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Conserved domains on  [gi|1415868345|emb|SPZ28165|]
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Sor operon activator [Raoultella planticola]

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];
14-317 5.23e-108

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


:

Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 316.30  E-value: 5.23e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1415868345  14 KVAQLYYEQDLTQAQIARELGIYRTTISRLLKRGREQGIVTIAINYDYNENLWLEQQLKQKFALKEAVVASCESSQEEDQ 93
Cdd:COG2390     1 RAAWLYYVEGLTQREIAERLGISRRTVSRLLAEAREEGLVRISITDPLAGLLELERELRERFGLKEVIVVPGDSDDDEEV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1415868345  94 LSTIGQHGAQLVDRLLEPGDIIGFSWGRAVRALVETLPqASQSRQVICVPIIGGPSGKleSRYHVNTLTYGAAARLKAES 173
Cdd:COG2390    81 LRALGRAAAEYLERLLKDGDVIGVGWGRTLAAVAEALP-PLPLPDVTVVPLRGGLGED--VEAQANEIARRLAEKLGGEY 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1415868345 174 HLADFPALLENTLIRNGIMQSQHFKTISSYWENLDVALVGIGSPAIRDGANWHAFYGSEESDDLNARHVAGDICSRFYDI 253
Cdd:COG2390   158 YLLPAPAIVDSAETREALLEEPSIREVLELARRADVALVGIGSADPDSTLARRGYLSEEELAELRAAGAVGDICGRFFDA 237

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1415868345 254 NGIAVETNMNEKTLSIDIARLKQVRYSVGIAIGEEKYTGIIGALRGGYINCLVTNRETAELLLK 317
Cdd:COG2390   238 DGRIVDTPLNDRTIGISLEDLRRIPRVIAVAGGEEKAEAILAALRGGYINVLITDEATARALLE 301
 
Name Accession Description Interval E-value
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
14-317 5.23e-108

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


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 316.30  E-value: 5.23e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1415868345  14 KVAQLYYEQDLTQAQIARELGIYRTTISRLLKRGREQGIVTIAINYDYNENLWLEQQLKQKFALKEAVVASCESSQEEDQ 93
Cdd:COG2390     1 RAAWLYYVEGLTQREIAERLGISRRTVSRLLAEAREEGLVRISITDPLAGLLELERELRERFGLKEVIVVPGDSDDDEEV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1415868345  94 LSTIGQHGAQLVDRLLEPGDIIGFSWGRAVRALVETLPqASQSRQVICVPIIGGPSGKleSRYHVNTLTYGAAARLKAES 173
Cdd:COG2390    81 LRALGRAAAEYLERLLKDGDVIGVGWGRTLAAVAEALP-PLPLPDVTVVPLRGGLGED--VEAQANEIARRLAEKLGGEY 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1415868345 174 HLADFPALLENTLIRNGIMQSQHFKTISSYWENLDVALVGIGSPAIRDGANWHAFYGSEESDDLNARHVAGDICSRFYDI 253
Cdd:COG2390   158 YLLPAPAIVDSAETREALLEEPSIREVLELARRADVALVGIGSADPDSTLARRGYLSEEELAELRAAGAVGDICGRFFDA 237

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1415868345 254 NGIAVETNMNEKTLSIDIARLKQVRYSVGIAIGEEKYTGIIGALRGGYINCLVTNRETAELLLK 317
Cdd:COG2390   238 DGRIVDTPLNDRTIGISLEDLRRIPRVIAVAGGEEKAEAILAALRGGYINVLITDEATARALLE 301
Sugar-bind pfam04198
Putative sugar-binding domain; This probable domain is found in bacterial transcriptional ...
 59-317 7.86e-93

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: 276.04  E-value: 7.86e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1415868345  59 YDYNENLWLEQQLKQKFALKEAVVASCESSQEEDQLSTIGQHGAQLVDRLLEPGDIIGFSWGRAVRALVETLPQaSQSRQ 138
Cdd:pfam04198   1 SPVEGCLDLEQRLKEKFGLKEAIVVPGDSDENDLVLERLGRAAAQYLESLLKDGDIVGVGWGRTLSAVAEALTP-KSLRN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1415868345 139 VICVPIIGGPSGKLEsrYHVNTLTYGAAARLKAESHLADFPALLENTLIRNGIMQSQHFKTISSYWENLDVALVGIGSPA 218
Cdd:pfam04198  80 LKFVPLIGGLGRDGS--AHSNTVIARLAQKFGGSYYLLPAPAYASNAALRRGLLAERSVKSVLDLARRADVAIVGIGSAS 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1415868345 219 IRDGANWHAFYGSEESDDLNARHVAGDICSRFYDINGIAVETNMNEKTLSIDIARLKQVRYSVGIAIGEEKYTGIIGALR 298
Cdd:pfam04198 158 EMAPLFRRGYLTEEELAELRELGAVGEIFGRFFDAEGRVVDTALNERVIGLDLEDLRDIPNVIAIAGGESKAEAILAALR 237

                         250
                  ....*....|....*....
gi 1415868345 299 GGYINCLVTNRETAELLLK 317
Cdd:pfam04198 238 GGYINVLITDESTARALLA 256
PRK15418 PRK15418
transcriptional regulator LsrR; Provisional
 11-317 1.45e-33

transcriptional regulator LsrR; Provisional


Pssm-ID: 237962 [Multi-domain]  Cd Length: 318  Bit Score: 125.22  E-value: 1.45e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1415868345  11 LIVKVAQLYYEQDLTQAQIARELGIYRTTISRLLKRGREQGIVTIAINYDYNENLWLEQQLKQKFALKEAVVASCESSQE 90
Cdd:PRK15418   17 LVARIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRFEGCLELENALRQHFSLQHIRVLPALADAD 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1415868345  91 EDQLSTIGqhGAQLVDRLLEPGDIIGFSWGRAVRALVETLPQASQSRQVICVPIIGGPS------GKLESRYHVNTLtyg 164
Cdd:PRK15418   97 IGGRLGIG--AAHMLMSLLQPQQLLAVGFGEATMNTLQHLSGFISSQQIRLVTLSGGVGpymtgiGQLDAACSVSII--- 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1415868345 165 aAARLKAEShlADFPALLEN-TLIRNGIMQSQHfktissywenLDVALVGIGSPAIRDGAN-WHAFYGSEESDDLNARHV 242
Cdd:PRK15418  172 -PAPLRASS--AEIARTLRNeNSVRDVMLAAQA----------ADVAIVGIGAVNQKDDATiLRSGYISQGEQLMIGRKG 238

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1415868345 243 A-GDICSRFYDINGIAVE-TNMNEKTLSIDIARLKQVRYSVGIAIGEEKYTGIIGALRGGYINCLVTNRETAELLLK 317
Cdd:PRK15418  239 AvGDILGYFFDADGELVPdIKIHNELIGLPLSSLKTIPTVIGVAGGEEKAEAIIAALKGGYINALVTDEKTARAILA 315
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 14-50 1.50e-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: 39.01  E-value: 1.50e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1415868345  14 KVAQLYYEQDLTQAQIARELGIYRTTISRLLKRGREQ 50
Cdd:cd06171    17 EVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKK 53
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 14-50 1.65e-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: 1.65e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1415868345  14 KVAQLYYEQDLTQAQIARELGIYRTTISRLLKRGREQ 50
Cdd:TIGR02937 117 EVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKK 153
HTH_CRP smart00419
helix_turn_helix, cAMP Regulatory protein;
23-55 3.65e-04

helix_turn_helix, cAMP Regulatory protein;


Pssm-ID: 128696 [Multi-domain]  Cd Length: 48  Bit Score: 37.80  E-value: 3.65e-04
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1415868345   23 DLTQAQIARELGIYRTTISRLLKRGREQGIVTI 55
Cdd:smart00419   8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISR 40
transpos_IS21 NF033546
IS21 family transposase;
17-47 4.58e-04

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 41.42  E-value: 4.58e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1415868345  17 QLYYEQDLTQAQIARELGIYRTTISRLLKRG 47
Cdd:NF033546    2 RLLFRQGLSIREIARELGISRNTVRKYLRRA 32
transpos_IS630 NF033545
IS630 family transposase;
14-52 1.04e-03

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 40.32  E-value: 1.04e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1415868345  14 KVAQLYYEQDLTQAQIARELGIYRTTISRLLKRGREQGI 52
Cdd:NF033545    3 ARILLLAAEGLSITEIAERLGVSRSTVYRWLKRFNEGGL 41
 
Name Accession Description Interval E-value
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
14-317 5.23e-108

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


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 316.30  E-value: 5.23e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1415868345  14 KVAQLYYEQDLTQAQIARELGIYRTTISRLLKRGREQGIVTIAINYDYNENLWLEQQLKQKFALKEAVVASCESSQEEDQ 93
Cdd:COG2390     1 RAAWLYYVEGLTQREIAERLGISRRTVSRLLAEAREEGLVRISITDPLAGLLELERELRERFGLKEVIVVPGDSDDDEEV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1415868345  94 LSTIGQHGAQLVDRLLEPGDIIGFSWGRAVRALVETLPqASQSRQVICVPIIGGPSGKleSRYHVNTLTYGAAARLKAES 173
Cdd:COG2390    81 LRALGRAAAEYLERLLKDGDVIGVGWGRTLAAVAEALP-PLPLPDVTVVPLRGGLGED--VEAQANEIARRLAEKLGGEY 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1415868345 174 HLADFPALLENTLIRNGIMQSQHFKTISSYWENLDVALVGIGSPAIRDGANWHAFYGSEESDDLNARHVAGDICSRFYDI 253
Cdd:COG2390   158 YLLPAPAIVDSAETREALLEEPSIREVLELARRADVALVGIGSADPDSTLARRGYLSEEELAELRAAGAVGDICGRFFDA 237

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1415868345 254 NGIAVETNMNEKTLSIDIARLKQVRYSVGIAIGEEKYTGIIGALRGGYINCLVTNRETAELLLK 317
Cdd:COG2390   238 DGRIVDTPLNDRTIGISLEDLRRIPRVIAVAGGEEKAEAILAALRGGYINVLITDEATARALLE 301
Sugar-bind pfam04198
Putative sugar-binding domain; This probable domain is found in bacterial transcriptional ...
 59-317 7.86e-93

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: 276.04  E-value: 7.86e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1415868345  59 YDYNENLWLEQQLKQKFALKEAVVASCESSQEEDQLSTIGQHGAQLVDRLLEPGDIIGFSWGRAVRALVETLPQaSQSRQ 138
Cdd:pfam04198   1 SPVEGCLDLEQRLKEKFGLKEAIVVPGDSDENDLVLERLGRAAAQYLESLLKDGDIVGVGWGRTLSAVAEALTP-KSLRN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1415868345 139 VICVPIIGGPSGKLEsrYHVNTLTYGAAARLKAESHLADFPALLENTLIRNGIMQSQHFKTISSYWENLDVALVGIGSPA 218
Cdd:pfam04198  80 LKFVPLIGGLGRDGS--AHSNTVIARLAQKFGGSYYLLPAPAYASNAALRRGLLAERSVKSVLDLARRADVAIVGIGSAS 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1415868345 219 IRDGANWHAFYGSEESDDLNARHVAGDICSRFYDINGIAVETNMNEKTLSIDIARLKQVRYSVGIAIGEEKYTGIIGALR 298
Cdd:pfam04198 158 EMAPLFRRGYLTEEELAELRELGAVGEIFGRFFDAEGRVVDTALNERVIGLDLEDLRDIPNVIAIAGGESKAEAILAALR 237

                         250
                  ....*....|....*....
gi 1415868345 299 GGYINCLVTNRETAELLLK 317
Cdd:pfam04198 238 GGYINVLITDESTARALLA 256
PRK15418 PRK15418
transcriptional regulator LsrR; Provisional
 11-317 1.45e-33

transcriptional regulator LsrR; Provisional


Pssm-ID: 237962 [Multi-domain]  Cd Length: 318  Bit Score: 125.22  E-value: 1.45e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1415868345  11 LIVKVAQLYYEQDLTQAQIARELGIYRTTISRLLKRGREQGIVTIAINYDYNENLWLEQQLKQKFALKEAVVASCESSQE 90
Cdd:PRK15418   17 LVARIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRFEGCLELENALRQHFSLQHIRVLPALADAD 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1415868345  91 EDQLSTIGqhGAQLVDRLLEPGDIIGFSWGRAVRALVETLPQASQSRQVICVPIIGGPS------GKLESRYHVNTLtyg 164
Cdd:PRK15418   97 IGGRLGIG--AAHMLMSLLQPQQLLAVGFGEATMNTLQHLSGFISSQQIRLVTLSGGVGpymtgiGQLDAACSVSII--- 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1415868345 165 aAARLKAEShlADFPALLEN-TLIRNGIMQSQHfktissywenLDVALVGIGSPAIRDGAN-WHAFYGSEESDDLNARHV 242
Cdd:PRK15418  172 -PAPLRASS--AEIARTLRNeNSVRDVMLAAQA----------ADVAIVGIGAVNQKDDATiLRSGYISQGEQLMIGRKG 238

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1415868345 243 A-GDICSRFYDINGIAVE-TNMNEKTLSIDIARLKQVRYSVGIAIGEEKYTGIIGALRGGYINCLVTNRETAELLLK 317
Cdd:PRK15418  239 AvGDILGYFFDADGELVPdIKIHNELIGLPLSSLKTIPTVIGVAGGEEKAEAIIAALKGGYINALVTDEKTARAILA 315
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 10-46 1.15e-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: 45.59  E-value: 1.15e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1415868345  10 RLIVkvaQLYYEQDLTQAQIARELGIYRTTISRLLKR 46
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 ...
 14-50 3.60e-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: 40.49  E-value: 3.60e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1415868345  14 KVAQLYYEQDLTQAQIARELGIYRTTISRLLKRGREQ 50
Cdd:pfam04545  11 QVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRK 47
MarR_2 pfam12802
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 16-54 1.07e-04

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: 39.49  E-value: 1.07e-04
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1415868345  16 AQLYYEQDLTQAQIARELGIYRTTISRLLKRGREQGIVT 54
Cdd:pfam12802  12 LALARNPGLTVAELARRLGISKQTVSRLVKRLEAKGLVE 50
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 14-50 1.50e-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: 39.01  E-value: 1.50e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1415868345  14 KVAQLYYEQDLTQAQIARELGIYRTTISRLLKRGREQ 50
Cdd:cd06171    17 EVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKK 53
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 14-50 1.65e-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: 1.65e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1415868345  14 KVAQLYYEQDLTQAQIARELGIYRTTISRLLKRGREQ 50
Cdd:TIGR02937 117 EVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKK 153
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 18-52 3.40e-04

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: 41.76  E-value: 3.40e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1415868345  18 LYYEQDLTQAQIARELGIYRTTISRLLKRGREQGI 52
Cdd:COG3415    33 LLLAEGLSVREIAERLGVSRSTVYRWLKRYREGGL 67
HTH_CRP smart00419
helix_turn_helix, cAMP Regulatory protein;
23-55 3.65e-04

helix_turn_helix, cAMP Regulatory protein;


Pssm-ID: 128696 [Multi-domain]  Cd Length: 48  Bit Score: 37.80  E-value: 3.65e-04
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1415868345   23 DLTQAQIARELGIYRTTISRLLKRGREQGIVTI 55
Cdd:smart00419   8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISR 40
transpos_IS21 NF033546
IS21 family transposase;
17-47 4.58e-04

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 41.42  E-value: 4.58e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1415868345  17 QLYYEQDLTQAQIARELGIYRTTISRLLKRG 47
Cdd:NF033546    2 RLLFRQGLSIREIARELGISRNTVRKYLRRA 32
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
17-48 5.14e-04

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


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 41.02  E-value: 5.14e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1415868345  17 QLYYEQDLTQAQIARELGIYRTTISRLLKRGR 48
Cdd:COG2826    16 EALLKAGLSVREIARRLGRSPSTISRELKRNS 47
HTH_28 pfam13518
Helix-turn-helix domain; This helix-turn-helix domain is often found in transposases and is ...
 18-52 6.37e-04

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: 37.19  E-value: 6.37e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1415868345  18 LYYEQDLTQAQIARELGIYRTTISRLLKRGREQGI 52
Cdd:pfam13518   7 LLALEGESIKEAARLFGISRSTVYRWIRRYREGGL 41
COG2512 COG2512
Predicted transcriptional regulator, contains CW (cell wall-binding) repeats and an HTH domain ...
 24-55 7.69e-04

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: 37.59  E-value: 7.69e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1415868345  24 LTQAQIARELGIYRTTISRLLKRGREQGIVTI 55
Cdd:COG2512    31 MTQSEIVKETGWSKSKVSRLLSRLEERGLIEK 62
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 6-54 9.54e-04

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: 37.28  E-value: 9.54e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1415868345   6 SDDIRLivKVAQLYYEQDLTQAQIARELGIYRTTISRLLKRGREQGIVT 54
Cdd:cd00090     5 SDPTRL--RILRLLLEGPLTVSELAERLGLSQSTVSRHLKKLEEAGLVE 51
HTH_Crp_2 pfam13545
Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain ...
 9-54 1.03e-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: 37.05  E-value: 1.03e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1415868345   9 IRLIVKVAQLYYEQDLTQAQIARELGIYRTTISRLLKRGREQGIVT 54
Cdd:pfam13545   8 LELAARDGGGRIDLPLTQEDLADLLGTTRETVSRVLSELRREGLIE 53
transpos_IS630 NF033545
IS630 family transposase;
14-52 1.04e-03

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 40.32  E-value: 1.04e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1415868345  14 KVAQLYYEQDLTQAQIARELGIYRTTISRLLKRGREQGI 52
Cdd:NF033545    3 ARILLLAAEGLSITEIAERLGVSRSTVYRWLKRFNEGGL 41
HTH_38 pfam13936
Helix-turn-helix domain; This helix-turn-helix domain is often found in transferases and is ...
 17-47 1.15e-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: 36.34  E-value: 1.15e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1415868345  17 QLYYEQDLTQAQIARELGIYRTTISRLLKRG 47
Cdd:pfam13936  14 ARLLAEGLSLREIARRLGRSPSTISRELRRN 44
InsE COG2963
Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons];
14-51 1.38e-03

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


Pssm-ID: 442203 [Multi-domain]  Cd Length: 93  Bit Score: 37.21  E-value: 1.38e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1415868345  14 KVAQLYYEQDLTQAQIARELGIYRTTISRLLKRGREQG 51
Cdd:COG2963    15 EAVRLVLEGGASVAEVARELGISPSTLYRWVRQYREGG 52
HTH_23 pfam13384
Homeodomain-like domain;
20-52 1.81e-03

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 35.71  E-value: 1.81e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1415868345  20 YEQDLTQAQIARELGIYRTTISRLLKRGREQGI 52
Cdd:pfam13384  14 LAEGLSVKEIAELLGVSRRTVYRWLKRYNEEGL 46
HTH_CRP cd00092
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic ...
 24-53 1.82e-03

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: 36.10  E-value: 1.82e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 1415868345  24 LTQAQIARELGIYRTTISRLLKRGREQGIV 53
Cdd:cd00092    26 LTRQEIADYLGLTRETVSRTLKELEEEGLI 55
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 24-55 2.65e-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: 38.43  E-value: 2.65e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1415868345  24 LTQAQIARELGIYRTTISRLLKRGREQGIVTI 55
Cdd:COG0664   159 LTQEEIASYLGLTRETVSRILKKLEKEGLIEL 190
PRK00118 PRK00118
putative DNA-binding protein; Validated
 17-94 2.71e-03

putative DNA-binding protein; Validated


Pssm-ID: 234647  Cd Length: 104  Bit Score: 36.76  E-value: 2.71e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1415868345  17 QLYYEQDLTQAQIARELGIYRTTISRLLKRgreqgivTIAINYDYNENLWLEQQLKQKFALKEAVVASCESSQEEDQL 94
Cdd:PRK00118   27 ELYYLDDYSLGEIAEEFNVSRQAVYDNIKR-------TEKLLEDYEEKLHLYEKFIERNELFDKIAYLKEKYPDDEEL 97
COG1356 COG1356
Transcriptional regulator [Transcription];
19-49 3.25e-03

Transcriptional regulator [Transcription];


Pssm-ID: 440967 [Multi-domain]  Cd Length: 139  Bit Score: 37.14  E-value: 3.25e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1415868345  19 YYEQDLTQAQIARELGIYRTTISRLLKRGRE 49
Cdd:COG1356    19 LRERGLTQQEIADILGTSRANVSSIEKSARE 49
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 18-50 3.48e-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: 35.12  E-value: 3.48e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1415868345  18 LYYEQDLTQAQIARELGIYRTTISRLLKRGREQ 50
Cdd:pfam08281  21 LRYLEGLSYAEIAELLGISEGTVKSRLSRARKK 53
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
16-54 6.63e-03

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


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 36.49  E-value: 6.63e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1415868345  16 AQLYYEQDLTQAQIARELGIYRTTISRLLKRGREQGIVT 54
Cdd:COG1846    45 AALAEAGGLTQSELAERLGLTKSTVSRLLDRLEEKGLVE 83
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 18-50 8.75e-03

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 36.51  E-value: 8.75e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1415868345  18 LYYEQDLTQAQIARELGIYRTTISRLLKRGREQ 50
Cdd:COG1595   138 LRYLEGLSYAEIAEILGISEGTVKSRLSRARKK 170
 
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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