hypothetical protein AMJ79_05845 [Phycisphaerae bacterium SM23_30]
Protein Classification
XylR family transcriptional regulator( domain architecture ID 11546740)
XylR family transcriptional regulator similar to xylose operon transcription regulator XylR, a DNA transcription repressor that regulates the xylBAFGHR operon and contains an N-terminal periplasmic-binding protein (PBP) fold ligand binding domain and a C-terminal AraC-like DNA binding domain
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| PBP1_XylR | cd01543 | ligand-binding domain of DNA transcription repressor specific for xylose (XylR); ... |
3-267 | 1.26e-134 | |||||
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: 385.02 E-value: 1.26e-134
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| HTH_ARAC | smart00342 | helix_turn_helix, arabinose operon control protein; |
292-374 | 3.15e-19 | |||||
helix_turn_helix, arabinose operon control protein; : Pssm-ID: 197666 [Multi-domain] Cd Length: 84 Bit Score: 81.45 E-value: 3.15e-19
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| Name | Accession | Description | Interval | E-value | |||||
| PBP1_XylR | cd01543 | ligand-binding domain of DNA transcription repressor specific for xylose (XylR); ... |
3-267 | 1.26e-134 | |||||
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: 385.02 E-value: 1.26e-134
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| Peripla_BP_3 | pfam13377 | Periplasmic binding protein-like domain; This domain is found in a variety of transcriptional ... |
104-267 | 2.05e-35 | |||||
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: 127.45 E-value: 2.05e-35
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| PurR | COG1609 | DNA-binding transcriptional regulator, LacI/PurR family [Transcription]; |
18-267 | 8.29e-33 | |||||
DNA-binding transcriptional regulator, LacI/PurR family [Transcription]; Pssm-ID: 441217 [Multi-domain] Cd Length: 335 Bit Score: 125.31 E-value: 8.29e-33
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| HTH_ARAC | smart00342 | helix_turn_helix, arabinose operon control protein; |
292-374 | 3.15e-19 | |||||
helix_turn_helix, arabinose operon control protein; Pssm-ID: 197666 [Multi-domain] Cd Length: 84 Bit Score: 81.45 E-value: 3.15e-19
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| AraC | COG2207 | AraC-type DNA-binding domain and AraC-containing proteins [Transcription]; |
292-377 | 7.38e-19 | |||||
AraC-type DNA-binding domain and AraC-containing proteins [Transcription]; Pssm-ID: 441809 [Multi-domain] Cd Length: 258 Bit Score: 85.22 E-value: 7.38e-19
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| HTH_18 | pfam12833 | Helix-turn-helix domain; |
297-375 | 6.77e-17 | |||||
Helix-turn-helix domain; Pssm-ID: 432818 [Multi-domain] Cd Length: 81 Bit Score: 74.93 E-value: 6.77e-17
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| PRK10703 | PRK10703 | HTH-type transcriptional repressor PurR; |
54-266 | 2.31e-11 | |||||
HTH-type transcriptional repressor PurR; Pssm-ID: 236739 [Multi-domain] Cd Length: 341 Bit Score: 64.36 E-value: 2.31e-11
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| PRK10219 | PRK10219 | superoxide response transcriptional regulator SoxS; |
281-374 | 4.72e-08 | |||||
superoxide response transcriptional regulator SoxS; Pssm-ID: 182314 [Multi-domain] Cd Length: 107 Bit Score: 50.69 E-value: 4.72e-08
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| Name | Accession | Description | Interval | E-value | |||||
| PBP1_XylR | cd01543 | ligand-binding domain of DNA transcription repressor specific for xylose (XylR); ... |
3-267 | 1.26e-134 | |||||
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: 385.02 E-value: 1.26e-134
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| Peripla_BP_3 | pfam13377 | Periplasmic binding protein-like domain; This domain is found in a variety of transcriptional ... |
104-267 | 2.05e-35 | |||||
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: 127.45 E-value: 2.05e-35
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| PurR | COG1609 | DNA-binding transcriptional regulator, LacI/PurR family [Transcription]; |
18-267 | 8.29e-33 | |||||
DNA-binding transcriptional regulator, LacI/PurR family [Transcription]; Pssm-ID: 441217 [Multi-domain] Cd Length: 335 Bit Score: 125.31 E-value: 8.29e-33
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| PBP1_LacI_sugar_binding-like | cd06267 | ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 ... |
48-255 | 1.19e-29 | |||||
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: 114.92 E-value: 1.19e-29
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| PBP1_Qymf-like | cd06291 | ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing ... |
54-266 | 5.29e-27 | |||||
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: 107.99 E-value: 5.29e-27
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| PBP1_EndR-like | cd19977 | periplasmic ligand-binding domain of putative repressor of the endoglucanase operon and its ... |
42-258 | 6.65e-23 | |||||
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: 96.44 E-value: 6.65e-23
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| PBP1_DegA_Like | cd19976 | ligand-binding domain of putative DNA transcription regulators highly similar to that of the ... |
48-266 | 1.47e-22 | |||||
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: 95.78 E-value: 1.47e-22
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| PBP1_sucrose_transcription_regulator | cd06288 | ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members ... |
52-266 | 2.47e-21 | |||||
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: 92.23 E-value: 2.47e-21
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| PBP1_LacI-like | cd06285 | ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ... |
52-267 | 2.82e-20 | |||||
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: 89.21 E-value: 2.82e-20
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| PBP1_LacI-like | cd19974 | ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ... |
42-266 | 3.99e-20 | |||||
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: 89.15 E-value: 3.99e-20
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| PBP1_MalR-like | cd06294 | ligand-binding domain of maltose transcription regulator MalR which is a member of the ... |
54-256 | 1.92e-19 | |||||
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: 86.87 E-value: 1.92e-19
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| PBP1_LacI-like | cd06284 | ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus ... |
48-255 | 2.42e-19 | |||||
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: 86.82 E-value: 2.42e-19
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| PBP1_GntR | cd01575 | ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of ... |
93-266 | 2.79e-19 | |||||
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: 86.39 E-value: 2.79e-19
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| HTH_ARAC | smart00342 | helix_turn_helix, arabinose operon control protein; |
292-374 | 3.15e-19 | |||||
helix_turn_helix, arabinose operon control protein; Pssm-ID: 197666 [Multi-domain] Cd Length: 84 Bit Score: 81.45 E-value: 3.15e-19
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| PBP1_CcpA-like | cd19975 | ligand-binding domain of putative DNA transcription regulators highly similar to that of the ... |
4-266 | 4.63e-19 | |||||
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: 86.07 E-value: 4.63e-19
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| PBP1_LacI | cd01574 | ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of ... |
5-266 | 4.89e-19 | |||||
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: 85.71 E-value: 4.89e-19
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| AraC | COG2207 | AraC-type DNA-binding domain and AraC-containing proteins [Transcription]; |
292-377 | 7.38e-19 | |||||
AraC-type DNA-binding domain and AraC-containing proteins [Transcription]; Pssm-ID: 441809 [Multi-domain] Cd Length: 258 Bit Score: 85.22 E-value: 7.38e-19
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| PBP1_AraR | cd01541 | ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a ... |
52-257 | 5.35e-18 | |||||
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: 82.99 E-value: 5.35e-18
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| PBP1_AglR-like | cd20010 | Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) and ... |
53-243 | 9.83e-18 | |||||
Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) and similar proteins; Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. Pssm-ID: 380665 [Multi-domain] Cd Length: 269 Bit Score: 82.21 E-value: 9.83e-18
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| PBP1_GalR | cd01544 | ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory ... |
34-266 | 4.33e-17 | |||||
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: 80.26 E-value: 4.33e-17
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| HTH_18 | pfam12833 | Helix-turn-helix domain; |
297-375 | 6.77e-17 | |||||
Helix-turn-helix domain; Pssm-ID: 432818 [Multi-domain] Cd Length: 81 Bit Score: 74.93 E-value: 6.77e-17
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| PBP1_GalS-like | cd06270 | ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory ... |
14-255 | 9.44e-17 | |||||
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: 79.10 E-value: 9.44e-17
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| PBP1_MalI-like | cd06289 | ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia ... |
52-255 | 1.07e-16 | |||||
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: 79.15 E-value: 1.07e-16
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| GlxA | COG4977 | Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ... |
270-377 | 1.13e-16 | |||||
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Pssm-ID: 444002 [Multi-domain] Cd Length: 318 Bit Score: 79.82 E-value: 1.13e-16
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| PBP1_CelR | cd06295 | ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly ... |
52-266 | 1.08e-15 | |||||
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: 76.52 E-value: 1.08e-15
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| PBP1_LacI-like | cd06293 | ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ... |
45-239 | 3.88e-15 | |||||
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: 74.62 E-value: 3.88e-15
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| PBP1_LacI-like | cd06273 | ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ... |
52-242 | 4.69e-15 | |||||
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: 74.47 E-value: 4.69e-15
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| PBP1_TreR-like | cd01542 | ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a ... |
48-254 | 1.03e-14 | |||||
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: 73.30 E-value: 1.03e-14
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| PBP1_PurR | cd06275 | ligand-binding domain of purine repressor, PurR, which functions as the master regulatory ... |
89-266 | 3.73e-14 | |||||
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: 71.90 E-value: 3.73e-14
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| PBP1_CcpA_TTHA0807 | cd06297 | ligand-binding domain of TTHA0807, a CcpA regulator, from Thermus thermophilus HB8 and its ... |
53-266 | 4.31e-14 | |||||
ligand-binding domain of TTHA0807, a CcpA regulator, from Thermus thermophilus HB8 and its close homologs; Ligand-binding domain of the uncharacterized transcription regulator TTHA0807 from the extremely thermophilic organism Thermus thermophilus HB8 and close homologs from other bacteria. Although its exact biological function is not known, the TTHA0807 belongs to the catabolite control protein A (CcpA)family of regulatory proteins. The CcpA functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators. Pssm-ID: 380520 [Multi-domain] Cd Length: 268 Bit Score: 71.73 E-value: 4.31e-14
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| PBP1_LacI-like | cd06290 | ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ... |
42-266 | 8.21e-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: 380513 [Multi-domain] Cd Length: 267 Bit Score: 70.72 E-value: 8.21e-14
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| PBP1_hexuronate_repressor-like | cd06272 | ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon ... |
54-244 | 2.78e-13 | |||||
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: 69.32 E-value: 2.78e-13
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| PBP1_LacI-like | cd06278 | ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ... |
36-266 | 1.39e-12 | |||||
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: 67.17 E-value: 1.39e-12
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| PBP1_AglR_RafR-like | cd06292 | Ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that ... |
13-267 | 1.41e-12 | |||||
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: 67.29 E-value: 1.41e-12
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| PBP1_LacI-like | cd06280 | ligand-binding domain of an uncharacterized transcription regulator from Staphylococcus ... |
52-251 | 3.79e-12 | |||||
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: 65.74 E-value: 3.79e-12
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| PBP1_repressor_sugar_binding-like | cd01537 | Ligand-binding domain of the LacI-GalR family of transcription regulators and the ... |
52-258 | 4.17e-12 | |||||
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: 65.73 E-value: 4.17e-12
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| PBP1_RegR_EndR_KdgR-like | cd06283 | ligand-binding domain of DNA transcription repressor RegR and other putative regulators such ... |
52-254 | 9.94e-12 | |||||
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: 64.49 E-value: 9.94e-12
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| PBP1_LacI-like | cd06281 | ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ... |
43-266 | 1.97e-11 | |||||
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: 63.80 E-value: 1.97e-11
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| PRK10703 | PRK10703 | HTH-type transcriptional repressor PurR; |
54-266 | 2.31e-11 | |||||
HTH-type transcriptional repressor PurR; Pssm-ID: 236739 [Multi-domain] Cd Length: 341 Bit Score: 64.36 E-value: 2.31e-11
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| PBP1_LacI-like | cd06282 | ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ... |
67-239 | 2.69e-11 | |||||
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: 63.46 E-value: 2.69e-11
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| PBP1_CatR-like | cd06296 | ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in ... |
52-267 | 4.47e-11 | |||||
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: 62.68 E-value: 4.47e-11
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| RbsB | COG1879 | ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH ... |
47-264 | 9.71e-11 | |||||
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: 62.25 E-value: 9.71e-11
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| PBP1_SalR | cd01545 | ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of ... |
7-266 | 1.05e-10 | |||||
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: 61.80 E-value: 1.05e-10
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| PBP1_AglR_RafR-like | cd06271 | ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and ... |
19-242 | 2.17e-10 | |||||
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: 60.52 E-value: 2.17e-10
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| PBP1_LacI-like | cd06299 | ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum ... |
14-243 | 4.81e-10 | |||||
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: 59.60 E-value: 4.81e-10
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| PBP1_ABC_sugar_binding-like | cd01536 | periplasmic sugar-binding domain of active transport systems that are members of the type 1 ... |
47-256 | 3.27e-09 | |||||
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: 57.19 E-value: 3.27e-09
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| PRK10423 | PRK10423 | transcriptional repressor RbsR; Provisional |
98-224 | 1.13e-08 | |||||
transcriptional repressor RbsR; Provisional Pssm-ID: 182448 [Multi-domain] Cd Length: 327 Bit Score: 55.86 E-value: 1.13e-08
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| PBP1_LacI-like | cd06279 | ligand-binding domain of an uncharacterized transcription regulator from Corynebacterium ... |
54-239 | 1.32e-08 | |||||
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: 55.68 E-value: 1.32e-08
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| PBP1_CcpB-like | cd06286 | ligand-binding domain of a novel transcription factor implicated in catabolite repression in ... |
88-247 | 1.99e-08 | |||||
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: 54.86 E-value: 1.99e-08
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| lacI | PRK09526 | lac repressor; Reviewed |
21-267 | 2.89e-08 | |||||
lac repressor; Reviewed Pssm-ID: 181929 [Multi-domain] Cd Length: 342 Bit Score: 55.00 E-value: 2.89e-08
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| PRK10219 | PRK10219 | superoxide response transcriptional regulator SoxS; |
281-374 | 4.72e-08 | |||||
superoxide response transcriptional regulator SoxS; Pssm-ID: 182314 [Multi-domain] Cd Length: 107 Bit Score: 50.69 E-value: 4.72e-08
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| ftrA | PRK09393 | transcriptional activator FtrA; Provisional |
283-377 | 2.01e-07 | |||||
transcriptional activator FtrA; Provisional Pssm-ID: 181818 [Multi-domain] Cd Length: 322 Bit Score: 52.27 E-value: 2.01e-07
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| PBP1_RafR-like | cd20009 | Ligand-binding domain of DNA transcription repressor specific for raffinose (RafR) and similar ... |
53-242 | 4.46e-07 | |||||
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: 50.61 E-value: 4.46e-07
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| PBP1_LacI-like | cd06277 | ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ... |
90-266 | 1.15e-06 | |||||
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: 49.55 E-value: 1.15e-06
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| PRK11041 | PRK11041 | DNA-binding transcriptional regulator CytR; Provisional |
167-239 | 2.31e-06 | |||||
DNA-binding transcriptional regulator CytR; Provisional Pssm-ID: 182923 [Multi-domain] Cd Length: 309 Bit Score: 48.84 E-value: 2.31e-06
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| PBP1_ABC_sugar_binding-like | cd06319 | periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ... |
47-210 | 2.37e-06 | |||||
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: 48.51 E-value: 2.37e-06
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| PRK14987 | PRK14987 | HTH-type transcriptional regulator GntR; |
5-242 | 2.44e-06 | |||||
HTH-type transcriptional regulator GntR; Pssm-ID: 184949 [Multi-domain] Cd Length: 331 Bit Score: 48.87 E-value: 2.44e-06
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| Peripla_BP_1 | pfam00532 | Periplasmic binding proteins and sugar binding domain of LacI family; This family includes the ... |
18-239 | 2.51e-06 | |||||
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: 48.66 E-value: 2.51e-06
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| PRK10572 | PRK10572 | arabinose operon transcriptional regulator AraC; |
274-377 | 2.53e-05 | |||||
arabinose operon transcriptional regulator AraC; Pssm-ID: 236717 [Multi-domain] Cd Length: 290 Bit Score: 45.35 E-value: 2.53e-05
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| PRK10371 | PRK10371 | transcriptional regulator MelR; |
277-375 | 6.57e-05 | |||||
transcriptional regulator MelR; Pssm-ID: 182416 [Multi-domain] Cd Length: 302 Bit Score: 44.43 E-value: 6.57e-05
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| PBP1_CcpA | cd06298 | ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major ... |
195-266 | 1.50e-04 | |||||
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: 43.05 E-value: 1.50e-04
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| PBP1_galactofuranose_YtfQ-like | cd06309 | periplasmic binding domain of ABC-type galactofuranose YtfQ-like transport systems; ... |
71-256 | 1.89e-04 | |||||
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: 42.98 E-value: 1.89e-04
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| PBP1_ABC_ThpA_XypA | cd06313 | periplasmic sugar-binding proteins (ThpA and XypA) of ABC-type transport systems; This group ... |
156-248 | 2.08e-04 | |||||
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: 42.64 E-value: 2.08e-04
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| HTH_AraC | pfam00165 | Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ... |
284-325 | 7.41e-04 | |||||
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added. Pssm-ID: 425497 [Multi-domain] Cd Length: 42 Bit Score: 36.75 E-value: 7.41e-04
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| PBP1_LacI-like | cd06287 | ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ... |
167-266 | 9.95e-04 | |||||
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: 40.48 E-value: 9.95e-04
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| PRK13502 | PRK13502 | HTH-type transcriptional activator RhaR; |
304-374 | 1.67e-03 | |||||
HTH-type transcriptional activator RhaR; Pssm-ID: 184093 [Multi-domain] Cd Length: 282 Bit Score: 40.04 E-value: 1.67e-03
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| PRK13500 | PRK13500 | HTH-type transcriptional activator RhaR; |
294-374 | 5.09e-03 | |||||
HTH-type transcriptional activator RhaR; Pssm-ID: 184091 [Multi-domain] Cd Length: 312 Bit Score: 38.54 E-value: 5.09e-03
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| PBP1_ABC_sugar_binding-like | cd06322 | periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ... |
90-211 | 6.60e-03 | |||||
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: 38.03 E-value: 6.60e-03
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