sigma-70, region 4 [Peptoniphilus sp. BV3AC2]
sigma-70 family RNA polymerase sigma factor( domain architecture ID 11495650)
sigma-70 family RNA polymerase sigma factor is a general transcription factor that reversibly binds RNA polymerase and mediates transcription.
List of domain hits
Name | Accession | Description | Interval | E-value | |||
RpoE | COG1595 | DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ... |
79-141 | 2.55e-12 | |||
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: 60.78 E-value: 2.55e-12
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Sig70_bacteroi1 super family | cl37203 | RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ... |
19-135 | 6.43e-06 | |||
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium. The actual alignment was detected with superfamily member TIGR02985: Pssm-ID: 274376 [Multi-domain] Cd Length: 161 Bit Score: 43.32 E-value: 6.43e-06
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Name | Accession | Description | Interval | E-value | |||
RpoE | COG1595 | DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ... |
79-141 | 2.55e-12 | |||
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: 60.78 E-value: 2.55e-12
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sigma70-ECF | TIGR02937 | RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ... |
77-135 | 6.14e-11 | |||
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: 56.59 E-value: 6.14e-11
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Sigma70_r4_2 | pfam08281 | Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ... |
79-123 | 2.55e-07 | |||
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: 44.75 E-value: 2.55e-07
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Sigma70_r4 | cd06171 | Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
78-120 | 3.29e-07 | |||
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: 44.40 E-value: 3.29e-07
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PRK09415 | PRK09415 | RNA polymerase factor sigma C; Reviewed |
81-138 | 7.09e-07 | |||
RNA polymerase factor sigma C; Reviewed Pssm-ID: 181835 [Multi-domain] Cd Length: 179 Bit Score: 46.28 E-value: 7.09e-07
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Sig70_bacteroi1 | TIGR02985 | RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ... |
19-135 | 6.43e-06 | |||
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium. Pssm-ID: 274376 [Multi-domain] Cd Length: 161 Bit Score: 43.32 E-value: 6.43e-06
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HTH_LUXR | smart00421 | helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon |
85-126 | 7.87e-03 | |||
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon Pssm-ID: 197715 [Multi-domain] Cd Length: 58 Bit Score: 32.88 E-value: 7.87e-03
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Name | Accession | Description | Interval | E-value | |||
RpoE | COG1595 | DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ... |
79-141 | 2.55e-12 | |||
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: 60.78 E-value: 2.55e-12
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sigma70-ECF | TIGR02937 | RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ... |
77-135 | 6.14e-11 | |||
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: 56.59 E-value: 6.14e-11
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FliA | COG1191 | DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ... |
79-137 | 9.01e-11 | |||
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: 57.53 E-value: 9.01e-11
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SigE-fam_strep | TIGR02983 | RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ... |
77-138 | 9.38e-09 | |||
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives. Pssm-ID: 132028 [Multi-domain] Cd Length: 162 Bit Score: 50.85 E-value: 9.38e-09
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Sigma70_r4_2 | pfam08281 | Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ... |
79-123 | 2.55e-07 | |||
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: 44.75 E-value: 2.55e-07
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Sigma70_r4 | cd06171 | Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
78-120 | 3.29e-07 | |||
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: 44.40 E-value: 3.29e-07
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PRK09415 | PRK09415 | RNA polymerase factor sigma C; Reviewed |
81-138 | 7.09e-07 | |||
RNA polymerase factor sigma C; Reviewed Pssm-ID: 181835 [Multi-domain] Cd Length: 179 Bit Score: 46.28 E-value: 7.09e-07
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PRK12543 | PRK12543 | RNA polymerase sigma factor; Provisional |
78-141 | 4.47e-06 | |||
RNA polymerase sigma factor; Provisional Pssm-ID: 183582 [Multi-domain] Cd Length: 179 Bit Score: 43.95 E-value: 4.47e-06
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Sig70_bacteroi1 | TIGR02985 | RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ... |
19-135 | 6.43e-06 | |||
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium. Pssm-ID: 274376 [Multi-domain] Cd Length: 161 Bit Score: 43.32 E-value: 6.43e-06
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Sigma70_r4 | pfam04545 | Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ... |
84-133 | 9.23e-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: 40.49 E-value: 9.23e-06
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PRK12517 | PRK12517 | RNA polymerase sigma factor; Provisional |
35-141 | 1.13e-05 | |||
RNA polymerase sigma factor; Provisional Pssm-ID: 183569 [Multi-domain] Cd Length: 188 Bit Score: 42.75 E-value: 1.13e-05
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PRK05602 | PRK05602 | RNA polymerase sigma factor; Reviewed |
69-116 | 1.43e-05 | |||
RNA polymerase sigma factor; Reviewed Pssm-ID: 235530 [Multi-domain] Cd Length: 186 Bit Score: 42.72 E-value: 1.43e-05
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PRK11924 | PRK11924 | RNA polymerase sigma factor; Provisional |
76-120 | 6.56e-05 | |||
RNA polymerase sigma factor; Provisional Pssm-ID: 183384 [Multi-domain] Cd Length: 179 Bit Score: 40.72 E-value: 6.56e-05
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PRK06288 | PRK06288 | RNA polymerase sigma factor WhiG; Reviewed |
80-120 | 2.05e-04 | |||
RNA polymerase sigma factor WhiG; Reviewed Pssm-ID: 235770 [Multi-domain] Cd Length: 268 Bit Score: 39.67 E-value: 2.05e-04
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PRK12519 | PRK12519 | RNA polymerase sigma factor; Provisional |
83-128 | 3.34e-04 | |||
RNA polymerase sigma factor; Provisional Pssm-ID: 237125 [Multi-domain] Cd Length: 194 Bit Score: 38.89 E-value: 3.34e-04
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PRK06811 | PRK06811 | RNA polymerase factor sigma-70; Validated |
76-138 | 7.15e-04 | |||
RNA polymerase factor sigma-70; Validated Pssm-ID: 180707 [Multi-domain] Cd Length: 189 Bit Score: 38.00 E-value: 7.15e-04
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PRK12538 | PRK12538 | RNA polymerase sigma factor; Provisional |
78-113 | 9.29e-04 | |||
RNA polymerase sigma factor; Provisional Pssm-ID: 139048 [Multi-domain] Cd Length: 233 Bit Score: 37.91 E-value: 9.29e-04
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PRK12513 | PRK12513 | RNA polymerase sigma factor; Provisional |
79-120 | 1.45e-03 | |||
RNA polymerase sigma factor; Provisional Pssm-ID: 183566 [Multi-domain] Cd Length: 194 Bit Score: 36.98 E-value: 1.45e-03
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CsgD | COG2771 | DNA-binding transcriptional regulator, CsgD family [Transcription]; |
92-134 | 1.49e-03 | |||
DNA-binding transcriptional regulator, CsgD family [Transcription]; Pssm-ID: 442052 [Multi-domain] Cd Length: 188 Bit Score: 37.04 E-value: 1.49e-03
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Csa3 | COG3415 | CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ... |
77-129 | 2.92e-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: 36.37 E-value: 2.92e-03
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LuxR_C_like | cd06170 | C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ... |
92-126 | 4.22e-03 | |||
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp. Pssm-ID: 99777 [Multi-domain] Cd Length: 57 Bit Score: 33.66 E-value: 4.22e-03
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PRK12527 | PRK12527 | RNA polymerase sigma factor; Reviewed |
79-128 | 5.33e-03 | |||
RNA polymerase sigma factor; Reviewed Pssm-ID: 171560 [Multi-domain] Cd Length: 159 Bit Score: 35.14 E-value: 5.33e-03
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Sig-70_X6 | TIGR02999 | RNA polymerase sigma factor, TIGR02999 family; This group of sigma factors are members of the ... |
78-123 | 7.29e-03 | |||
RNA polymerase sigma factor, TIGR02999 family; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five. Pssm-ID: 132044 [Multi-domain] Cd Length: 183 Bit Score: 34.99 E-value: 7.29e-03
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PRK09641 | PRK09641 | RNA polymerase sigma factor SigW; Provisional |
83-120 | 7.71e-03 | |||
RNA polymerase sigma factor SigW; Provisional Pssm-ID: 182012 [Multi-domain] Cd Length: 187 Bit Score: 35.06 E-value: 7.71e-03
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HTH_LUXR | smart00421 | helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon |
85-126 | 7.87e-03 | |||
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon Pssm-ID: 197715 [Multi-domain] Cd Length: 58 Bit Score: 32.88 E-value: 7.87e-03
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Blast search parameters | ||||
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