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Conserved domains on  [gi|488978946|ref|WP_002889794|]
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MULTISPECIES: DNA-binding transcriptional regulator CsiR [Klebsiella]

Protein Classification

DNA-binding transcriptional regulator CsiR( domain architecture ID 11485384)

DNA-binding transcriptional regulator CsiR negatively regulates the expression of the glaH-lhgD-gabDTP operon in a temporal manner during entry into stationary phase or during the first few hours of carbon starvation

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PRK11534 PRK11534
DNA-binding transcriptional regulator CsiR; Provisional
1-224 1.43e-157

DNA-binding transcriptional regulator CsiR; Provisional


:

Pssm-ID: 183181 [Multi-domain]  Cd Length: 224  Bit Score: 435.48  E-value: 1.43e-157
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946   1 MTAIPQATAIDGYRWLKNDIICGVYHPDEKLRMSLLTSRYGLGVGPLREALSQLVAERLVTVVNQKGYRVAPMSEQELLD 80
Cdd:PRK11534   1 MTAPMQITALDGYRWLKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRVASMSEQELLD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946  81 IFDARANMEAMLVRLAIERGGDEWEAELLARAHLLNKLESCEASEHLLDEWDQRHQAFHTAIVAGCGSQYLLQMRERLFD 160
Cdd:PRK11534  81 IFDARANMEAMLVSLAIARGGDEWEADVLAKAHLLSKLEACDASEKMLDEWDLRHQAFHTAIVAGCGSHYLLQMRERLFD 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488978946 161 LAARYRFIWLRTTVLSVEMLEDKHVQHQTLVDAILARDAEQASALMREHLLTPIPIIQQAMAGK 224
Cdd:PRK11534 161 LAARYRFIWLRRTVLSVEMLEDKHDQHQTLTAAILARDTARASELMRQHLLTPIPIIQQAMAGN 224
 
Name Accession Description Interval E-value
PRK11534 PRK11534
DNA-binding transcriptional regulator CsiR; Provisional
1-224 1.43e-157

DNA-binding transcriptional regulator CsiR; Provisional


Pssm-ID: 183181 [Multi-domain]  Cd Length: 224  Bit Score: 435.48  E-value: 1.43e-157
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946   1 MTAIPQATAIDGYRWLKNDIICGVYHPDEKLRMSLLTSRYGLGVGPLREALSQLVAERLVTVVNQKGYRVAPMSEQELLD 80
Cdd:PRK11534   1 MTAPMQITALDGYRWLKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRVASMSEQELLD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946  81 IFDARANMEAMLVRLAIERGGDEWEAELLARAHLLNKLESCEASEHLLDEWDQRHQAFHTAIVAGCGSQYLLQMRERLFD 160
Cdd:PRK11534  81 IFDARANMEAMLVSLAIARGGDEWEADVLAKAHLLSKLEACDASEKMLDEWDLRHQAFHTAIVAGCGSHYLLQMRERLFD 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488978946 161 LAARYRFIWLRTTVLSVEMLEDKHVQHQTLVDAILARDAEQASALMREHLLTPIPIIQQAMAGK 224
Cdd:PRK11534 161 LAARYRFIWLRRTVLSVEMLEDKHDQHQTLTAAILARDTARASELMRQHLLTPIPIIQQAMAGN 224
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
13-222 1.48e-47

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


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 156.24  E-value: 1.48e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946  13 YRWLKNDIICGVYHPDEKLRMSLLTSRYGLGVGPLREALSQLVAERLVTVVNQKGYRVAPMSEQELLDIFDARANMEAML 92
Cdd:COG1802   17 YEALREAILSGELPPGERLSEAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARVAPLSPEEIRELYEVRAALEGLA 96
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946  93 VRLAIERGGDEWEAELLArahLLNKLESCEASEHlLDEWDQRHQAFHTAIVAGCGSQYLLQMRERLFDLAARYRFIWLRT 172
Cdd:COG1802   97 ARLAAERATPADLARLRA---LLEELEAAAAAGD-VAAYLELDREFHRALVEAAGNPRLAELLRRLRARLRRYRRLSLRS 172
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 488978946 173 TvlsvEMLEDKHVQHQTLVDAILARDAEQASALMREHLLTPIPIIQQAMA 222
Cdd:COG1802  173 P----GRLEESLAEHRAILDALEAGDAEAAAAALRAHLERARERLLEALA 218
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
80-210 1.78e-21

This entry represents the C-terminal ligand binding domain of many members of the GntR family; This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain. This domain is found in and that are regulators of sugar biosynthesis operons. Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector binding or oligomerisation domain at the C terminus. The winged-helix DNA-binding domain is well conserved in structure for the whole of the GntR family, and is similar in structure to other transcriptional regulator families. The C-terminal effector-binding and oligomerisation domains are more variable and are consequently used to define the subfamilies. Based on the sequence and structure of the C-terminal domains, the GtnR family can be divided into four major groups, as represented by FadR, HutC, MocR and YtrA, as well as some minor groups such as those represented by AraR and PlmA.


Pssm-ID: 214892 [Multi-domain]  Cd Length: 123  Bit Score: 85.87  E-value: 1.78e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946    80 DIFDARANMEAMLVRLAIERGGDEWEAELlarAHLLNKLESCEASEHLLDEWDQRHQAFHTAIVAGCGSQYLLQMRERLF 159
Cdd:smart00895   1 ELYEVRRALEPLAARLAAERATDEDLAAL---EALLDAMEAAAAAGDDLEEFAELDREFHRALAEAAGNPVLLELLESLR 77
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 488978946   160 DLAARYRFIwlrttvlSVEMLEDKHVQHQTLVDAILARDAEQASALMREHL 210
Cdd:smart00895  78 ARLRRLRRL-------SLEAARRALDEHRAILDAIRARDAEAARAAMREHL 121
FCD pfam07729
FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR ...
80-208 3.04e-19

FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR family. This domain binds to a range of effector molecules, including Lactate, Zn(II), Ni(II), Ca(II), Mg(II), citrate, sugar acids, sialic acid and N-acetylglucosamine-6-P, that regulate the transcription of genes through the action of the N-terminal DNA-binding domain pfam00392 (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). This domain is found in Swiss:P45427 and Swiss:P31460 that are regulators of sugar biosynthesis operons. It is also in the known structure of FadR where it binds to acyl-coA, the domain is alpha helical. This family has been named as FCD for (FadR C-terminal Domain).


Pssm-ID: 429623 [Multi-domain]  Cd Length: 121  Bit Score: 80.11  E-value: 3.04e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946   80 DIFDARANMEAMLVRLAIERGGDEWEAELLARAHLLNKLesceASEHLLDEWDQRHQAFHTAIVAGCGSQYLLQMRERLF 159
Cdd:pfam07729   1 ELYELRAALEPLAARLAAERATDEDLAELEALLEALEAA----ADAGDLEAFAEADREFHLALAEAAGNPVLARMLESLW 76
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 488978946  160 DLAARYRFIWLRTTVLSVEMLEdkhvQHQTLVDAILARDAEQASALMRE 208
Cdd:pfam07729  77 DRLRRLRRLLLSSPGRLRASLE----EHRAILDAIRARDPEAARAAMRR 121
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
13-71 1.27e-08

Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is presumed to result in a conformational change that regulates the DNA-binding affinity of the repressor. The GntR-like proteins bind as dimers, where each monomer recognizes a half-site of 2-fold symmetric DNA sequences.


Pssm-ID: 153418 [Multi-domain]  Cd Length: 66  Bit Score: 50.14  E-value: 1.27e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946  13 YRWLKNDIICGVYHPDEKLR-MSLLTSRYGLGVGPLREALSQLVAERLVTVVNQKGYRVA 71
Cdd:cd07377    7 ADQLREAILSGELKPGDRLPsERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFVA 66
 
Name Accession Description Interval E-value
PRK11534 PRK11534
DNA-binding transcriptional regulator CsiR; Provisional
1-224 1.43e-157

DNA-binding transcriptional regulator CsiR; Provisional


Pssm-ID: 183181 [Multi-domain]  Cd Length: 224  Bit Score: 435.48  E-value: 1.43e-157
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946   1 MTAIPQATAIDGYRWLKNDIICGVYHPDEKLRMSLLTSRYGLGVGPLREALSQLVAERLVTVVNQKGYRVAPMSEQELLD 80
Cdd:PRK11534   1 MTAPMQITALDGYRWLKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRVASMSEQELLD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946  81 IFDARANMEAMLVRLAIERGGDEWEAELLARAHLLNKLESCEASEHLLDEWDQRHQAFHTAIVAGCGSQYLLQMRERLFD 160
Cdd:PRK11534  81 IFDARANMEAMLVSLAIARGGDEWEADVLAKAHLLSKLEACDASEKMLDEWDLRHQAFHTAIVAGCGSHYLLQMRERLFD 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488978946 161 LAARYRFIWLRTTVLSVEMLEDKHVQHQTLVDAILARDAEQASALMREHLLTPIPIIQQAMAGK 224
Cdd:PRK11534 161 LAARYRFIWLRRTVLSVEMLEDKHDQHQTLTAAILARDTARASELMRQHLLTPIPIIQQAMAGN 224
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
13-222 1.48e-47

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


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 156.24  E-value: 1.48e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946  13 YRWLKNDIICGVYHPDEKLRMSLLTSRYGLGVGPLREALSQLVAERLVTVVNQKGYRVAPMSEQELLDIFDARANMEAML 92
Cdd:COG1802   17 YEALREAILSGELPPGERLSEAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARVAPLSPEEIRELYEVRAALEGLA 96
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946  93 VRLAIERGGDEWEAELLArahLLNKLESCEASEHlLDEWDQRHQAFHTAIVAGCGSQYLLQMRERLFDLAARYRFIWLRT 172
Cdd:COG1802   97 ARLAAERATPADLARLRA---LLEELEAAAAAGD-VAAYLELDREFHRALVEAAGNPRLAELLRRLRARLRRYRRLSLRS 172
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 488978946 173 TvlsvEMLEDKHVQHQTLVDAILARDAEQASALMREHLLTPIPIIQQAMA 222
Cdd:COG1802  173 P----GRLEESLAEHRAILDALEAGDAEAAAAALRAHLERARERLLEALA 218
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
13-222 4.83e-26

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 100.78  E-value: 4.83e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946  13 YRWLKNDIICGVYHPDEKL---RMslLTSRYGLGVGPLREALSQLVAERLVTVVNQKGYRVAPMSEQELL---------- 79
Cdd:COG2186   13 AEQLRELILSGELKPGDRLpseRE--LAEQLGVSRTTVREALRALEALGLVEVRQGGGTFVREPSPWALLdplalllald 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946  80 -----DIFDARANMEAMLVRLAIERGGDEweaellARAHLLNKLESCEASEHLLDEWDQRHQAFHTAIVAGCGSQYLLQM 154
Cdd:COG2186   91 daslrDLLEARLALEPEAARLAAERATDE------DLARLEAALAEMEAAADDGEAFAEADLAFHRAIAEASGNPLLALL 164
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488978946 155 RERLFDLAARYRfiwlRTTVLSVEMLEDKHVQHQTLVDAILARDAEQASALMREHLLTPIPIIQQAMA 222
Cdd:COG2186  165 LESLRELLRRSV----RLTLRSPEARERSLAEHRAILDAIRAGDPEAARAAMRAHLEAVRERLREALA 228
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
80-210 1.78e-21

This entry represents the C-terminal ligand binding domain of many members of the GntR family; This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain. This domain is found in and that are regulators of sugar biosynthesis operons. Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector binding or oligomerisation domain at the C terminus. The winged-helix DNA-binding domain is well conserved in structure for the whole of the GntR family, and is similar in structure to other transcriptional regulator families. The C-terminal effector-binding and oligomerisation domains are more variable and are consequently used to define the subfamilies. Based on the sequence and structure of the C-terminal domains, the GtnR family can be divided into four major groups, as represented by FadR, HutC, MocR and YtrA, as well as some minor groups such as those represented by AraR and PlmA.


Pssm-ID: 214892 [Multi-domain]  Cd Length: 123  Bit Score: 85.87  E-value: 1.78e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946    80 DIFDARANMEAMLVRLAIERGGDEWEAELlarAHLLNKLESCEASEHLLDEWDQRHQAFHTAIVAGCGSQYLLQMRERLF 159
Cdd:smart00895   1 ELYEVRRALEPLAARLAAERATDEDLAAL---EALLDAMEAAAAAGDDLEEFAELDREFHRALAEAAGNPVLLELLESLR 77
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 488978946   160 DLAARYRFIwlrttvlSVEMLEDKHVQHQTLVDAILARDAEQASALMREHL 210
Cdd:smart00895  78 ARLRRLRRL-------SLEAARRALDEHRAILDAIRARDAEAARAAMREHL 121
FCD pfam07729
FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR ...
80-208 3.04e-19

FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR family. This domain binds to a range of effector molecules, including Lactate, Zn(II), Ni(II), Ca(II), Mg(II), citrate, sugar acids, sialic acid and N-acetylglucosamine-6-P, that regulate the transcription of genes through the action of the N-terminal DNA-binding domain pfam00392 (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). This domain is found in Swiss:P45427 and Swiss:P31460 that are regulators of sugar biosynthesis operons. It is also in the known structure of FadR where it binds to acyl-coA, the domain is alpha helical. This family has been named as FCD for (FadR C-terminal Domain).


Pssm-ID: 429623 [Multi-domain]  Cd Length: 121  Bit Score: 80.11  E-value: 3.04e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946   80 DIFDARANMEAMLVRLAIERGGDEWEAELLARAHLLNKLesceASEHLLDEWDQRHQAFHTAIVAGCGSQYLLQMRERLF 159
Cdd:pfam07729   1 ELYELRAALEPLAARLAAERATDEDLAELEALLEALEAA----ADAGDLEAFAEADREFHLALAEAAGNPVLARMLESLW 76
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 488978946  160 DLAARYRFIWLRTTVLSVEMLEdkhvQHQTLVDAILARDAEQASALMRE 208
Cdd:pfam07729  77 DRLRRLRRLLLSSPGRLRASLE----EHRAILDAIRARDPEAARAAMRR 121
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
13-70 7.63e-12

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 58.74  E-value: 7.63e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 488978946    13 YRWLKNDIICGVYHPDEKLR-MSLLTSRYGLGVGPLREALSQLVAERLVTVVNQKGYRV 70
Cdd:smart00345   2 AERLREDIVSGELRPGDKLPsERELAAQLGVSRTTVREALSRLEAEGLVQRRPGSGTFV 60
PRK03837 PRK03837
transcriptional regulator NanR; Provisional
16-210 4.29e-09

transcriptional regulator NanR; Provisional


Pssm-ID: 235166 [Multi-domain]  Cd Length: 241  Bit Score: 55.03  E-value: 4.29e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946  16 LKNDIICGVYHPDEKL---RMslLTSRYGLGVGPLREALSQLVAERLVTVVNQKGYRV------------APMSEQEL-- 78
Cdd:PRK03837  22 LEQMIRSGEFGPGDQLpseRE--LMAFFGVGRPAVREALQALKRKGLVQISHGERARVsrpsadtiigqlSGMAKDFLsq 99
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946  79 ----LDIFD-ARANMEAMLVRLAIERGGDEWEAELLARahllnkLESCEASEHLLDEWDQRHQAFHTAIVAGCGSQYLLQ 153
Cdd:PRK03837 100 spdgLAHLKqARLFFESSLARYAAEHATDEQIALLRKA------LERNSQSLGDNAAFIRSDMEFHRVIAEIPGNPIFMA 173
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 488978946 154 MRERLFDLAARYRfiwlrTTVLSVEMLEDK-HVQHQTLVDAILARDAEQASALMREHL 210
Cdd:PRK03837 174 IHEALLDWLIEAR-----PEVVILHGHENVtLQEHIAIVDAIRAHDPDEADRALQSHL 226
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
13-71 1.27e-08

Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is presumed to result in a conformational change that regulates the DNA-binding affinity of the repressor. The GntR-like proteins bind as dimers, where each monomer recognizes a half-site of 2-fold symmetric DNA sequences.


Pssm-ID: 153418 [Multi-domain]  Cd Length: 66  Bit Score: 50.14  E-value: 1.27e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946  13 YRWLKNDIICGVYHPDEKLR-MSLLTSRYGLGVGPLREALSQLVAERLVTVVNQKGYRVA 71
Cdd:cd07377    7 ADQLREAILSGELKPGDRLPsERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFVA 66
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
13-70 7.32e-08

Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerization domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor.


Pssm-ID: 306822 [Multi-domain]  Cd Length: 64  Bit Score: 47.99  E-value: 7.32e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 488978946   13 YRWLKNDIICGVYHPDEKL-RMSLLTSRYGLGVGPLREALSQLVAERLVTVVNQKGYRV 70
Cdd:pfam00392   6 YARLREDILSGRLRPGDKLpSERELAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
PRK10421 PRK10421
DNA-binding transcriptional repressor LldR; Provisional
42-210 3.93e-07

DNA-binding transcriptional repressor LldR; Provisional


Pssm-ID: 236690 [Multi-domain]  Cd Length: 253  Bit Score: 49.38  E-value: 3.93e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946  42 LGVG--PLREALSQLVAERLVTVVNQKG----YRVAPMSEQELLDIF------DARANMEAMLVRLAIErGGDEWEAELL 109
Cdd:PRK10421  36 LGVSrnSLREALAKLVSEGVLLSRRGGGtfirWRHETWSEQNIVQPLktlmadDPDYSFDILEARHAIE-ASTAWHAAMR 114
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946 110 ARAHLLNKLESCeASEHLLDEWDQRHQA---FHTAIVAGCGSQYLLQMRERLFDLAaRYRFIWLRTTVLSVEMLEDK-HV 185
Cdd:PRK10421 115 ATPGDKEKIQLC-FEATLSEDPDLASQAdvrFHLAIAEASHNVVLLQTMRGFFDVL-QSSVKQSRQRMYLVPPVFSQlTE 192
                        170       180
                 ....*....|....*....|....*
gi 488978946 186 QHQTLVDAILARDAEQASALMREHL 210
Cdd:PRK10421 193 QHQAVMDAILAGDAEGARKAMMAHL 217
PRK09990 PRK09990
DNA-binding transcriptional regulator GlcC; Provisional
36-210 7.78e-06

DNA-binding transcriptional regulator GlcC; Provisional


Pssm-ID: 182186 [Multi-domain]  Cd Length: 251  Bit Score: 45.53  E-value: 7.78e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946  36 LTSRYGLGVGPLREALSQLVAERLVTVVNQKGYRVAPMSEQE---------------LLDIFDARANMEAMLVRLAIERG 100
Cdd:PRK09990  37 LCEKLGFSRSALREGLTVLRGRGIIETAQGRGSFVARLNRVQdasplmhlfssqprtLYDLLEVRALLEGESARLAALRG 116
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946 101 GD--------EWEaELLArAHLLNKleSCEASEHLldewdQRHQAFHTAIVAGCGSQYLLQMRERLFDLAaryrfiwLRT 172
Cdd:PRK09990 117 TQadfvlitrRYE-EMLA-AHENNK--EIDPIEHA-----RLDHAFHLAICEASHNPVLVHTLQSLTDLM-------LSS 180
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 488978946 173 TVLSVEML-----EDKHV--QHQTLVDAILARDAEQASALMREHL 210
Cdd:PRK09990 181 VFASVNNLyhrpqQKKQIdrQHARLYNAVLQRLPEQAQRAARDHI 225
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
13-109 3.91e-05

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


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 43.31  E-value: 3.91e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946  13 YRWLKNDIICGVYHPDEKL-RMSLLTSRYGLGVGPLREALSQLVAERLVTVVNQKGYRVA-PMSEQELLDIFDARANMEA 90
Cdd:COG2188   11 ADALRERIESGELPPGDRLpSERELAEEFGVSRMTVRKALDELVEEGLLERRQGRGTFVAePKIEYPLSRLTSFTEELRA 90
                         90       100
                 ....*....|....*....|....*.
gi 488978946  91 M-------LVRLAIERgGDEWEAELL 109
Cdd:COG2188   91 RgrepstrVLSAERVP-ADEEVAEAL 115
PRK11414 PRK11414
GntR family transcriptional regulator;
16-119 8.03e-05

GntR family transcriptional regulator;


Pssm-ID: 183126 [Multi-domain]  Cd Length: 221  Bit Score: 42.16  E-value: 8.03e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488978946  16 LKNDIICGVYHPDEKLRMSLLTSRYGLGVGPLREALSQLVAERLVTVVNQKGYRVAPMSEQELLDIFDARANMEAMLVRL 95
Cdd:PRK11414  20 LKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQAFTVPEVSKRQLDEINRIRYELELMAVAL 99
                         90       100
                 ....*....|....*....|....
gi 488978946  96 AIERGGDEWEAELLArahLLNKLE 119
Cdd:PRK11414 100 AVENLTPQDLAELQE---LLEKLQ 120
 
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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