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Conserved domains on  [gi|1134749482|ref|NP_313031|]
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sor-operon regulator [Escherichia coli O157:H7 str. Sakai]

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];
12-315 5.55e-113

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


:

Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 329.01  E-value: 5.55e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482  12 KIAQLYYEQDMTQAQIARELGIYRTNISRLLKRGRDQGIVTIAINYDYNENLWLEQQLKQKFGLKDVVVVSGNDEDEETQ 91
Cdd:COG2390     1 RAAWLYYVEGLTQREIAERLGISRRTVSRLLAEAREEGLVRISITDPLAGLLELERELRERFGLKEVIVVPGDSDDDEEV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482  92 LAMMGLHGAQLLDRLLEPGDIVGFSWGRAVSALVENLPqAGQSRQLICVPIIGGPSGKleSRYHVNTLTYSAAAKLKGES 171
Cdd:COG2390    81 LRALGRAAAEYLERLLKDGDVIGVGWGRTLAAVAEALP-PLPLPDVTVVPLRGGLGED--VEAQANEIARRLAEKLGGEY 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482 172 HLADFPALLDNPLIRNGIMQSQHFKTISAYWDNLDVALVGIGSPAIRDGANWHAFYGGEESDDLNARQVAGDICSRFFDI 251
Cdd:COG2390   158 YLLPAPAIVDSAETREALLEEPSIREVLELARRADVALVGIGSADPDSTLARRGYLSEEELAELRAAGAVGDICGRFFDA 237

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1134749482 252 HGEMVETNMSEKTLSIEMNKLKQARYSIGIAMSEEKYSGIIGALRGKYINCLVTNSSTAELLLK 315
Cdd:COG2390   238 DGRIVDTPLNDRTIGISLEDLRRIPRVIAVAGGEEKAEAILAALRGGYINVLITDEATARALLE 301
 
Name Accession Description Interval E-value
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
12-315 5.55e-113

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


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 329.01  E-value: 5.55e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482  12 KIAQLYYEQDMTQAQIARELGIYRTNISRLLKRGRDQGIVTIAINYDYNENLWLEQQLKQKFGLKDVVVVSGNDEDEETQ 91
Cdd:COG2390     1 RAAWLYYVEGLTQREIAERLGISRRTVSRLLAEAREEGLVRISITDPLAGLLELERELRERFGLKEVIVVPGDSDDDEEV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482  92 LAMMGLHGAQLLDRLLEPGDIVGFSWGRAVSALVENLPqAGQSRQLICVPIIGGPSGKleSRYHVNTLTYSAAAKLKGES 171
Cdd:COG2390    81 LRALGRAAAEYLERLLKDGDVIGVGWGRTLAAVAEALP-PLPLPDVTVVPLRGGLGED--VEAQANEIARRLAEKLGGEY 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482 172 HLADFPALLDNPLIRNGIMQSQHFKTISAYWDNLDVALVGIGSPAIRDGANWHAFYGGEESDDLNARQVAGDICSRFFDI 251
Cdd:COG2390   158 YLLPAPAIVDSAETREALLEEPSIREVLELARRADVALVGIGSADPDSTLARRGYLSEEELAELRAAGAVGDICGRFFDA 237

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1134749482 252 HGEMVETNMSEKTLSIEMNKLKQARYSIGIAMSEEKYSGIIGALRGKYINCLVTNSSTAELLLK 315
Cdd:COG2390   238 DGRIVDTPLNDRTIGISLEDLRRIPRVIAVAGGEEKAEAILAALRGGYINVLITDEATARALLE 301
Sugar-bind pfam04198
Putative sugar-binding domain; This probable domain is found in bacterial transcriptional ...
 57-315 5.67e-95

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: 281.43  E-value: 5.67e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482  57 YDYNENLWLEQQLKQKFGLKDVVVVSGNDEDEETQLAMMGLHGAQLLDRLLEPGDIVGFSWGRAVSALVENLPQAgQSRQ 136
Cdd:pfam04198   1 SPVEGCLDLEQRLKEKFGLKEAIVVPGDSDENDLVLERLGRAAAQYLESLLKDGDIVGVGWGRTLSAVAEALTPK-SLRN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482 137 LICVPIIGGPSGKLEsrYHVNTLTYSAAAKLKGESHLADFPALLDNPLIRNGIMQSQHFKTISAYWDNLDVALVGIGSPA 216
Cdd:pfam04198  80 LKFVPLIGGLGRDGS--AHSNTVIARLAQKFGGSYYLLPAPAYASNAALRRGLLAERSVKSVLDLARRADVAIVGIGSAS 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482 217 IRDGANWHAFYGGEESDDLNARQVAGDICSRFFDIHGEMVETNMSEKTLSIEMNKLKQARYSIGIAMSEEKYSGIIGALR 296
Cdd:pfam04198 158 EMAPLFRRGYLTEEELAELRELGAVGEIFGRFFDAEGRVVDTALNERVIGLDLEDLRDIPNVIAIAGGESKAEAILAALR 237

                         250
                  ....*....|....*....
gi 1134749482 297 GKYINCLVTNSSTAELLLK 315
Cdd:pfam04198 238 GGYINVLITDESTARALLA 256
PRK15418 PRK15418
transcriptional regulator LsrR; Provisional
 9-315 1.29e-36

transcriptional regulator LsrR; Provisional


Pssm-ID: 237962 [Multi-domain]  Cd Length: 318  Bit Score: 133.31  E-value: 1.29e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482   9 LIVKIAQLYYEQDMTQAQIARELGIYRTNISRLLKRGRDQGIVTIAINYDYNENLWLEQQLKQKFGLKDVVVVSG-NDED 87
Cdd:PRK15418   17 LVARIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRFEGCLELENALRQHFSLQHIRVLPAlADAD 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482  88 EETQLammGLHGAQLLDRLLEPGDIVGFSWGRAVSALVENLPQAGQSRQLICVPIIGGPS------GKLESRYHVNTL-- 159
Cdd:PRK15418   97 IGGRL---GIGAAHMLMSLLQPQQLLAVGFGEATMNTLQHLSGFISSQQIRLVTLSGGVGpymtgiGQLDAACSVSIIpa 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482 160 -----TYSAAAKLKGESHladfpalldnplIRNGIMQSQHfktisaywdnLDVALVGIGSPAIRDGAN-WHAFYGGEESD 233
Cdd:PRK15418  174 plrasSAEIARTLRNENS------------VRDVMLAAQA----------ADVAIVGIGAVNQKDDATiLRSGYISQGEQ 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482 234 DLNARQVA-GDICSRFFDIHGEMVE-TNMSEKTLSIEMNKLKQARYSIGIAMSEEKYSGIIGALRGKYINCLVTNSSTAE 311
Cdd:PRK15418  232 LMIGRKGAvGDILGYFFDADGELVPdIKIHNELIGLPLSSLKTIPTVIGVAGGEEKAEAIIAALKGGYINALVTDEKTAR 311


                  ....
gi 1134749482 312 LLLK 315
Cdd:PRK15418  312 AILA 315
SigBFG TIGR02980
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ...
 12-44 6.18e-05

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: 43.37  E-value: 6.18e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1134749482  12 KIAQLYYEQDMTQAQIARELGIYRTNISRLLKR 44
Cdd:TIGR02980 185 RILLLRFFEDKTQSEIAERLGISQMHVSRLLRR 217
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 4-52 9.54e-05

Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.


Pssm-ID: 238042 [Multi-domain]  Cd Length: 78  Bit Score: 40.36  E-value: 9.54e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1134749482   4 SDDIRLivKIAQLYYEQDMTQAQIARELGIYRTNISRLLKRGRDQGIVT 52
Cdd:cd00090     5 SDPTRL--RILRLLLEGPLTVSELAERLGLSQSTVSRHLKKLEEAGLVE 51
HTH_CRP smart00419
helix_turn_helix, cAMP Regulatory protein;
21-53 1.45e-03

helix_turn_helix, cAMP Regulatory protein;


Pssm-ID: 128696 [Multi-domain]  Cd Length: 48  Bit Score: 35.88  E-value: 1.45e-03
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1134749482   21 DMTQAQIARELGIYRTNISRLLKRGRDQGIVTI 53
Cdd:smart00419   8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISR 40
 
Name Accession Description Interval E-value
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
12-315 5.55e-113

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


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 329.01  E-value: 5.55e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482  12 KIAQLYYEQDMTQAQIARELGIYRTNISRLLKRGRDQGIVTIAINYDYNENLWLEQQLKQKFGLKDVVVVSGNDEDEETQ 91
Cdd:COG2390     1 RAAWLYYVEGLTQREIAERLGISRRTVSRLLAEAREEGLVRISITDPLAGLLELERELRERFGLKEVIVVPGDSDDDEEV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482  92 LAMMGLHGAQLLDRLLEPGDIVGFSWGRAVSALVENLPqAGQSRQLICVPIIGGPSGKleSRYHVNTLTYSAAAKLKGES 171
Cdd:COG2390    81 LRALGRAAAEYLERLLKDGDVIGVGWGRTLAAVAEALP-PLPLPDVTVVPLRGGLGED--VEAQANEIARRLAEKLGGEY 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482 172 HLADFPALLDNPLIRNGIMQSQHFKTISAYWDNLDVALVGIGSPAIRDGANWHAFYGGEESDDLNARQVAGDICSRFFDI 251
Cdd:COG2390   158 YLLPAPAIVDSAETREALLEEPSIREVLELARRADVALVGIGSADPDSTLARRGYLSEEELAELRAAGAVGDICGRFFDA 237

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1134749482 252 HGEMVETNMSEKTLSIEMNKLKQARYSIGIAMSEEKYSGIIGALRGKYINCLVTNSSTAELLLK 315
Cdd:COG2390   238 DGRIVDTPLNDRTIGISLEDLRRIPRVIAVAGGEEKAEAILAALRGGYINVLITDEATARALLE 301
Sugar-bind pfam04198
Putative sugar-binding domain; This probable domain is found in bacterial transcriptional ...
 57-315 5.67e-95

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: 281.43  E-value: 5.67e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482  57 YDYNENLWLEQQLKQKFGLKDVVVVSGNDEDEETQLAMMGLHGAQLLDRLLEPGDIVGFSWGRAVSALVENLPQAgQSRQ 136
Cdd:pfam04198   1 SPVEGCLDLEQRLKEKFGLKEAIVVPGDSDENDLVLERLGRAAAQYLESLLKDGDIVGVGWGRTLSAVAEALTPK-SLRN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482 137 LICVPIIGGPSGKLEsrYHVNTLTYSAAAKLKGESHLADFPALLDNPLIRNGIMQSQHFKTISAYWDNLDVALVGIGSPA 216
Cdd:pfam04198  80 LKFVPLIGGLGRDGS--AHSNTVIARLAQKFGGSYYLLPAPAYASNAALRRGLLAERSVKSVLDLARRADVAIVGIGSAS 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482 217 IRDGANWHAFYGGEESDDLNARQVAGDICSRFFDIHGEMVETNMSEKTLSIEMNKLKQARYSIGIAMSEEKYSGIIGALR 296
Cdd:pfam04198 158 EMAPLFRRGYLTEEELAELRELGAVGEIFGRFFDAEGRVVDTALNERVIGLDLEDLRDIPNVIAIAGGESKAEAILAALR 237

                         250
                  ....*....|....*....
gi 1134749482 297 GKYINCLVTNSSTAELLLK 315
Cdd:pfam04198 238 GGYINVLITDESTARALLA 256
PRK15418 PRK15418
transcriptional regulator LsrR; Provisional
 9-315 1.29e-36

transcriptional regulator LsrR; Provisional


Pssm-ID: 237962 [Multi-domain]  Cd Length: 318  Bit Score: 133.31  E-value: 1.29e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482   9 LIVKIAQLYYEQDMTQAQIARELGIYRTNISRLLKRGRDQGIVTIAINYDYNENLWLEQQLKQKFGLKDVVVVSG-NDED 87
Cdd:PRK15418   17 LVARIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRFEGCLELENALRQHFSLQHIRVLPAlADAD 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482  88 EETQLammGLHGAQLLDRLLEPGDIVGFSWGRAVSALVENLPQAGQSRQLICVPIIGGPS------GKLESRYHVNTL-- 159
Cdd:PRK15418   97 IGGRL---GIGAAHMLMSLLQPQQLLAVGFGEATMNTLQHLSGFISSQQIRLVTLSGGVGpymtgiGQLDAACSVSIIpa 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482 160 -----TYSAAAKLKGESHladfpalldnplIRNGIMQSQHfktisaywdnLDVALVGIGSPAIRDGAN-WHAFYGGEESD 233
Cdd:PRK15418  174 plrasSAEIARTLRNENS------------VRDVMLAAQA----------ADVAIVGIGAVNQKDDATiLRSGYISQGEQ 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134749482 234 DLNARQVA-GDICSRFFDIHGEMVE-TNMSEKTLSIEMNKLKQARYSIGIAMSEEKYSGIIGALRGKYINCLVTNSSTAE 311
Cdd:PRK15418  232 LMIGRKGAvGDILGYFFDADGELVPdIKIHNELIGLPLSSLKTIPTVIGVAGGEEKAEAIIAALKGGYINALVTDEKTAR 311


                  ....
gi 1134749482 312 LLLK 315
Cdd:PRK15418  312 AILA 315
SigBFG TIGR02980
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ...
 12-44 6.18e-05

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: 43.37  E-value: 6.18e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1134749482  12 KIAQLYYEQDMTQAQIARELGIYRTNISRLLKR 44
Cdd:TIGR02980 185 RILLLRFFEDKTQSEIAERLGISQMHVSRLLRR 217
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 8-44 7.33e-05

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: 43.27  E-value: 7.33e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1134749482   8 RLIVkiaQLYYEQDMTQAQIARELGIYRTNISRLLKR 44
Cdd:COG1191   192 RLVL---SLYYFEELTLKEIAEVLGVSESRVSRLHKK 225
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 12-48 7.84e-05

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: 39.72  E-value: 7.84e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1134749482  12 KIAQLYYEQDMTQAQIARELGIYRTNISRLLKRGRDQ 48
Cdd:pfam04545  11 QVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRK 47
MarR_2 pfam12802
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 13-52 8.78e-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: 8.78e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1134749482  13 IAQLYYEQDMTQAQIARELGIYRTNISRLLKRGRDQGIVT 52
Cdd:pfam12802  11 LLALARNPGLTVAELARRLGISKQTVSRLVKRLEAKGLVE 50
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 4-52 9.54e-05

Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.


Pssm-ID: 238042 [Multi-domain]  Cd Length: 78  Bit Score: 40.36  E-value: 9.54e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1134749482   4 SDDIRLivKIAQLYYEQDMTQAQIARELGIYRTNISRLLKRGRDQGIVT 52
Cdd:cd00090     5 SDPTRL--RILRLLLEGPLTVSELAERLGLSQSTVSRHLKKLEEAGLVE 51
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 12-48 1.92e-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: 41.18  E-value: 1.92e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1134749482  12 KIAQLYYEQDMTQAQIARELGIYRTNISRLLKRGRDQ 48
Cdd:TIGR02937 117 EVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKK 153
COG1356 COG1356
Transcriptional regulator [Transcription];
17-47 5.50e-04

Transcriptional regulator [Transcription];


Pssm-ID: 440967 [Multi-domain]  Cd Length: 139  Bit Score: 39.45  E-value: 5.50e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1134749482  17 YYEQDMTQAQIARELGIYRTNISRLLKRGRD 47
Cdd:COG1356    19 LRERGLTQQEIADILGTSRANVSSIEKSARE 49
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 16-48 7.88e-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: 37.08  E-value: 7.88e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1134749482  16 LYYEQDMTQAQIARELGIYRTNISRLLKRGRDQ 48
Cdd:cd06171    21 LRFGEGLSYEEIAEILGISRSTVRQRLHRALKK 53
HTH_CRP smart00419
helix_turn_helix, cAMP Regulatory protein;
21-53 1.45e-03

helix_turn_helix, cAMP Regulatory protein;


Pssm-ID: 128696 [Multi-domain]  Cd Length: 48  Bit Score: 35.88  E-value: 1.45e-03
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1134749482   21 DMTQAQIARELGIYRTNISRLLKRGRDQGIVTI 53
Cdd:smart00419   8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISR 40
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 16-50 2.46e-03

CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein Csa3, CARF domain is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 442641 [Multi-domain]  Cd Length: 325  Bit Score: 39.06  E-value: 2.46e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1134749482  16 LYYEQDMTQAQIARELGIYRTNISRLLKRGRDQGI 50
Cdd:COG3415    33 LLLAEGLSVREIAERLGVSRSTVYRWLKRYREGGL 67
COG2512 COG2512
Predicted transcriptional regulator, contains CW (cell wall-binding) repeats and an HTH domain ...
 22-53 3.29e-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: 3.29e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1134749482  22 MTQAQIARELGIYRTNISRLLKRGRDQGIVTI 53
Cdd:COG2512    31 MTQSEIVKETGWSKSKVSRLLSRLEERGLIEK 62
HTH_ARSR smart00418
helix_turn_helix, Arsenical Resistance Operon Repressor;
12-52 3.51e-03

helix_turn_helix, Arsenical Resistance Operon Repressor;


Pssm-ID: 197713 [Multi-domain]  Cd Length: 66  Bit Score: 35.26  E-value: 3.51e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1134749482   12 KIAQLYYEQDMTQAQIARELGIYRTNISRLLKRGRDQGIVT 52
Cdd:smart00418   1 KILKLLAEGELCVCELAEILGLSQSTVSHHLKKLREAGLVE 41
HTH_38 pfam13936
Helix-turn-helix domain; This helix-turn-helix domain is often found in transferases and is ...
 11-45 4.59e-03

Helix-turn-helix domain; This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.


Pssm-ID: 433591 [Multi-domain]  Cd Length: 44  Bit Score: 34.41  E-value: 4.59e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1134749482  11 VKIAQLYyEQDMTQAQIARELGIYRTNISRLLKRG 45
Cdd:pfam13936  11 EEIARLL-AEGLSLREIARRLGRSPSTISRELRRN 44
tfx PRK03975
putative transcriptional regulator; Provisional
 17-46 5.20e-03

putative transcriptional regulator; Provisional


Pssm-ID: 179690 [Multi-domain]  Cd Length: 141  Bit Score: 36.79  E-value: 5.20e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 1134749482  17 YYEQDMTQAQIARELGIYRTNISRLLKRGR 46
Cdd:PRK03975   17 LRERGLTQQEIADILGTSRANVSSIEKRAR 46
HTH_Crp_2 pfam13545
Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain ...
 21-52 5.66e-03

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: 34.74  E-value: 5.66e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1134749482  21 DMTQAQIARELGIYRTNISRLLKRGRDQGIVT 52
Cdd:pfam13545  22 PLTQEDLADLLGTTRETVSRVLSELRREGLIE 53
HTH_28 pfam13518
Helix-turn-helix domain; This helix-turn-helix domain is often found in transposases and is ...
 16-50 5.87e-03

Helix-turn-helix domain; This helix-turn-helix domain is often found in transposases and is likely to be DNA-binding.


Pssm-ID: 463908 [Multi-domain]  Cd Length: 52  Bit Score: 34.49  E-value: 5.87e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1134749482  16 LYYEQDMTQAQIARELGIYRTNISRLLKRGRDQGI 50
Cdd:pfam13518   7 LLALEGESIKEAARLFGISRSTVYRWIRRYREGGL 41
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 8-53 5.95e-03

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: 37.27  E-value: 5.95e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1134749482   8 RLIVKIAQLYYEQ---DMTQAQIARELGIYRTNISRLLKRGRDQGIVTI 53
Cdd:COG0664   142 RFLLELADRLDGRidlPLTQEEIASYLGLTRETVSRILKKLEKEGLIEL 190
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 16-46 6.18e-03

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.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 34.35  E-value: 6.18e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1134749482  16 LYYEQDMTQAQIARELGIYRTNISRLLKRGR 46
Cdd:pfam08281  21 LRYLEGLSYAEIAELLGISEGTVKSRLSRAR 51
InsE COG2963
Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons];
12-49 6.88e-03

Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442203 [Multi-domain]  Cd Length: 93  Bit Score: 35.29  E-value: 6.88e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1134749482  12 KIAQLYYEQDMTQAQIARELGIYRTNISRLLKRGRDQG 49
Cdd:COG2963    15 EAVRLVLEGGASVAEVARELGISPSTLYRWVRQYREGG 52
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
11-49 7.75e-03

Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 37.55  E-value: 7.75e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1134749482  11 VKIAQLYyEQDMTQAQIARELGIYRTNISRLLKRGRDQG 49
Cdd:COG2826    13 EEIEALL-KAGLSVREIARRLGRSPSTISRELKRNSGRR 50
 
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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