Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2053339036  70 AWRIWRGLSQQDVAEKLGISQSAVSQLESPDSRPQKRTREKLAALYDCQPEQL 122
Cdd:cd00093     6 ELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2053339036  69 AAWRIWRGLSQQDVAEKLGISQSAVSQLESPDSRPQKRTREKLAALYDCQPEQL 122
Cdd:pfam01381   2 KELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2053339036  71 WRIWRGLSQQDVAEKLGISQSAVSQLespdsrpQKRTREKLAALY 115
Cdd:TIGR02937 121 LRYLEGLSYKEIAEILGISVGTVKRR-------LKRARKKLRELL 158

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2053339036  70 AWRIWRGLSQQDVAEKLGISQSAVSQLESPDSRPQKRTREKLAALYDCQPEQL 122
Cdd:cd00093     6 ELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2053339036  70 AWRIWRGLSQQDVAEKLGISQSAVSQLESPDSRPQKRTREKLAALYDCQPEQLI 123
Cdd:COG1476    11 ELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELF 64

Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain CBS pair) [Transcription];

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2053339036  59 ISVEQNVSLQAAWRIWR---GLSQQDVAEKLGISQSAVSQLESPDSRPQKRTREKLAALYDCQPEQLIL 124
Cdd:COG3620    10 VTVSPDDTLGEALRLMRkelGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLV 78

Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2053339036  69 AAWRIWRGLSQQDVAEKLGISQSAVSQLES-PDSRPQKRTREKLAALYDCQPEQL 122
Cdd:pfam13560   7 RRLRERAGLSQEALARRLGVSRSTLSRLETgRRGRPSPAVVERLARALGVDGAER 61

DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2053339036  69 AAWRIWRGLSQQDVAEKLGISQSAVSQLESPDSRPQKRTREKLAALYDcQPEQL 122
Cdd:COG2944    12 RALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEK-HPELL 64

Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to DNA.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2053339036  75 RGLSQQDVAEKLGISQSAVSQLES-PDSRPQKRTREKLAALYDCQPEQLILY 125
Cdd:pfam13443   9 RGISKSDLARATGISRATLSRLRKgKPKRVSLDTLDKICDALGCQPGDLLEY 60

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2053339036  72 RIWRGLSQQDVAEKLGISQSAVSQLEspdsrpqKRTREKL 111
Cdd:pfam04545  16 RYGEGLTLEEIGERLGISRERVRQIE-------KRALRKL 48

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).

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2053339036  71 WRIWRGLSQQDVAEKLGISQSAVSQLEspdsrpqKRTREKL 111
Cdd:cd06171    21 LRFGEGLSYEEIAEILGISRSTVRQRL-------HRALKKL 54

transcriptional repressor DicA; Reviewed

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2053339036  76 GLSQQDVAEKLGISQSAVSQLESPDSRPQKRTREKLAALYDCQP 119
Cdd:PRK09706   18 KLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSP 61

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2053339036  71 WRIWRGLSQQDVAEKLGISQSAVSQLespdsrpQKRTREKLAALY 115
Cdd:TIGR02937 121 LRYLEGLSYKEIAEILGISVGTVKRR-------LKRARKKLRELL 158

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

                          10        20
                  ....*....|....*....|..
gi 2053339036  75 RGLSQQDVAEKLGISQSAVSQL 96
Cdd:COG3093    21 LGLSQTELAKALGVSRQRISEI 42

bifunctional HTH-domain containing protein/aminotransferase; Provisional

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2053339036  75 RGLSQQDV---AEKLGI--SQSAVSQLESPDSRPQKRTREKLAALYDCQPEQLI 123
Cdd:PRK13355   15 RGLKQEDLvhaAEARGVklGKSHISQYVSGKTGPRRDVLPFLAAILGVSEDWLL 68