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Conserved domains on  [gi|490588946|ref|WP_004453966|]
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sugar-binding transcriptional regulator [Clostridioides difficile]

Protein Classification

sugar-binding transcriptional regulator( domain architecture ID 11457260)

sugar-binding transcriptional regulator similar to Priestia megaterium central glycolytic genes regulator, in the absence of glucose, which represses the transcription of the gapA operon that encodes five key glycolytic enzymes

CATH:  1.10.10.60|3.40.50.1360
Gene Ontology:  GO:0030246|GO:0003677|GO:0006355
PubMed:  19232357
SCOP:  4002188

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
12-314 3.27e-116

DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];


:

Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 337.10  E-value: 3.27e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490588946  12 KCCSLYYEDNLNQQEIANQLGISRPTISRILKEAFEQGIVKIQIVDVLkNDYQKIERSLERKYKLKEVIVV-DDKQDALT 90
Cdd:COG2390    1 RAAWLYYVEGLTQREIAERLGISRRTVSRLLAEAREEGLVRISITDPL-AGLLELERELRERFGLKEVIVVpGDSDDDEE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490588946  91 QKQELARAVSEYLTRVVKENDIIGVSIGTTLKEIPRYVEKSNCKNVTFIPLLGGIGDNeIDIHANQIAVSLARAFGGDFK 170
Cdd:COG2390   80 VLRALGRAAAEYLERLLKDGDVIGVGWGRTLAAVAEALPPLPLPDVTVVPLRGGLGED-VEAQANEIARRLAEKLGGEYY 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490588946 171 LLHAPAVMSDLSTKEKLCKDEKIKEVLDLIDKTTIAIVGIGNPMSlNSTIMASGYMNEADIEDLKKYNSIGAICLQAFDK 250
Cdd:COG2390  159 LLPAPAIVDSAETREALLEEPSIREVLELARRADVALVGIGSADP-DSTLARRGYLSEEELAELRAAGAVGDICGRFFDA 237

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490588946 251 EGKTSILEFNQRVLGVKLEDLKKIKRTIGVASGDEKIEAIKASLKAKFINSLAINHSLALKLLE 314
Cdd:COG2390  238 DGRIVDTPLNDRTIGISLEDLRRIPRVIAVAGGEEKAEAILAALRGGYINVLITDEATARALLE 301
 
Name Accession Description Interval E-value
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
12-314 3.27e-116

DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 337.10  E-value: 3.27e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490588946  12 KCCSLYYEDNLNQQEIANQLGISRPTISRILKEAFEQGIVKIQIVDVLkNDYQKIERSLERKYKLKEVIVV-DDKQDALT 90
Cdd:COG2390    1 RAAWLYYVEGLTQREIAERLGISRRTVSRLLAEAREEGLVRISITDPL-AGLLELERELRERFGLKEVIVVpGDSDDDEE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490588946  91 QKQELARAVSEYLTRVVKENDIIGVSIGTTLKEIPRYVEKSNCKNVTFIPLLGGIGDNeIDIHANQIAVSLARAFGGDFK 170
Cdd:COG2390   80 VLRALGRAAAEYLERLLKDGDVIGVGWGRTLAAVAEALPPLPLPDVTVVPLRGGLGED-VEAQANEIARRLAEKLGGEYY 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490588946 171 LLHAPAVMSDLSTKEKLCKDEKIKEVLDLIDKTTIAIVGIGNPMSlNSTIMASGYMNEADIEDLKKYNSIGAICLQAFDK 250
Cdd:COG2390  159 LLPAPAIVDSAETREALLEEPSIREVLELARRADVALVGIGSADP-DSTLARRGYLSEEELAELRAAGAVGDICGRFFDA 237

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490588946 251 EGKTSILEFNQRVLGVKLEDLKKIKRTIGVASGDEKIEAIKASLKAKFINSLAINHSLALKLLE 314
Cdd:COG2390  238 DGRIVDTPLNDRTIGISLEDLRRIPRVIAVAGGEEKAEAILAALRGGYINVLITDEATARALLE 301
Sugar-bind pfam04198
Putative sugar-binding domain; This probable domain is found in bacterial transcriptional ...
 65-314 3.88e-65

Putative sugar-binding domain; This probable domain is found in bacterial transcriptional regulators such as DeoR and SorC. These proteins have an amino-terminal helix-turn-helix pfam00325 that binds to DNA. This domain is probably the ligand regulator binding region. SorC is regulated by sorbose and other members of this family are likely to be regulated by other sugar substrates.


Pssm-ID: 427778  Cd Length: 256  Bit Score: 205.55  E-value: 3.88e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490588946   65 KIERSLERKYKLKEVIVVDDKQDAL-TQKQELARAVSEYLTRVVKENDIIGVSIGTTLKEIPRYVEKSNCKNVTFIPLLG 143
Cdd:pfam04198   8 DLEQRLKEKFGLKEAIVVPGDSDENdLVLERLGRAAAQYLESLLKDGDIVGVGWGRTLSAVAEALTPKSLRNLKFVPLIG 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490588946  144 GIGDNeIDIHANQIAVSLARAFGGDFKLLHAPAVMSDLSTKEKLCKDEKIKEVLDLIDKTTIAIVGIGNpMSLNSTIMAS 223
Cdd:pfam04198  88 GLGRD-GSAHSNTVIARLAQKFGGSYYLLPAPAYASNAALRRGLLAERSVKSVLDLARRADVAIVGIGS-ASEMAPLFRR 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490588946  224 GYMNEADIEDLKKYNSIGAICLQAFDKEGKTSILEFNQRVLGVKLEDLKKIKRTIGVASGDEKIEAIKASLKAKFINSLA 303
Cdd:pfam04198 166 GYLTEEELAELRELGAVGEIFGRFFDAEGRVVDTALNERVIGLDLEDLRDIPNVIAIAGGESKAEAILAALRGGYINVLI 245

                         250
                  ....*....|.
gi 490588946  304 INHSLALKLLE 314
Cdd:pfam04198 246 TDESTARALLA 256
PRK15418 PRK15418
transcriptional regulator LsrR; Provisional
 17-313 1.77e-28

transcriptional regulator LsrR; Provisional


Pssm-ID: 237962 [Multi-domain]  Cd Length: 318  Bit Score: 111.74  E-value: 1.77e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490588946  17 YYEDNLNQQEIANQLGISRPTISRILKEAFEQGIVKIQIvdvlKNDYQ---KIERSLERKYKLKEVIVVDDKQDAlTQKQ 93
Cdd:PRK15418  25 YYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQI----NSRFEgclELENALRQHFSLQHIRVLPALADA-DIGG 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490588946  94 ELARAVSEYLTRVVKENDIIGVSIG-TTLKEIPRYVEKSNCKNVTFIPLLGGIGDNEIDIHANQIAVSLArafggdfkLL 172
Cdd:PRK15418 100 RLGIGAAHMLMSLLQPQQLLAVGFGeATMNTLQHLSGFISSQQIRLVTLSGGVGPYMTGIGQLDAACSVS--------II 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490588946 173 HAPAVMSDLSTKEKLCKDEKIKEVLDLIDKTTIAIVGIGnpmSLN----STIMASGYMNEADIEDLKKYNSIGAICLQAF 248
Cdd:PRK15418 172 PAPLRASSAEIARTLRNENSVRDVMLAAQAADVAIVGIG---AVNqkddATILRSGYISQGEQLMIGRKGAVGDILGYFF 248

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490588946 249 DKEGK-TSILEFNQRVLGVKLEDLKKIKRTIGVASGDEKIEAIKASLKAKFINSLAINHSLALKLL 313
Cdd:PRK15418 249 DADGElVPDIKIHNELIGLPLSSLKTIPTVIGVAGGEEKAEAIIAALKGGYINALVTDEKTARAIL 314
HTH_CRP smart00419
helix_turn_helix, cAMP Regulatory protein;
22-54 1.57e-06

helix_turn_helix, cAMP Regulatory protein;


Pssm-ID: 128696 [Multi-domain]  Cd Length: 48  Bit Score: 44.35  E-value: 1.57e-06
                           10        20        30
                   ....*....|....*....|....*....|...
gi 490588946    22 LNQQEIANQLGISRPTISRILKEAFEQGIVKIQ 54
Cdd:smart00419   9 LTRQEIAELLGLTRETVSRTLKRLEKEGLISRE 41
HTH_CRP cd00092
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic ...
 22-54 4.29e-05

helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.


Pssm-ID: 238044 [Multi-domain]  Cd Length: 67  Bit Score: 40.73  E-value: 4.29e-05
                         10        20        30
                 ....*....|....*....|....*....|...
gi 490588946  22 LNQQEIANQLGISRPTISRILKEAFEQGIVKIQ 54
Cdd:cd00092   26 LTRQEIADYLGLTRETVSRTLKELEEEGLISRR 58
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 16-45 2.55e-04

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 40.79  E-value: 2.55e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 490588946   16 LYYEDNLNQQEIANQLGISRPTISRILKEA 45
Cdd:TIGR02937 121 LRYLEGLSYKEIAEILGISVGTVKRRLKRA 150
transpos_IS21 NF033546
IS21 family transposase;
16-45 1.63e-03

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 39.50  E-value: 1.63e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 490588946  16 LYYEDNLNQQEIANQLGISRPTISRILKEA 45
Cdd:NF033546   3 LLFRQGLSIREIARELGISRNTVRKYLRRA 32
 
Name Accession Description Interval E-value
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
12-314 3.27e-116

DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 337.10  E-value: 3.27e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490588946  12 KCCSLYYEDNLNQQEIANQLGISRPTISRILKEAFEQGIVKIQIVDVLkNDYQKIERSLERKYKLKEVIVV-DDKQDALT 90
Cdd:COG2390    1 RAAWLYYVEGLTQREIAERLGISRRTVSRLLAEAREEGLVRISITDPL-AGLLELERELRERFGLKEVIVVpGDSDDDEE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490588946  91 QKQELARAVSEYLTRVVKENDIIGVSIGTTLKEIPRYVEKSNCKNVTFIPLLGGIGDNeIDIHANQIAVSLARAFGGDFK 170
Cdd:COG2390   80 VLRALGRAAAEYLERLLKDGDVIGVGWGRTLAAVAEALPPLPLPDVTVVPLRGGLGED-VEAQANEIARRLAEKLGGEYY 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490588946 171 LLHAPAVMSDLSTKEKLCKDEKIKEVLDLIDKTTIAIVGIGNPMSlNSTIMASGYMNEADIEDLKKYNSIGAICLQAFDK 250
Cdd:COG2390  159 LLPAPAIVDSAETREALLEEPSIREVLELARRADVALVGIGSADP-DSTLARRGYLSEEELAELRAAGAVGDICGRFFDA 237

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490588946 251 EGKTSILEFNQRVLGVKLEDLKKIKRTIGVASGDEKIEAIKASLKAKFINSLAINHSLALKLLE 314
Cdd:COG2390  238 DGRIVDTPLNDRTIGISLEDLRRIPRVIAVAGGEEKAEAILAALRGGYINVLITDEATARALLE 301
Sugar-bind pfam04198
Putative sugar-binding domain; This probable domain is found in bacterial transcriptional ...
 65-314 3.88e-65

Putative sugar-binding domain; This probable domain is found in bacterial transcriptional regulators such as DeoR and SorC. These proteins have an amino-terminal helix-turn-helix pfam00325 that binds to DNA. This domain is probably the ligand regulator binding region. SorC is regulated by sorbose and other members of this family are likely to be regulated by other sugar substrates.


Pssm-ID: 427778  Cd Length: 256  Bit Score: 205.55  E-value: 3.88e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490588946   65 KIERSLERKYKLKEVIVVDDKQDAL-TQKQELARAVSEYLTRVVKENDIIGVSIGTTLKEIPRYVEKSNCKNVTFIPLLG 143
Cdd:pfam04198   8 DLEQRLKEKFGLKEAIVVPGDSDENdLVLERLGRAAAQYLESLLKDGDIVGVGWGRTLSAVAEALTPKSLRNLKFVPLIG 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490588946  144 GIGDNeIDIHANQIAVSLARAFGGDFKLLHAPAVMSDLSTKEKLCKDEKIKEVLDLIDKTTIAIVGIGNpMSLNSTIMAS 223
Cdd:pfam04198  88 GLGRD-GSAHSNTVIARLAQKFGGSYYLLPAPAYASNAALRRGLLAERSVKSVLDLARRADVAIVGIGS-ASEMAPLFRR 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490588946  224 GYMNEADIEDLKKYNSIGAICLQAFDKEGKTSILEFNQRVLGVKLEDLKKIKRTIGVASGDEKIEAIKASLKAKFINSLA 303
Cdd:pfam04198 166 GYLTEEELAELRELGAVGEIFGRFFDAEGRVVDTALNERVIGLDLEDLRDIPNVIAIAGGESKAEAILAALRGGYINVLI 245

                         250
                  ....*....|.
gi 490588946  304 INHSLALKLLE 314
Cdd:pfam04198 246 TDESTARALLA 256
PRK15418 PRK15418
transcriptional regulator LsrR; Provisional
 17-313 1.77e-28

transcriptional regulator LsrR; Provisional


Pssm-ID: 237962 [Multi-domain]  Cd Length: 318  Bit Score: 111.74  E-value: 1.77e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490588946  17 YYEDNLNQQEIANQLGISRPTISRILKEAFEQGIVKIQIvdvlKNDYQ---KIERSLERKYKLKEVIVVDDKQDAlTQKQ 93
Cdd:PRK15418  25 YYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQI----NSRFEgclELENALRQHFSLQHIRVLPALADA-DIGG 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490588946  94 ELARAVSEYLTRVVKENDIIGVSIG-TTLKEIPRYVEKSNCKNVTFIPLLGGIGDNEIDIHANQIAVSLArafggdfkLL 172
Cdd:PRK15418 100 RLGIGAAHMLMSLLQPQQLLAVGFGeATMNTLQHLSGFISSQQIRLVTLSGGVGPYMTGIGQLDAACSVS--------II 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490588946 173 HAPAVMSDLSTKEKLCKDEKIKEVLDLIDKTTIAIVGIGnpmSLN----STIMASGYMNEADIEDLKKYNSIGAICLQAF 248
Cdd:PRK15418 172 PAPLRASSAEIARTLRNENSVRDVMLAAQAADVAIVGIG---AVNqkddATILRSGYISQGEQLMIGRKGAVGDILGYFF 248

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490588946 249 DKEGK-TSILEFNQRVLGVKLEDLKKIKRTIGVASGDEKIEAIKASLKAKFINSLAINHSLALKLL 313
Cdd:PRK15418 249 DADGElVPDIKIHNELIGLPLSSLKTIPTVIGVAGGEEKAEAIIAALKGGYINALVTDEKTARAIL 314
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 8-45 4.25e-07

DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 50.21  E-value: 4.25e-07
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 490588946   8 RLMMkccSLYYEDNLNQQEIANQLGISRPTISRILKEA 45
Cdd:COG1191  192 RLVL---SLYYFEELTLKEIAEVLGVSESRVSRLHKKA 226
HTH_CRP smart00419
helix_turn_helix, cAMP Regulatory protein;
22-54 1.57e-06

helix_turn_helix, cAMP Regulatory protein;


Pssm-ID: 128696 [Multi-domain]  Cd Length: 48  Bit Score: 44.35  E-value: 1.57e-06
                           10        20        30
                   ....*....|....*....|....*....|...
gi 490588946    22 LNQQEIANQLGISRPTISRILKEAFEQGIVKIQ 54
Cdd:smart00419   9 LTRQEIAELLGLTRETVSRTLKRLEKEGLISRE 41
HTH_Crp_2 pfam13545
Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain ...
 7-58 3.80e-06

Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain that is likely to bind DNA.


Pssm-ID: 463917 [Multi-domain]  Cd Length: 68  Bit Score: 43.98  E-value: 3.80e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 490588946    7 LRLMMKCCSLYYEDNLNQQEIANQLGISRPTISRILKEAFEQGIV---KIQIVDV 58
Cdd:pfam13545   8 LELAARDGGGRIDLPLTQEDLADLLGTTRETVSRVLSELRREGLIergRITILDP 62
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 15-48 6.31e-06

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 42.80  E-value: 6.31e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 490588946   15 SLYYEDNLNQQEIANQLGISRPTISRILKEAFEQ 48
Cdd:pfam04545  14 VLRYGEGLTLEEIGERLGISRERVRQIEKRALRK 47
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 21-58 1.99e-05

cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms];


Pssm-ID: 440428 [Multi-domain]  Cd Length: 207  Bit Score: 44.59  E-value: 1.99e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 490588946  21 NLNQQEIANQLGISRPTISRILKEAFEQGIV-----KIQIVDV 58
Cdd:COG0664  158 PLTQEEIASYLGLTRETVSRILKKLEKEGLIelergRITILDR 200
COG1342 COG1342
Predicted DNA-binding protein, UPF0251 family [General function prediction only];
7-45 2.33e-05

Predicted DNA-binding protein, UPF0251 family [General function prediction only];


Pssm-ID: 440953  Cd Length: 99  Bit Score: 42.43  E-value: 2.33e-05
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 490588946   7 LRLMmkccslYYEdNLNQQEIANQLGISRPTISRILKEA 45
Cdd:COG1342   42 IRLV------DLE-GLTQEEAAEKMGVSRPTFQRILKSA 73
HTH_CRP cd00092
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic ...
 22-54 4.29e-05

helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.


Pssm-ID: 238044 [Multi-domain]  Cd Length: 67  Bit Score: 40.73  E-value: 4.29e-05
                         10        20        30
                 ....*....|....*....|....*....|...
gi 490588946  22 LNQQEIANQLGISRPTISRILKEAFEQGIVKIQ 54
Cdd:cd00092   26 LTRQEIADYLGLTRETVSRTLKELEEEGLISRR 58
MarR_2 pfam12802
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 16-54 7.05e-05

MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.


Pssm-ID: 432797 [Multi-domain]  Cd Length: 60  Bit Score: 39.88  E-value: 7.05e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 490588946   16 LYYEDNLNQQEIANQLGISRPTISRILKEAFEQGIVKIQ 54
Cdd:pfam12802  14 LARNPGLTVAELARRLGISKQTVSRLVKRLEAKGLVERE 52
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 16-45 2.55e-04

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 40.79  E-value: 2.55e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 490588946   16 LYYEDNLNQQEIANQLGISRPTISRILKEA 45
Cdd:TIGR02937 121 LRYLEGLSYKEIAEILGISVGTVKRRLKRA 150
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 16-48 3.76e-04

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 37.85  E-value: 3.76e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 490588946  16 LYYEDNLNQQEIANQLGISRPTISRILKEAFEQ 48
Cdd:cd06171   21 LRFGEGLSYEEIAEILGISRSTVRQRLHRALKK 53
MarR pfam01047
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 14-51 1.00e-03

MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.


Pssm-ID: 426012 [Multi-domain]  Cd Length: 59  Bit Score: 36.76  E-value: 1.00e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 490588946   14 CSLYYEDNLNQQEIANQLGISRPTISRILKEAFEQGIV 51
Cdd:pfam01047  10 RILYEHGPLTVSELAEKLGVSKSTVTRVLDRLEKKGLI 47
transpos_IS21 NF033546
IS21 family transposase;
16-45 1.63e-03

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 39.50  E-value: 1.63e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 490588946  16 LYYEDNLNQQEIANQLGISRPTISRILKEA 45
Cdd:NF033546   3 LLFRQGLSIREIARELGISRNTVRKYLRRA 32
SigBFG TIGR02980
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ...
 16-48 1.86e-03

RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.


Pssm-ID: 274373 [Multi-domain]  Cd Length: 227  Bit Score: 39.13  E-value: 1.86e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 490588946   16 LYYEDNLNQQEIANQLGISRPTISRILKEAFEQ 48
Cdd:TIGR02980 189 LRFFEDKTQSEIAERLGISQMHVSRLLRRALKK 221
COG3398 COG3398
Predicted transcriptional regulator, contains two HTH domains [Transcription];
16-51 3.16e-03

Predicted transcriptional regulator, contains two HTH domains [Transcription];


Pssm-ID: 442625 [Multi-domain]  Cd Length: 159  Bit Score: 37.55  E-value: 3.16e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 490588946  16 LYYEDNLNQQEIANQLGISRPTISRILKEAFEQGIV 51
Cdd:COG3398  106 LLENPGATNKELAEELGISRSTVSWHLKRLEEDGLV 141
COG4584 COG4584
Transposase [Mobilome: prophages, transposons];
1-47 3.31e-03

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 443641 [Multi-domain]  Cd Length: 484  Bit Score: 39.05  E-value: 3.31e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 490588946   1 MKKIGDLRLMMKccslYYEDNLNQQEIANQLGISRPTISRILKEAFE 47
Cdd:COG4584    1 MLTMEQIREIRR----LLREGLSIREIARELGISRNTVRKYLRRAEE 43
COG2512 COG2512
Predicted transcriptional regulator, contains CW (cell wall-binding) repeats and an HTH domain ...
 22-53 3.35e-03

Predicted transcriptional regulator, contains CW (cell wall-binding) repeats and an HTH domain [General function prediction only];


Pssm-ID: 442002 [Multi-domain]  Cd Length: 80  Bit Score: 36.04  E-value: 3.35e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 490588946  22 LNQQEIANQLGISRPTISRILKEAFEQGIVKI 53
Cdd:COG2512   31 MTQSEIVKETGWSKSKVSRLLSRLEERGLIEK 62
HTH_23 pfam13384
Homeodomain-like domain;
6-50 3.83e-03

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 34.94  E-value: 3.83e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 490588946    6 DLRLMMKCCSLY-YEDNLNQQEIANQLGISRPTISRILKEAFEQGI 50
Cdd:pfam13384   1 SARERRRARALLlLAEGLSVKEIAELLGVSRRTVYRWLKRYNEEGL 46
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
21-55 6.08e-03

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 35.36  E-value: 6.08e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 490588946  21 NLNQQEIANQLGISRPTISRIlkeafEQGIVKIQI 55
Cdd:COG1396   20 GLTQEELAERLGVSRSTISRI-----ERGRRNPSL 49
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
16-52 6.69e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 36.49  E-value: 6.69e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 490588946  16 LYYEDNLNQQEIANQLGISRPTISRILKEAFEQGIVK 52
Cdd:COG1846   47 LAEAGGLTQSELAERLGLTKSTVSRLLDRLEEKGLVE 83
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 21-44 7.46e-03

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 35.17  E-value: 7.46e-03
                         10        20
                 ....*....|....*....|....
gi 490588946  21 NLNQQEIANQLGISRPTISRILKE 44
Cdd:COG3093   22 GLSQTELAKALGVSRQRISEILNG 45
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
14-54 8.91e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 35.26  E-value: 8.91e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 490588946    14 CSLYYEDNLNQQEIANQLGISRPTISRILKEAFEQGIVKIQ 54
Cdd:smart00347  17 RILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLVRRE 57
 
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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