Cdd:cd06297  80 ----PVVL-----IDANSmgyDCVYVDNVKGGFMATEYLAGLGEREYVFFGIEEDtvftETVFREREQGFLEALNKAGRP 150
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 210 IPDGYEVTGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASfmTPPLTTI 289
Cdd:cd06297 151 ISSSRMFRIDNSSKKAECLARELLKKADNPAAFFAAADLVALGLIRAAQSLGLRVGEDVAVIGFDGQPWAA--SPGLTTV 228
                       250       260       270       280
                ....*....|....*....|....*....|....*....|
gi 16131621 290 HQPKDELGELAIDVLIHRITQPTLQQQRLQLTPILMERGS 329
Cdd:cd06297 229 RQPVEEMGEAAAKLLLKRLNEYGGPPRSLKFEPELIVRES 268
HTH_LACI smart00354
helix_turn _helix lactose operon repressor;
2-71 8.20e-34

helix_turn _helix lactose operon repressor;


Pssm-ID: 197675 [Multi-domain]  Cd Length: 70  Bit Score: 118.84  E-value: 8.20e-34
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621      2 ATMKDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSALARSLKLNQTHTIGMLITASTN 71
Cdd:smart00354   1 ATIKDVARLAGVSKATVSRVLNGKGRVSEETREKVLAAMEELGYIPNRVARSLKGKKTKTIGLIVPDITN 70
Peripla_BP_1 pfam00532
Periplasmic binding proteins and sugar binding domain of LacI family; This family includes the ...
59-321 6.04e-33

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: 123.39  E-value: 6.04e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621    59 THTIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYP 138
Cdd:pfam00532   1 TLKLGALVPQLDEPFFQDLVKGITKAAKDHGFDVFLLAVGDGEDTLTNAIDLLLASGADGIIITTPAPSGDDITAKAEGY 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   139 TVPTVMMDWApFDGDSDL---IQDNSLLgGDLATQYLIDKGHTR-IACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGY 214
Cdd:pfam00532  81 GIPVIAADDA-FDNPDGVpcvMPDDTQA-GYESTQYLIAEGHKRpIAVMAGPASALTARERVQGFMAALAAAGREVKIYH 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   215 EVTGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALY-QAELQVPQDI-----AVIGYDDIELAS---FMTPP 285
Cdd:pfam00532 159 VATGDNDIPDAALAANAMLVSHPTIDAIVAMNDEAAMGAVRALLkQGRVKIPDIVgiginSVVGFDGLSKAQdtgLYLSP 238
                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 16131621   286 LTTIHQPKDELGELAIDVLIHRITQPTLQQQRLQLT 321
Cdd:pfam00532 239 LTVIQLPRQLLGIKASDMVYQWIPKFREHPRVLLIP 274
PBP1_AglR_RafR-like cd06271
ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and ...
71-308 1.27e-32

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: 121.76  E-value: 1.27e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  71 NPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMN-RNLetLMQKRVDGLLLLCTETHQPSREIMQRyPTVPTVMMD--- 146
Cdd:cd06271  14 NGTVSE*VSGITEEAGTTGYHLLVWPFEEAES*VPiRDL--VETGSADGVILSEIEPNDPRVQFLTK-QNFPFVAHGrsd 90
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 147 ------WAPFDGDSdliqdnsllGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLnipDGYEVTGDF 220
Cdd:cd06271  91 *pighaWVDIDNEA---------GAYEAVERLAGLGHRRIAFIVPPARYSPHDRRLQGYVRA*RDAGL---TGYPLDADT 158
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 221 EFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFM-TPPLTTIHQPKDELGEL 299
Cdd:cd06271 159 TLEAGRAAAQRLLALSPRPTAIVTMNDSATIGLVAGLQAAGLKIGEDVSIIGKDSAPFLGAMiTPPLTTVHAPIAEAGRE 238

                ....*....
gi 16131621 300 AIDVLIHRI 308
Cdd:cd06271 239 LAKALLARI 247
PRK14987 PRK14987
HTH-type transcriptional regulator GntR;
4-329 2.11e-32

HTH-type transcriptional regulator GntR;


Pssm-ID: 184949 [Multi-domain]  Cd Length: 331  Bit Score: 122.83  E-value: 2.11e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621    4 MKDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSALARSLKLNQTHTIGMLITASTNPFYSELVRGVER 83
Cdd:PRK14987   8 LQDVADRVGVTKMTVSRFLRNPEQVSVALRGKIAAALDELGYIPNRAPDILSNATSRAIGVLLPSLTNQVFAEVLRGIES 87
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   84 SCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGlLLLCTETHQPSREIMQRYPTVPTV-MMDWAPFDGDSDLIQDNsL 162
Cdd:PRK14987  88 VTDAHGYQTMLAHYGYKPEMEQERLESMLSWNIDG-LILTERTHTPRTLKMIEVAGIPVVeLMDSQSPCLDIAVGFDN-F 165
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  163 LGGDLATQYLIDKGHTRIACITGPLDKTPArLRLEGYRAAMKRAGLnIPDGYEVTGDFEFNGGFDAMRQLLSHPLRPQAV 242
Cdd:PRK14987 166 EAARQMTTAIIARGHRHIAYLGARLDERTI-IKQKGYEQAMLDAGL-VPYSVMVEQSSSYSSGIELIRQARREYPQLDGV 243
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  243 FTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGELAIDVLIHRITQPTLQQQRLQLTP 322
Cdd:PRK14987 244 FCTNDDLAVGAAFECQRLGLKVPDDMAIAGFHGHDIGQVMEPRLASVLTPRERMGSIGAERLLARIRGESVTPKMLDLGF 323

                 ....*..
gi 16131621  323 ILMERGS 329
Cdd:PRK14987 324 TLSPGGS 330
PRK10339 PRK10339
DNA-binding transcriptional repressor EbgR; Provisional
1-308 8.34e-31

DNA-binding transcriptional repressor EbgR; Provisional


Pssm-ID: 182389 [Multi-domain]  Cd Length: 327  Bit Score: 118.71  E-value: 8.34e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621    1 MATMKDVARLAGVSTSTVSHVINKDRFVS--EAITAKVEAAIKELNYAPSALAR-SLKLNQTHTIGMLIT----ASTN-P 72
Cdd:PRK10339   1 MATLKDIAIEAGVSLATVSRVLNDDPTLNvkEETKHRILEIAEKLEYKTSSARKlQTGAVNQHHILAIYSyqqeLEINdP 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   73 FYSELVRGVERSCFERGYSLVLC-NTEGDEQrmnrnletlmQKRVDGLLLLCTETHQPSREIMQRypTVPTVMMDWAPFD 151
Cdd:PRK10339  81 YYLAIRHGIETQCEKLGIELTNCyEHSGLPD----------IKNVTGILIVGKPTPALRAAASAL--TDNICFIDFHEPG 148
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  152 GDSDLIQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGL-NIPDGYEvtGDFEFNGGFDAMR 230
Cdd:PRK10339 149 SGYDAVDIDLARISKEIIDFYINQGVNRIGFIGGEDEPGKADIREVAFAEYGRLKQVvREEDIWR--GGFSSSSGYELAK 226
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16131621  231 QLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGELAIDVLIHRI 308
Cdd:PRK10339 227 QMLAREDYPKALFVASDSIAIGVLRAIHERGLNIPQDISLISVNDIPTARFTFPPLSTVRIHSEMMGSQGVNLLYEKA 304
RbsB COG1879
ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH ...
31-308 3.73e-30

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: 116.18  E-value: 3.73e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  31 AITAKVEAAIKELNYAPSALARSLKLNQTHTIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLET 110
Cdd:COG1879   5 LLAAVLALALALAACGSAAAEAAAAAAKGKTIGFVVKTLGNPFFVAVRKGAEAAAKELGVELIVVDAEGDAAKQISQIED 84
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 111 LMQKRVDGLLLLCTEtHQPSREIMQRY-----PTVpTVMMDWAPFDGDSDLIQDNsLLGGDLATQYLID--KGHTRIACI 183
Cdd:COG1879  85 LIAQGVDAIIVSPVD-PDALAPALKKAkaagiPVV-TVDSDVDGSDRVAYVGSDN-YAAGRLAAEYLAKalGGKGKVAIL 161
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 184 TGPLDKTPARLRLEGYRAAMKRA-GLNIPDgyEVTGDFEFNGGFDAMRQLL-SHPlRPQAVFTGNDAMAVGVYQALYQAE 261
Cdd:COG1879 162 TGSPGAPAANERTDGFKEALKEYpGIKVVA--EQYADWDREKALEVMEDLLqAHP-DIDGIFAANDGMALGAAQALKAAG 238
                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|
gi 16131621 262 LQvpQDIAVIGYDDIE--LASFMTPPLT-TIHQPKDELGELAIDVLIHRI 308
Cdd:COG1879 239 RK--GDVKVVGFDGSPeaLQAIKDGTIDaTVAQDPYLQGYLAVDAALKLL 286
PBP1_ABC_sugar_binding-like cd01536
periplasmic sugar-binding domain of active transport systems that are members of the type 1 ...
61-309 7.75e-29

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: 111.89  E-value: 7.75e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTEThQPSREIMQRYPT- 139
Cdd:cd01536   1 KIGVVVKDLTNPFWVAVKKGAEAAAKELGVELVVLDAQGDVAKQISQIEDLIAQGVDAIIIAPVDS-EALVPAVKKANAa 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 140 -VPTVMMDwAPFDGDSDLI----QDNSlLGGDLATQYLIDK--GHTRIACITGPLDKTPARLRLEGYRAAMKRAGlNIPD 212
Cdd:cd01536  80 gIPVVAVD-TDIDGGGDVVafvgTDNY-EAGKLAGEYLAEAlgGKGKVAILEGPPGSSTAIDRTKGFKEALKKYP-DIEI 156
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 213 GYEVTGDFEFNGGFDAMRQLL-SHPlRPQAVFTGNDAMAVGVYQALYQAELQvpQDIAVIGYDDIE--LASFMTPPLT-T 288
Cdd:cd01536 157 VAEQPANWDRAKALTVTENLLqANP-DIDAVFAANDDMALGAAEALKAAGRT--GDIKIVGVDGTPeaLKAIKDGELDaT 233
                       250       260
                ....*....|....*....|.
gi 16131621 289 IHQPKDELGELAIDVLIHRIT 309
Cdd:cd01536 234 VAQDPYLQGYLAVEAAVKLLN 254
PRK11303 PRK11303
catabolite repressor/activator;
4-315 1.27e-27

catabolite repressor/activator;


Pssm-ID: 236897 [Multi-domain]  Cd Length: 328  Bit Score: 109.97  E-value: 1.27e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621    4 MK--DVARLAGVSTSTVSHVIN---KDRFVSEAITAKVEAAIKELNYAPSALARSLKLNQTHTIGMLITASTNPFYSELV 78
Cdd:PRK11303   1 MKldEIARLAGVSRTTASYVINgkaKQYRVSDKTVEKVMAVVREHNYHPNAVAAGLRAGRTRSIGLIIPDLENTSYARIA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   79 RGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLlcTETHQPSREIMQRYPT--VPTVMMDWAPfdgDSDL 156
Cdd:PRK11303  81 KYLERQARQRGYQLLIACSDDQPDNEMRCAEHLLQRQVDALIV--STSLPPEHPFYQRLQNdgLPIIALDRAL---DREH 155
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  157 IqdNSLLGGDLA-----TQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYevTGDFEFNGGFDAMRQ 231
Cdd:PRK11303 156 F--TSVVSDDQDdaemlAESLLKFPAESILLLGALPELSVSFEREQGFRQALKDDPREVHYLY--ANSFEREAGAQLFEK 231
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  232 LLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGELAIDVLIHRITQP 311
Cdd:PRK11303 232 WLETHPMPDALFTTSYTLLQGVLDVLLERPGELPSDLAIATFGDNELLDFLPCPVNAVAQQHRLIAERALELALAALDEP 311

                 ....
gi 16131621  312 TLQQ 315
Cdd:PRK11303 312 RKPK 315
PBP1_FruR cd06274
ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its ...
61-318 7.59e-27

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: 106.52  E-value: 7.59e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLL-CTETHQPSREIMQRypT 139
Cdd:cd06274   1 TIGLIVPDLANRFFARLAEALERLARERGLQLLIACSDDDPEQERRLVENLIARQVDGLIVApSTPPDDIYYLCQAA--G 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 140 VPTVMMDwAPFDGDSD--LIQDNSLLGGDLaTQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVT 217
Cdd:cd06274  79 LPVVFLD-RPFSGSDApsVVSDNRAGARAL-TEKLLAAGPGEIYFLGGRPELPSTAERIRGFRAALAEAGITEGDDWILA 156
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 218 GDFEFNGGFDAMRQLLSHPLR-PQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDEL 296
Cdd:cd06274 157 EGYDRESGYQLMAELLARLGGlPQALFTSSLTLLEGVLRFLRERLGAIPSDLVLGTFDDHPLLDFLPNPVDSVRQDHDEI 236
                       250       260
                ....*....|....*....|..
gi 16131621 297 GELAIDVLIHRITQPTLQQQRL 318
Cdd:cd06274 237 AEHAFELLDALIEGQPEPGVII 258
PBP1_RafR-like cd20009
Ligand-binding domain of DNA transcription repressor specific for raffinose (RafR) and similar ...
167-319 3.12e-26

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: 104.93  E-value: 3.12e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 167 LATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMRQLLSHPLRPQAVFTGN 246
Cdd:cd20009 108 EAVRRLAARGRRRIALVAPPRELTYAQHRLRGFRRALAEAGLEVEPLLIVTLDSSAEAIRAAARRLLRQPPRPDGIICAS 187
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16131621 247 DAMAVGVYQALYQAELQVPQDIAVIGYDDIELASFMTPPLTTIHQPKDELGELAIDVLIHRITQPTLQQ-QRLQ 319
Cdd:cd20009 188 EIAALGALAGLEDAGLVVGRDVDVVAKETSPILDYFRPPIDTLYEDIEEAGRFLAEALLRRIEGEPAEPlQTLE 261
PBP1_hexuronate_repressor-like cd06272
ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon ...
115-327 3.64e-26

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: 104.76  E-value: 3.64e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 115 RVDGLLLlcTETHQPSREIMQR-YPTVPTVMMDwAPFDGDSDLIQDNSLLGgDLATQYLIDKGHTRIACITGPLDKTPAR 193
Cdd:cd06272  56 RFDGVIV--FGISDSDIEYLNKnKPKIPIVLYN-RESPKYSTVNVDNEKAG-RLAVLLLIQKGHKSIAYIGNPNSNRNQT 131
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 194 LRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGY 273
Cdd:cd06272 132 LRGKGFIETCEKHGIHLSDSIIDSRGLSIEGGDNAAKKLLKKKTLPKAIFCNSDDIALGVLRVLKENGISIPEDISIVSY 211
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....
gi 16131621 274 DDIELASFMTPPLTTIHQPKDELGELAIDVLIHRITQPTLQQQRLQLTPILMER 327
Cdd:cd06272 212 DNIPQEARSDPPLTVVGVPIEKIAEESLRLILKLIEGRENEIQQLILYPELIFR 265
PBP1_ABC_sugar_binding-like cd06319
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
61-305 4.36e-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: 99.36  E-value: 4.36e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTethqpSREIMqryPTV 140
Cdd:cd06319   1 KIGYSVYDLDNPFWQIMERGVQAAAEELGYEFVTYDQKNSANEQVTNANDLIAQGVDGIIISPT-----NSSAA---PTV 72
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 141 ---------PTVMMDWAPFDGDSD--LIQDNsLLGGDLATQYLIDK------GHTRIACITGPLDKTPARLRLEGYRAAM 203
Cdd:cd06319  73 ldlaneakiPVVIADIGTGGGDYVsyIISDN-YDGGYQAGEYLAEAlkengwGGGSVGIIAIPQSRVNGQARTAGFEDAL 151
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 204 KRAGLNIPdGYEVTGDFEFNGGFDAMRQLL-SHP-LRpqAVFTGNDAMAVGVYQALYQAELQvpQDIAVIGYDDIELASF 281
Cdd:cd06319 152 EEAGVEEV-ALRQTPNSTVEETYSAAQDLLaANPdIK--GIFAQNDQMAQGALQAIEEAGRT--GDILVVGFDGDPEALD 226
                       250       260
                ....*....|....*....|....*..
gi 16131621 282 MTPPLT---TIHQPKDELGELAIDVLI 305
Cdd:cd06319 227 LIKDGKldgTVAQQPFGMGARAVELAI 253
PBP1_ribose_binding cd06323
periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose ...
61-316 5.49e-22

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: 93.13  E-value: 5.49e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCT--ETHQPSREIMQRyP 138
Cdd:cd06323   1 TIGLSVSTLNNPFFVSLKDGAQAEAKELGVELVVLDAQNDPAKQLSQVEDLIVRKVDALLINPTdsDAVSPAVEEANE-A 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 139 TVPTVMMDWAPFDGD--SDLIQDNsLLGGDLATQYLIDKGHTR--IACITGPLDKTPARLRLEGYRAAMKRA-GLNIPDg 213
Cdd:cd06323  80 GIPVITVDRSVTGGKvvSHIASDN-VAGGEMAAEYIAKKLGGKgkVVELQGIPGTSAARERGKGFHNAIAKYpKINVVA- 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 214 yEVTGDFEFNGGFDAMRQLL-SHPlRPQAVFTGNDAMAVGVYQALYQAElqvPQDIAVIGYDDIE--LASFMTPPLT-TI 289
Cdd:cd06323 158 -SQTADFDRTKGLNVMENLLqAHP-DIDAVFAHNDEMALGAIQALKAAG---RKDVIVVGFDGTPdaVKAVKDGKLAaTV 232
                       250       260
                ....*....|....*....|....*..
gi 16131621 290 HQPKDELGELAIDVLIHRITQPTLQQQ 316
Cdd:cd06323 233 AQQPEEMGAKAVETADKYLKGEKVPKK 259
PBP1_galactofuranose_YtfQ-like cd06309
periplasmic binding domain of ABC-type galactofuranose YtfQ-like transport systems; ...
61-276 7.99e-22

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: 93.05  E-value: 7.99e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPS---REIMQRy 137
Cdd:cd06309   1 TVGFSQAGSESPWRVANTKSIKEAAKKRGYELVYTDANQDQEKQINDIRDLIAQGVDAILISPIDATGWDpvlKEAKDA- 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 138 pTVPTVMMD----------WAPFDGdSDLIQDNSLLGGDLATQYLIDKGHtrIACITGPLDKTPARLRLEGYRAAMKRAG 207
Cdd:cd06309  80 -GIPVILVDrtidgedgslYVTFIG-SDFVEEGRRAAEWLVKNYKGGKGN--VVELQGTAGSSVAIDRSKGFREVIKKHP 155
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 208 lNIPDGYEVTGDFEFNGGFDAMRQLL-SHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDI 276
Cdd:cd06309 156 -NIKIVASQSGNFTREKGQKVMENLLqAGPGDIDVIYAHNDDMALGAIQALKEAGLKPGKDVLVVGIDGQ 224
Periplasmic_Binding_Protein_type1 cd01391
Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This ...
62-306 2.79e-21

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: 91.56  E-value: 2.79e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  62 IGMLITA---STNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYP 138
Cdd:cd01391   2 IGVVTSSlhqIREQFGIQRVEAIFHTADKLGASVEIRDSCWHGSVALEQSIEFIRDNIAGVIGPGSSSVAIVIQNLAQLF 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 139 TVPTVMMDWAPFDGDSDLIQDNSL-------LGGDLATQYLIDKGHTRIACITGPLDKTpARLRLEGYRAAMKRAGLnIP 211
Cdd:cd01391  82 DIPQLALDATSQDLSDKTLYKYFLsvvfsdtLGARLGLDIVKRKNWTYVAAIHGEGLNS-GELRMAGFKELAKQEGI-CI 159
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 212 DGYEVTGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALyqAELQVPQDIAVIGYDDIELA-----SFMTPPL 286
Cdd:cd01391 160 VASDKADWNAGEKGFDRALRKLREGLKARVIVCANDMTARGVLSAM--RRLGLVGDVSVIGSDGWADRdevgyEVEANGL 237
                       250       260
                ....*....|....*....|
gi 16131621 287 TTIHQPKDELGELAIDVLIH 306
Cdd:cd01391 238 TTIKQQKMGFGITAIKAMAD 257
LacI pfam00356
Bacterial regulatory proteins, lacI family;
3-48 2.58e-20

Bacterial regulatory proteins, lacI family;


Pssm-ID: 306791 [Multi-domain]  Cd Length: 46  Bit Score: 82.69  E-value: 2.58e-20
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 16131621     3 TMKDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPS 48
Cdd:pfam00356   1 TIKDVARLAGVSKSTVSRVLNNPGRVSEETRERVEAAMEELNYIPN 46
HTH_LacI cd01392
Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; ...
5-55 1.80e-19

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: 80.53  E-value: 1.80e-19
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 16131621   5 KDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSALARSLK 55
Cdd:cd01392   1 KDIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYRPNAAARSLR 51
PRK10653 PRK10653
ribose ABC transporter substrate-binding protein RbsB;
32-302 1.71e-16

ribose ABC transporter substrate-binding protein RbsB;


Pssm-ID: 182620 [Multi-domain]  Cd Length: 295  Bit Score: 78.59  E-value: 1.71e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   32 ITAKVEAAIKELNYAPSALARSlklnqthTIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETL 111
Cdd:PRK10653   6 LATLVSAVALSATVSANAMAKD-------TIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDL 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  112 MQKRVDGLLLLCTETHQPSREI-MQRYPTVPTVMMDWAPFDGD--SDLIQDNsLLGGDLATQYLIDK--GHTRIACITGP 186
Cdd:PRK10653  79 TVRGTKILLINPTDSDAVGNAVkMANQANIPVITLDRGATKGEvvSHIASDN-VAGGKMAGDFIAKKlgEGAKVIQLEGI 157
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  187 LDKTPARLRLEGYRAAMKRAGLNI----PdgyevtGDFEFNGGFDAMRQLL-SHPlRPQAVFTGNDAMAVGVYQALYQAE 261
Cdd:PRK10653 158 AGTSAARERGEGFKQAVAAHKFNVlasqP------ADFDRTKGLNVMQNLLtAHP-DVQAVFAQNDEMALGALRALQTAG 230
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 16131621  262 lqvPQDIAVIGYDDIE--LASFMTPPL-TTIHQPKDELGELAID 302
Cdd:PRK10653 231 ---KSDVMVVGFDGTPdgIKAVNRGKLaATIAQQPDQIGAIGVE 271
Peripla_BP_4 pfam13407
Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic ...
62-304 3.77e-16

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: 76.96  E-value: 3.77e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621    62 IGMLITASTNPFYSELVRGVERSCFERGY-SLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTEtHQPSREIMQRYP-- 138
Cdd:pfam13407   1 IGVVPKSTGNPFFQAAEEGAEEAAKELGGeVIVVGPAEADAAEQVAQIEDAIAQGVDAIIVAPVD-PTALAPVLKKAKda 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   139 TVPTVMMDwAPFDGDSDL--IQDNSLLGGDLATQYLID--KGHTRIACITGPLDKTPARLRLEGYRAAMKR--AGLNIPD 212
Cdd:pfam13407  80 GIPVVTFD-SDAPSSPRLayVGFDNEAAGEAAGELLAEalGGKGKVAILSGSPGDPNANERIDGFKKVLKEkyPGIKVVA 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   213 GYEVTGDfEFNGGFDAMRQLLS---HPLrpQAVFTGNDAMAVGVYQALyqAELQVPQDIAVIGYD--DIELASFMTPPLT 287
Cdd:pfam13407 159 EVEGTNW-DPEKAQQQMEALLTaypNPL--DGIISPNDGMAGGAAQAL--EAAGLAGKVVVTGFDatPEALEAIKDGTID 233
                         250
                  ....*....|....*...
gi 16131621   288 -TIHQPKDELGELAIDVL 304
Cdd:pfam13407 234 aTVLQDPYGQGYAAVELA 251
PBP1_XylR cd01543
ligand-binding domain of DNA transcription repressor specific for xylose (XylR); ...
62-326 4.09e-16

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: 76.86  E-value: 4.09e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  62 IGMLITASTNPFYsELVRGVERSCFERGY-SLVLcntegDEQRMNRNLETLMQKRVDGLLLLcTETHQPSREIMQRypTV 140
Cdd:cd01543   2 VALLLETSRGYGR-RLLRGIARYAREHGPwSLYL-----EPPGYEELLDLLKGWKGDGIIAR-LDDPELAEALRRL--GI 72
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 141 PTVMMDWA-PFDGDSDLIQDNSLLGgDLATQYLIDKGHTRIACItGPLDKTPARLRLEGYRAAMKRAGLNIpDGYEVTGD 219
Cdd:cd01543  73 PVVNVSGSrPEPGFPRVTTDNEAIG-RMAAEHLLERGFRHFAFC-GFRNAAWSRERGEGFREALREAGYEC-HVYESPPS 149
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 220 FEFNGGFDA----MRQLLSHPlRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYDDIEL-ASFMTPPLTTIHQPKD 294
Cdd:cd01543 150 GSSRSWEEEreelADWLKSLP-KPVGIFACNDDRARQVLEACREAGIRVPEEVAVLGVDNDELiCELSSPPLSSIALDAE 228
                       250       260       270
                ....*....|....*....|....*....|..
gi 16131621 295 ELGELAIDVLiHRItqptLQQQRLQLTPILME 326
Cdd:cd01543 229 QIGYEAAELL-DRL----MRGERVPPEPILIP 255
PBP1_ABC_sugar_binding-like cd06321
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
61-281 4.16e-16

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: 76.94  E-value: 4.16e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYS--LVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQ-RY 137
Cdd:cd06321   1 VIGVTVQDLGNPFFVAMVRGAEEAAAEINPGakVTVVDARYDLAKQFSQIDDFIAQGVDLILLNAADSAGIEPAIKRaKD 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 138 PTVPTVMMDwAPFDGDSDLIQDNSLLGGDLATQYLIDK--GHTRIACITGPlDKTPARLRLEGYRAAMKRA-GLNIPDGY 214
Cdd:cd06321  81 AGIIVVAVD-VAAEGADATVTTDNVQAGYLACEYLVEQlgGKGKVAIIDGP-PVSAVIDRVNGCKEALAEYpGIKLVDDQ 158
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16131621 215 EvtGDFEFNGGFDAMRQLLS-HPlRPQAVFTGNDAMAVGVYQALYQAelqvpqdiaviGYDDIELASF 281
Cdd:cd06321 159 N--GKGSRAGGLSVMTRMLTaHP-DVDGVFAINDPGAIGALLAAQQA-----------GRDDIVITSV 212
PBP1_sensor_kinase-like cd06308
periplasmic binding domain of two-component sensor kinase signaling systems; Periplasmic ...
61-274 2.65e-15

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: 74.51  E-value: 2.65e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVER-SCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETH---QPSREIMQR 136
Cdd:cd06308   1 VIGFSQCSLNDPWRAAMNEEIKAeAAKYPNVELIVTDAQGDAAKQIADIEDLIAQGVDLLIVSPNEADaltPVVKKAYDA 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 137 ypTVPTVMMDwAPFDGDsdliQDNSLLGGD------LATQYLID--KGHTRIACITGPLDKTPARLRLEGYRAAMKRAGl 208
Cdd:cd06308  81 --GIPVIVLD-RKVSGD----DYTAFIGADnveigrQAGEYIAEllNGKGNVVEIQGLPGSSPAIDRHKGFLEAIAKYP- 152
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 16131621 209 NIPDGYEVTGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALyqAELQVPQDIAVIGYD 274
Cdd:cd06308 153 GIKIVASQDGDWLRDKAIKVMEDLLQAHPDIDAVYAHNDEMALGAYQAL--KKAGREKEIKIIGVD 216
PBP1_ABC_sugar_binding-like cd06322
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
61-274 1.05e-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: 380545 [Multi-domain]  Cd Length: 270  Bit Score: 73.08  E-value: 1.05e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETH--QPSREIMQRyP 138
Cdd:cd06322   1 TIGVSLLTLQHPFFVDIKDAMKKEAAELGVKVVVADANGDLAKQLSQIEDFIQQGVDAIILAPVDSGgiVPAIEAANE-A 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 139 TVPTVMMDWAPFDGDSD-LIQDNSLLGGDLATQYL---IDKGHTRIACITGPlDKTPARLRLEGYRAAMKR-AGLNIPDg 213
Cdd:cd06322  80 GIPVFTVDVKADGAKVVtHVGTDNYAGGKLAGEYAlkaLLGGGGKIAIIDYP-EVESVVLRVNGFKEAIKKyPNIEIVA- 157
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 16131621 214 yEVTGDFEFNGGFDAMRQLL-SHPlRPQAVFTGNDAMAVGVYQALYQAELQvpQDIAVIGYD 274
Cdd:cd06322 158 -EQPGDGRREEALAATEDMLqANP-DLDGIFAIGDPAALGALTAIESAGKE--DKIKVIGFD 215
PBP1_LacI-like cd06287
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
73-329 7.02e-14

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: 70.53  E-value: 7.02e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  73 FYSELVRGVERSCFERGYSLVLCNTEGDeqrmNRNLETLmqkRVDGLLLLCTETHQP-SREIMQRypTVPTVMMDWAP-F 150
Cdd:cd06287  21 FMMEVAAAAAEEALEHDLALVLVPPLHH----VSMLDAL---DVDGAIVVEPTVEDPiLARLRQR--GVPVVSIGRAPgT 91
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 151 DGDSDLIQDNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRAGLNiPDGYEVTGDFEFNGGFDAMR 230
Cdd:cd06287  92 DEPVPYVDLQSAATARLLLEHLHGAGARQVALLTGSSRRNSSLESEAAYLRFAQEYGTT-PVVYKVPESEGERAGYEAAA 170
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 231 QLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIG-YDDIElASFMTPPLTTIHQPKDELGELAIDVLIHRIT 309
Cdd:cd06287 171 ALLAAHPDIDAVCVPVDAFAVGAMRAARDSGRSVPEDLMVVTrYDGIR-ARTADPPLTAVDLHLDRVARTAIDLLFASLS 249
                       250       260
                ....*....|....*....|
gi 16131621 310 QPTlQQQRLQLTPILMERGS 329
Cdd:cd06287 250 GEE-RSVEVGPAPELVVRAS 268
PBP1_ABC_sugar_binding-like cd19970
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
61-302 9.52e-14

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: 70.36  E-value: 9.52e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFER-GYSLVL--CNTEGDEQRMNRNLETLMQKRVDGLLLLCTETH---QPSREIM 134
Cdd:cd19970   1 KVALVMKSLANEFFIEMEKGARKHAKEAnGYELLVkgIKQETDIEQQIAIVENLIAQKVDAIVIAPADSKalvPVLKKAV 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 135 QRypTVPTVMMDWApFDGD---SDLIQ------DNSLlGGDLATQYLIDK--GHTRIACITGPLDKTPARLRLEGYRAAM 203
Cdd:cd19970  81 DA--GIAVINIDNR-LDADalkEGGINvpfvgpDNRQ-GAYLAGDYLAKKlgKGGKVAIIEGIPGADNAQQRKAGFLKAF 156
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 204 KRAGLNIPDgyEVTGDFEFNGGFDAMRQLLS-HPlRPQAVFTGNDAMAVGVYQALyqAELQVPQDIAVIGYDDIELASfm 282
Cdd:cd19970 157 EEAGMKIVA--SQSANWEIDEANTVAANLLTaHP-DIRGILCANDNMALGAIKAV--DAAGKAGKVLVVGFDNIPAVR-- 229
                       250       260
                ....*....|....*....|....*.
gi 16131621 283 tPPLT------TIHQPKDELGELAID 302
Cdd:cd19970 230 -PLLKdgkmlaTIDQHPAKQAVYGIE 254
PBP1_ABC_IbpA-like cd19968
periplasmic sugar-binding protein IbpA of an ABC transporter and similar proteins; The ...
61-274 2.92e-13

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: 68.95  E-value: 2.92e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYPT- 139
Cdd:cd19968   1 KIGFSFPNLSFPFFVYMHEQAVDEAAKLGVKLVVLDAQNSSSKQASDLENAIAQGVDGIIVSPIDVKALVPAIEAAIKAg 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 140 VPTVMMDWApFDGDSDL--IQDNSLLGGDLATQYLIDK--GHTRIACITGPLDKTPARLRLEGYRAAMKrAGLNIPDGYE 215
Cdd:cd19968  81 IPVVTVDRR-AEGAAPVphVGADNVAGGREVAKFVVDKlpNGAKVIELTGTPGSSPAIDRTKGFHEELA-AGPKIKVVFE 158
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 216 VTGDFEFNGGFDAMRQLL-SHPLRPQAVFTGNDAMAVGVYQALYQAELQVpQDIAVIGYD 274
Cdd:cd19968 159 QTGNFERDEGLTVMENILtSLPGPPDAIICANDDMALGAIEAMRAAGLDL-KKVKVIGFD 217
PBP1_TmRBP-like cd19967
D-ribose ABC transporter substrate-binding protein such as Thermoanaerobacter tengcongensis ...
64-302 6.38e-13

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: 67.73  E-value: 6.38e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  64 MLITAS-TNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTE---THQPSREIMQRypT 139
Cdd:cd19967   3 AVIVSTpNNPFFVVEAEGAKEKAKELGYEVTVFDHQNDTAKEAELFDTAIASGAKAIILDPADadaSIAAVKKAKDA--G 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 140 VPTVMMDWAPFDGDSDLIQ--DNSLLGGDLATQYLIDK--GHTRIACITGPLDKTPARLRLEGYRAAMKRaglnIPDGYE 215
Cdd:cd19967  81 IPVFLIDREINAEGVAVAQivSDNYQGAVLLAQYFVKLmgEKGLYVELLGKESDTNAQLRSQGFHSVIDQ----YPELKM 156
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 216 V---TGDFEFNGGFDAMRQLL-SHPlRPQAVFTGNDAMAVGVYQALYQAelQVPQDIAVIGYD--DIELASFMTPPLT-T 288
Cdd:cd19967 157 VaqqSADWDRTEAFEKMESILqANP-DIKGVICGNDEMALGAIAALKAA--GRAGDVIIVGFDgsNDVRDAIKEGKISaT 233
                       250
                ....*....|....
gi 16131621 289 IHQPKDELGELAID 302
Cdd:cd19967 234 VLQPAKLIARLAVE 247
PBP1_ABC_sugar_binding-like cd19972
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
61-321 1.37e-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: 380627 [Multi-domain]  Cd Length: 269  Bit Score: 66.70  E-value: 1.37e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLL---CTETHQPSReiMQRY 137
Cdd:cd19972   1 TIGLAVANLQADFFNQIKQSVEAEAKKKGYKVITVDAKGDSATQVNQIQDLITQNIDALIYIpagATAAAVPVK--AARA 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 138 PTVPTVMMDWAPFDGDSD-LIQDNSLLG-GDLATqYLIDK--GHTRIACITGPLDKTPARLRLEGYRAAMKRA-GLNIPD 212
Cdd:cd19972  79 AGIPVIAVDRNPEDAPGDtFIATDSVAAaKELGE-WVIKQtgGKGEIAILHGQLGTTPEVDRTKGFQEALAEApGIKVVA 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 213 gyEVTGDFEFNGGFDAMRQLLS-HPlRPQAVFTGNDAMAVGVYQALYQAELqvPQDIAVIGYD-DIELASFMTPPLT--T 288
Cdd:cd19972 158 --EQTADWDQDEGFKVAQDMLQaNP-NITVFFGQSDAMALGAAQAVKVAGL--DHKIWVVGFDgDVAGLKAVKDGVLdaT 232
                       250       260       270
                ....*....|....*....|....*....|....*.
gi 16131621 289 IHQPKDELGELAIDV---LIHRITQPTLQQQRLQLT 321
Cdd:cd19972 233 MTQQTQKMGRLAVDSaidLLNGKAVPKEQLQDAVLT 268
PBP1_ABC_sugar_binding-like cd19971
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
61-274 2.04e-11

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: 63.37  E-value: 2.04e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLL--LCTETHQPSREIMQRYp 138
Cdd:cd19971   1 KFGFSYMTMNNPFFIAINDGIKKAVEANGDELITRDPQLDQNKQNEQIEDMINQGVDAIFLnpVDSEGIRPALEAAKEA- 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 139 TVPTVMMDwAPFDgDSDLIQ-----DN----SLLGGDLATQYLiDKGhtRIACITGPLDKTpARLRLEGYRAAMKR-AGL 208
Cdd:cd19971  80 GIPVINVD-TPVK-DTDLVDstiasDNynagKLCGEDMVKKLP-EGA--KIAVLDHPTAES-CVDRIDGFLDAIKKnPKF 153
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16131621 209 NIPDGYEVTGDFEfnGGFDAMRQLL-SHPlRPQAVFTGNDAMAVGVYQALYQAELQvpQDIAVIGYD 274
Cdd:cd19971 154 EVVAQQDGKGQLE--VAMPIMEDILqAHP-DLDAVFALNDPSALGALAALKAAGKL--GDILVYGVD 215
PBP1_ABC_D-talitol-like cd06318
periplasmic D-talitol-binding protein of an ABC transport system and similar proteins; ...
72-306 1.28e-10

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: 61.27  E-value: 1.28e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  72 PFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLlctETHQPS--REIMQRYPT--VPTVMMDw 147
Cdd:cd06318  12 PYYAALVAAAKAEAKKLGVELVVTDAQNDLTKQISDVEDLITRGVDVLIL---NPVDPEglTPAVKAAKAagIPVITVD- 87
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 148 APFDGDSDL---IQDNSLLGGDLATQYLID---KGHTRIACITGPLDKTPARLR----LEGYRAAMKR----AGLNIPDG 213
Cdd:cd06318  88 SALDPSANVatqVGRDNKQNGVLVGKEAAKalgGDPGKIIELSGDKGNEVSRDRrdgfLAGVNEYQLRkygkSNIKVVAQ 167
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 214 -YevtGDFEFNGGFDAMRQLL-SHPlRPQAVFTGNDAMAVGVYQALYQAELQvpQDIAVIGYDD-------IELASFMTp 284
Cdd:cd06318 168 pY---GNWIRSGAVAAMEDLLqAHP-DINVVYAENDDMALGAMKALKAAGML--DKVKVAGADGqkealklIKDGKYVA- 240
                       250       260
                ....*....|....*....|..
gi 16131621 285 plTTIHQPkDELGELAIDVLIH 306
Cdd:cd06318 241 --TGLNDP-DLLGKTAVDTAAK 259
PBP1_ABC_ThpA_XypA cd06313
periplasmic sugar-binding proteins (ThpA and XypA) of ABC-type transport systems; This group ...
61-305 5.17e-10

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: 59.21  E-value: 5.17e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQ----R 136
Cdd:cd06313   1 KIGFTVYGLSSEFITNLVEAMKAVAKELNVDLVVLDGNGDVSTQINQVDTLIAQGVDAIIVVPVDADALAPAVEKakeaG 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 137 YPTVPTVMM----DWAPFDGDSDliqdnsLLGGDLATQYLIDK--GHTRIACITGPLDKTPARLRLEGYRAAMKRA-GLN 209
Cdd:cd06313  81 IPLVGVNALieneDLTAYVGSDD------VVAGELEGQAVADRlgGKGNVVILEGPIGQSAQIDRGKGIENVLKKYpDIK 154
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 210 IPDgyEVTGDFEFNGGFDAMRQLLS-HPLRPQAVFTGNDAMAVGVYQALYQAELqvpQDIAVIGYDDIELASFMTPP--- 285
Cdd:cd06313 155 VLA--EQTANWSRDEAMSLMENWLQaYGDEIDGIIAQNDDMALGALQAVKAAGR---DDIPVVGIDGIEDALQAVKSgel 229
                       250       260
                ....*....|....*....|
gi 16131621 286 LTTIHQPKDELGELAIDVLI 305
Cdd:cd06313 230 IATVLQDAEAQGKGAVEVAV 249
PBP1_allose_binding cd06320
periplasmic allose-binding domain of bacterial transport systems that function as a primary ...
62-305 8.74e-10

periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis; Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily. Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta 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.


Pssm-ID: 380543 [Multi-domain]  Cd Length: 283  Bit Score: 58.81  E-value: 8.74e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  62 IGMLITASTNPFYSELVRGVERSCFERGYSLVL--CNTEGDEQRMNRNLETLMQKRVDGLLLL---CTETHQPSREIMQR 136
Cdd:cd06320   2 IGVVLKTLSNPFWVAMKDGIEAEAKKLGVKVDVqaAPSETDTQGQLNLLETMLNKGYDAILVSpisDTNLIPPIEKANKK 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 137 ypTVPTVMMDWA--PFDGDSDLIQDNSLLGGD------LATQYLIDK--GHTRIACITGPLDKTPARLRLEGYRAAMKRA 206
Cdd:cd06320  82 --GIPVINLDDAvdADALKKAGGKVTSFIGTDnvaagaLAAEYIAEKlpGGGKVAIIEGLPGNAAAEARTKGFKETFKKA 159
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 207 GlnipdGYEV----TGDFEFNGGFDAMRQLL-SHP-LRpqAVFTGNDAMAVGVYQALYQAELQvpQDIAVIGYDDIELA- 279
Cdd:cd06320 160 P-----GLKLvasqPADWDRTKALDAATAILqAHPdLK--GIYAANDTMALGAVEAVKAAGKT--GKVLVVGTDGIPEAk 230
                       250       260
                ....*....|....*....|....*...
gi 16131621 280 -SFMTPPLT-TIHQPKDELGELAIDVLI 305
Cdd:cd06320 231 kSIKAGELTaTVAQYPYLEGAMAVEAAL 258
PBP1_GGBP cd01539
periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and ...
61-279 5.62e-09

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: 56.44  E-value: 5.62e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERG-YSLVLCNTEGDEQRMNRNLETLMQKRVDGLLL-----LCTET-------- 126
Cdd:cd01539   2 KIGVFIYNYDDTFISSVRKALEKAAKAGGkIELEIYDAQNDQSTQNDQIDTMIAKGVDLLVVnlvdrTAAQTiidkakaa 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 127 --------HQPSREIMQRYPTVPTVMMDWApfdgDSDLIQdnsllgGDLATQYL-----IDK---GHTRIACITGPLDKT 190
Cdd:cd01539  82 nipviffnREPSREDLKSYDKAYYVGTDAE----ESGIMQ------GEIIADYWkanpeIDKngdGKIQYVMLKGEPGHQ 151
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 191 PARLRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMRQLLS-HPLRPQAVFTGNDAMAVGVYQALYQAEL---QVPQ 266
Cdd:cd01539 152 DAIARTKYSVKTLNDAGIKTEQLAEDTANWDRAQAKDKMDAWLSkYGDKIELVIANNDDMALGAIEALKAAGYntgDGDK 231
                       250
                ....*....|...
gi 16131621 267 DIAVIGYDDIELA 279
Cdd:cd01539 232 YIPVFGVDATPEA 244
PBP1_ABC_sugar_binding-like cd06310
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
61-274 2.12e-08

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: 380533 [Multi-domain]  Cd Length: 272  Bit Score: 54.27  E-value: 2.12e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVL--CNTEGDEQRMNRNLETLMQKRVDGLLLLCTETH---QPSREIMQ 135
Cdd:cd06310   1 KIGVVLKGTTSAFWRTVREGAEAAAKDLGVKIIFvgPESEEDVAGQNSLLEELINKKPDAIVVAPLDSEdlvDPLKDAKD 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 136 RYPTVPTVMMDWAPFDGDSDLIQDNsLLGGDLATQYLIDK--GHTRIACITGPLDKTPARLRLEGYRAAMKR--AGLN-I 210
Cdd:cd06310  81 KGIPVIVIDSGIKGDAYLSYIATDN-YAAGRLAAQKLAEAlgGKGKVAVLSLTAGNSTTDQREEGFKEYLKKhpGGIKvL 159
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 16131621 211 PDGYevtGDFEFNGGFDAMRQLLSHplRPQA--VFTGNDAMAVGVYQALYQAELQvpQDIAVIGYD 274
Cdd:cd06310 160 ASQY---AGSDYAKAANETEDLLGK--YPDIdgIFATNEITALGAAVAIKSRKLS--GQIKIVGFD 218
PBP1_ABC_sugar_binding-like cd06324
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
98-274 2.58e-08

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: 54.53  E-value: 2.58e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  98 EGDEQRMNRNLETLMQ--KRVDGLLLlcTETHQPSREIM---QRYPtVPTVMMDWAPFDGDSDLIQ-------------- 158
Cdd:cd06324  39 NRNRFKMLELAEELLArpPKPDYLIL--VNEKGVAPELLelaEQAK-IPVFLINNDLTDEERALLGkprekfkywlgsiv 115
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 159 -DNSLLGGDLAtQYLIDKGHT-------RIACITGPLDKTPARLRLEGYRAAMKRAglniPDGY---EVTGDFEFNGGFD 227
Cdd:cd06324 116 pDNEQAGYLLA-KALIKAARKksddgkiRVLAISGDKSTPASILREQGLRDALAEH----PDVTllqIVYANWSEDEAYQ 190
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*...
gi 16131621 228 AMRQLLS-HPlRPQAVFTGNDAMAVGVYQALYQAELQVPQDIAVIGYD 274
Cdd:cd06324 191 KTEKLLQrYP-DIDIVWAANDAMALGAIDALEEAGLKPGKDVLVGGID 237
PBP1_rhizopine_binding-like cd06301
periplasmic binding proteins specific to rhizopines; Periplasmic binding proteins specific to ...
87-276 3.76e-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: 53.77  E-value: 3.76e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  87 ERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREI-MQRYPTVPTVMMDWAPFDGDSDL--IQDNSLL 163
Cdd:cd06301  29 YPGVKLVIVDAQSDAAKQLSQVENFIAQGVDAIIVNPVDTDASAPAVdAAADAGIPLVYVNREPDSKPKGVafVGSDDIE 108
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 164 GGDLATQYLIDK--GHTRIACITGPLDKTPARLRLEGYRAAMKR-AGLNIPDgyEVTGDFEFNGGFDAMRQLLSHPLRPQ 240
Cdd:cd06301 109 SGELQMEYLAKLlgGKGNIAILDGVLGHEAQILRTEGNKDVLAKyPGMKIVA--EQTANWSREKAMDIVENWLQSGDKID 186
                       170       180       190
                ....*....|....*....|....*....|....*.
gi 16131621 241 AVFTGNDAMAVGVYQALYQAELQVpqDIAVIGYDDI 276
Cdd:cd06301 187 AIVANNDEMAIGAILALEAAGKKD--DILVAGIDAT 220
PBP1_ABC_sugar_binding-like cd06311
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
61-260 2.65e-07

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: 51.21  E-value: 2.65e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERG---YSLVlcnTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQ---PSREIM 134
Cdd:cd06311   1 TIGISIPSADHGWTAGVAYYAEKQAKELAdleYKLV---TSSNANEQVSQLEDLIAQKVDAIVILPQDSEEltvAAQKAK 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 135 QRYptVPTVMMDwapfDGDSDLIQDNSLLG-----GDLATQYLIDK--GHTRIACITGPLDKTPARLRLEGYRAAMK-RA 206
Cdd:cd06311  78 DAG--IPVVNFD----RGLNVLIYDLYVAGdnpgmGVVSAEYIGKKlgGKGNVVVLEVPSSGSVNEERVAGFKEVIKgNP 151
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....
gi 16131621 207 GLNIPDGYEvtGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQA 260
Cdd:cd06311 152 GIKILAMQA--GDWTREDGLKVAQDILTKNKKIDAVWAADDDMAIGVLQAIKEA 203
PBP1_ABC_sugar_binding-like cd20004
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
61-274 4.47e-07

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: 50.31  E-value: 4.47e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVL--CNTEGDEQRMNRNLETLMQKRVDGLLLLCTETH---QPSREIMQ 135
Cdd:cd20004   1 CIAVIPKGTTHDFWKSVKAGAEKAAQELGVEIYWrgPSREDDVEAQIQIIEYFIDQGVDGIVLAPLDRKalvAPVERARA 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 136 RypTVPTVMMDwAPFDGDSDL--IQDNSLLGGDLATQYLIDKGHTRIACITGPLDK--TPARLRLEGYRAAMKRA--GLN 209
Cdd:cd20004  81 Q--GIPVVIID-SDLGGDAVIsfVATDNYAAGRLAAKRMAKLLNGKGKVALLRLAKgsASTTDRERGFLEALKKLapGLK 157
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16131621 210 IPDGYEVTGDFEfnGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELqvPQDIAVIGYD 274
Cdd:cd20004 158 VVDDQYAGGTVG--EARSSAENLLNQYPDVDGIFTPNESTTIGALRALRRLGL--AGKVKFIGFD 218
PBP1_ABC_xylose_binding-like cd19992
periplasmic xylose-like sugar-binding component of the ABC-type transport systems; Periplasmic ...
62-314 1.79e-06

periplasmic xylose-like sugar-binding component of the ABC-type transport systems; Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein 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: 380647 [Multi-domain]  Cd Length: 284  Bit Score: 48.73  E-value: 1.79e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  62 IGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLC--TETHQPSREiMQRYPT 139
Cdd:cd19992   2 IGVSFPTQQEERWQKDKEYMEEEAKELGVELIFQVADNDAKTQASQVENLLAQGIDVLIIAPvdAGAAANIVD-KAKAAG 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 140 VPTVMMDWAPFDGDSDLI--QDNSLLGgDLATQYLID---KGHtrIACITGPLDKTPARLRLEGYRAAMKraglNIPDGY 214
Cdd:cd19992  81 VPVISYDRLILNADVDLYvgRDNYKVG-QLQAEYALEavpKGN--YVILSGDPGDNNAQLITAGAMDVLQ----PAIDSG 153
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 215 EVT--GDfEFNGGFD---AMRQ----LLSHPLRPQAVFTGNDAMAVGVYQALyqAELQVPQDIAVIGyDDIELASF---- 281
Cdd:cd19992 154 DIKivLD-QYVKGWSpdeAMKLvenaLTANNNNIDAVLAPNDGMAGGAIQAL--KAQGLAGKVFVTG-QDAELAALkriv 229
                       250       260       270
                ....*....|....*....|....*....|....*.
gi 16131621 282 ---MTpplTTIHQPKDELGELAIDVLIHRITQPTLQ 314
Cdd:cd19992 230 egtQT---MTVWKDLKELARAAADAAVKLAKGEKPQ 262
PBP1_sugar_binding cd06307
periplasmic sugar-binding domain of uncharacterized transport systems; Periplasmic ...
62-308 1.90e-05

periplasmic sugar-binding domain of uncharacterized transport systems; Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes.


Pssm-ID: 380530 [Multi-domain]  Cd Length: 275  Bit Score: 45.63  E-value: 1.90e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  62 IGMLITASTNPFYSELVRGVERSCFERGY----SLVLCNTEGDEQRMNRNLETLMqKRVDGLLLLCTEtHQPSREIMQRY 137
Cdd:cd06307   2 FGFLLPSPENPFYELLRRAIEAAAAALRDrrvrLRIHFVDSLDPEALAAALRRLA-AGCDGVALVAPD-HPLVRAAIDEL 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 138 PT--VPTVMMdwapfdgDSDLIQ---------DNSLLG---GDLATQYLIDKGHtRIACITGPLDKTPARLRLEGYRAAM 203
Cdd:cd06307  80 AArgIPVVTL-------VSDLPGsrrlayvgiDNRAAGrtaAWLMGRFLGRRPG-KVLVILGSHRFRGHEEREAGFRSVL 151
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 204 --KRAGLNIPDGYEVTGDFEFNggFDAMRQLL-SHP-LRpqAVFT---GNDamavGVYQALyqAELQVPQDIAVIGYDDI 276
Cdd:cd06307 152 reRFPDLTVLEVLEGLDDDELA--YELLRELLaRHPdLV--GIYNaggGNE----GIARAL--REAGRARRVVFIGHELT 221
                       250       260       270
                ....*....|....*....|....*....|....*...
gi 16131621 277 E------LASFMTpplTTIHQPKDELGELAIDVLIHRI 308
Cdd:cd06307 222 PetrrllRDGTID---AVIDQDPELQARRAIEVLLAHL 256
PBP1_methylthioribose_binding-like cd06305
similar to methylthioribose-binding protein of ABC-type transport systems that belong to a ...
61-278 8.71e-05

similar to methylthioribose-binding protein of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily; Proteins similar to methylthioribose-binding protein of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) 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. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.


Pssm-ID: 380528 [Multi-domain]  Cd Length: 273  Bit Score: 43.44  E-value: 8.71e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLC--TETHQPS-REIMQRy 137
Cdd:cd06305   1 TIAVVRNGTSGDWDQQALQGAVAEAEKLGGTVIVFDANGDDARMADQIQQAITQKVDAIIISHgdADALDPKlKKALDA- 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 138 pTVPTVMMDWAPFDGDSDLIQDNSLLGGDLATQYLID--KGHTRIACITG----PLDKtparlRLEGYRAAMKrAGLNIP 211
Cdd:cd06305  80 -GIPVVTFDTDSQVPGVNNITQDDYALGTLSLGQLVKdlNGEGNIAVFNVfgvpPLDK-----RYDIYKAVLK-ANPGIK 152
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16131621 212 DGYEVTGDFEFNGGFDAMRQLLShpLRPQ-------AVFTGNDAMAVGVYQALYQAELqvpQDIAVIGYD----DIEL 278
Cdd:cd06305 153 KIVAELGDVTPNTAADAQTQVEA--LLKKypeggidAIWAAWDEPAKGAVQALEEAGR---TDIKVYGVDisnqDLEL 225
PBP1_arabinose_binding cd01540
periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose ...
62-272 8.81e-05

periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily; Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such as LacI and GalR.


Pssm-ID: 380482 [Multi-domain]  Cd Length: 294  Bit Score: 43.43  E-value: 8.81e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  62 IGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLlCTETHQPSREIMQR----- 136
Cdd:cd01540   2 IGFIVKQPDQPWFQDEWKGAKKAAKELGFEVIKIDAKMDGEKVLSAIDNLIAQGAQGIVI-CTPDQKLGPAIAAKakaag 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 137 ---------------YPTVPTVMMDwapfdgDSDLIQDN-SLLGGDLATQYLIDKGHTRIACITgpLDKTP-ARLRLEGY 199
Cdd:cd01540  81 ipviavddqlvdadpMKIVPFVGID------AYKIGEAVgEWLAKEMKKRGWDDVKEVGVLAIT--MDTLSvCVDRTDGA 152
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16131621 200 RAAMKRAGL---NIPDGYEVTGDFEfnGGFDAMRQLL-SHP-LRPQAVFTGNDAMAVGVYQALYQAELQvPQDIAVIG 272
Cdd:cd01540 153 KDALKAAGFpedQIFQAPYKGTDTE--GAFNAANAVItAHPeVKHWLVVGCNDEGVLGAVRALEQAGFD-AEDIIGVG 227
PBP1_tmGBP cd06314
periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and ...
61-277 1.71e-04

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: 42.57  E-value: 1.71e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLC-NTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYPT 139
Cdd:cd06314   1 TFALVPKGLNNPFWDLAEAGAEKAAKELGVNVEFVgPQKSDAAEQVQLIEDLIARGVDGIAISPNDPEAVTPVINKAADK 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 140 -VPTVMmdwapFDGDSD-------LIQDNSLLG---GDLATQYLIDKGhtRIACITGPLDKTPARLRLEGYRAAMK-RAG 207
Cdd:cd06314  81 gIPVIT-----FDSDAPdskrlayIGTDNYEAGreaGELMKKALPGGG--KVAIITGGLGADNLNERIQGFKDALKgSPG 153
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16131621 208 LNIPDGYEVTGDfeFNGGFDAMRQLLS-HPlrpqavftGNDAMaVGVYQ------ALYQAELQVPQDIAVIGYDDIE 277
Cdd:cd06314 154 IEIVDPLSDNDD--IAKAVQNVEDILKaNP--------DLDAI-FGVGAyngpaiAAALKDAGKVGKVKIVGFDTLP 219
PBP1_ABC_sugar_binding-like cd20007
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
61-274 1.84e-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: 42.61  E-value: 1.84e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVlcnTEG----DEQRMNRNLETLMQKRVDGLLLLCTETHQ---PSREI 133
Cdd:cd20007   1 TIALVPGVTGDPFYITMQCGAEAAAKELGVELD---VQGpptfDPTLQTPIVNAVIAKKPDALLIAPTDPQAliaPLKRA 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 134 MQRypTVPTVMMDwaPFDGDSDL----IQDNSLLGGDLATQYLID----KGhtRIACITGPLDKTPARLRLEGYRAAMKR 205
Cdd:cd20007  78 ADA--GIKVVTVD--TTLGDPSFvlsqIASDNVAGGALAAEALAEliggKG--KVLVINSTPGVSTTDARVKGFAEEMKK 151
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16131621 206 AGLNIPDGYEVTGDfEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQAELQvpQDIAVIGYD 274
Cdd:cd20007 152 YPGIKVLGVQYSEN-DPAKAASIVAAALQANPDLAGIFGTNTFSAEGAAAALRNAGKT--GKVKVVGFD 217
PRK09701 PRK09701
D-allose transporter substrate-binding protein;
52-305 2.29e-04

D-allose transporter substrate-binding protein;


Pssm-ID: 182037 [Multi-domain]  Cd Length: 311  Bit Score: 42.17  E-value: 2.29e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621   52 RSLKLNQTHTIGMLITAST--------------NPFYSELVRGVERSCFERGYS--LVLCNTEGDEQRMNRNLETLMQKR 115
Cdd:PRK09701   3 KYLKYFSGTLVGLMLSTSAfaaaeyavvlktlsNPFWVDMKKGIEDEAKTLGVSvdIFASPSEGDFQSQLQLFEDLSNKN 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  116 VDGLLLlctethQPsreiMQRYPTVPTVMMDWAP------FDGDSDLIQ--------------DNSLLGGDLAtQYLIDK 175
Cdd:PRK09701  83 YKGIAF------AP----LSSVNLVMPVARAWKKgiylvnLDEKIDMDNlkkaggnveafvttDNVAVGAKGA-SFIIDK 151
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  176 -GHT--RIACITGPLDKTPARLRLEGYRAAMKRAGlNIPDGYEVTGDFEFNGGFDAMRQLLSHPLRPQAVFTGNDAMAVG 252
Cdd:PRK09701 152 lGAEggEVAIIEGKAGNASGEARRNGATEAFKKAS-QIKLVASQPADWDRIKALDVATNVLQRNPNIKAIYCANDTMAMG 230
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 16131621  253 VYQALYQAELQvpQDIAVIGYDDIELASFMTPP--LT-TIHQPKDELGELAIDVLI 305
Cdd:PRK09701 231 VAQAVANAGKT--GKVLVVGTDGIPEARKMVEAgqMTaTVAQNPADIGATGLKLMV 284
PBP1_ABC_sugar_binding-like cd19973
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
61-260 5.38e-04

monosaccharide ABC transporter substrate-binding protein; 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: 380628 [Multi-domain]  Cd Length: 285  Bit Score: 40.91  E-value: 5.38e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLC--NTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQ-RY 137
Cdd:cd19973   1 TIGLITKTDTNPFFVKMKEGAQKAAKALGIKLMTAagKIDGDNATQVTAIENMIAAGAKGILITPSDTKAIVPAVKKaRD 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 138 PTVPTVMMDwAPFD----GDSDLIQDNsLLGGDLATQYLIDKGHTR---IACITGPLDKTPARLRLEGYRAAMKRAGLNI 210
Cdd:cd19973  81 AGVLVIALD-TPTDpidaADATFATDN-FKAGVLIGEWAKAALGAKdakIATLDLTPGHTVGVLRHQGFLKGFGIDEKDP 158
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 16131621 211 PDGY-----EVTGDFEFNG----GFDAMRQLLSHPLRPQAVFTGNDAMAVGVYQALYQA 260
Cdd:cd19973 159 ESNEdeddsQVVGSADTNGdqakGQTAMENLLQKDPDINLVYTINEPAAAGAYQALKAA 217
PBP1_ABC_xylose_binding-like cd01538
periplasmic xylose-like sugar-binding component of the ABC-type transport systems that belong ...
61-312 3.67e-03

periplasmic xylose-like sugar-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily; Periplasmic xylose-like sugar-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein 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: 380480 [Multi-domain]  Cd Length: 283  Bit Score: 38.56  E-value: 3.67e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQ-RYPT 139
Cdd:cd01538   1 KIGVSLPNLREARWQTDRDIMVEQLEEKGAKVLVQSADGDKAKQASQIENLLTQGADVLVLAPVDGQALSPVVAEaKAEG 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 140 VPTVMMDWAPFDGDSDLIQ--DNSLLGGDLATQYLIDKGHTRIACITGPLDKTPARLRLEGYRAAMKRA----GLNIPDG 213
Cdd:cd01538  81 IKVIAYDRLILNADVDYYIsfDNEKVGELQAQALLDAKPEGNYVLIGGSPTDNNAKLFRDGQMKVLQPAidsgKIKVVGD 160
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 214 YEVTgDFEFNGGFDAMRQLL-SHPLRPQAVFTGNDAMAVGVYQALYQAELQvpQDIAVIGyDDIELAS---FMTPPLT-T 288
Cdd:cd01538 161 QWVD-DWLPANAQQIMENALtANGNNVDAVVASNDGTAGGAIAALKAQGLS--GGVPVSG-QDADLAAikrILAGTQTmT 236
                       250       260
                ....*....|....*....|....*.
gi 16131621 289 IHQPKDELGELAIDVLIH--RITQPT 312
Cdd:cd01538 237 VYKDIRLLADAAAEVAVAlmRGEKPP 262
PBP1_ABC_sugar_binding-like cd20008
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
61-279 6.11e-03

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: 37.98  E-value: 6.11e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621  61 TIGMLITASTNPFYSELVRGVERSCFERGYSLVLC--NTEGDEQRMNRNLETLMQKRVDGLLLLCTETHQPSREIMQRYP 138
Cdd:cd20008   1 KIAVIVKDTDSEYWQTVLKGAEKAAKELGVEVTFLgpATEADIAGQVNLVENAISRKPDAIVLAPNDTAALVPAVEAADA 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131621 139 TVPTVMMDWA--PFDGDSDLIQDNsLLGGDLATQYLID------KGHTRIACITGPLDKTPARLRLEGYRAAMKraglNI 210
Cdd:cd20008  81 GIPVVLVDSGanTDDYDAFLATDN-VAAGALAADELAEllkasgGGKGKVAIISFQAGSQTLVDREEGFRDYIK----EK 155
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16131621 211 PDGYEVTGDFEFNGgfD---AMRQ----LLSHP-LRpqAVFTGNDAMAVGVYQALyqAELQVPQDIAVIGYD--DIELA 279
Cdd:cd20008 156 YPDIEIVDVQYSDG--DiakALNQttdlLTANPdLV--GIFGANNPSAVGVAQAL--AEAGKAGKIVLVGFDssPDEVA 228
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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