RegulonDB

RegulonDB RegulonDB 11.1: Operon Form

thrS-infC-rpmI-rplT-pheMST-ihfA operon and associated TUs in Escherichia coli K-12 genome

Operon
Name:	thrS-infC-rpmI-rplT-pheMST-ihfA
This page displays every known transcription unit of this operon and their known regulation.

Transcription unit

Name:	ihfA
Synonym(s):	OP00240, himA
Gene(s):	ihfA Genome Browser M3D Gene expression COLOMBOS
Reference(s):	[1] Aviv M., et al., 1994
Promoter
Name:	ihfAp4
+1:	1795721
Sigma Factor:	Sigma38 Sigmulon
Distance from start of the gene:	169
Sequence:	gatattttatccgaatgtaagaaagttggcgtaaatcaggtagttggcgtaaacttatttGacgtgtaccgcggtaagggt -35 -10 +1
Evidence:	[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[1] Aviv M., et al., 1994 [2] Huerta AM., et al., 2003 [3] Mechulam Y., et al., 1987
Terminator(s)
Type:	rho-independent
Sequence:	agtgaaaagaAAAAAGGCCGCAGAGCGGCCTTTTtagttagatc
Reference(s):	[4] Mechulam Y., et al., 1985

TF binding sites (TFBSs)

[IHF,-] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
remote	IHF	repressor	ihfAp4	1795662	1795674	54.0	agagcctcgcCATAAGCCTGATCctgcaagata	nd	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	nd	[1], [5]
proximal	IHF	repressor	ihfAp4	1795736	1795748	-21.0	agttggcgtaAATCAGGTAGTTGgcgtaaactt	nd	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	nd	[1], [5]
proximal	IHF	repressor	ihfAp4	1795762	1795774	-47.0	gcggatatttTATCCGAATGTAAgaaagttggc	nd	[COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	nd	[1], [5]

Transcription factor	Function	Promoter	Binding Sites	Evidence (Confirmed, Strong, Weak)	Reference(s)
IHF	repressor	ihfAp4	1795762	1795774	-47.0	gcggatatttTATCCGAATGTAAgaaagttggc	nd	[1], [5]
IHF	repressor	ihfAp4	1795736	1795748	-21.0	agttggcgtaAATCAGGTAGTTGgcgtaaactt	nd	[1], [5]
IHF	repressor	ihfAp4	1795662	1795674	54.0	agagcctcgcCATAAGCCTGATCctgcaagata	nd	[1], [5]

Transcription unit

Name:	pheM
Gene(s):	pheM Genome Browser M3D Gene expression COLOMBOS
Note(s):	The pheM ORF codes for the leader peptide that controls pheMST operon expression in response to phenylalanine availability, through an attenuation mechanism Springer M,1983. Therefore, the transcription sometimes ends behind pheM Fayat G,1983. The RNA produced by the pheM gene has been observed mainly in the poles of the cell Kannaiah S, Livny J, Amster-Choder O,2019.
Evidence:	[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s):	[6] Fayat G., et al., 1983
Promoter
Name:	pheMp
+1:	1799301
Distance from start of the gene:	31
Sequence:	tttcgtttcaacgccatcaaaacattgacttttatcgccgtagccttttcaataaaggtcTtttgaagagtaccaaaaggt
Evidence:	[COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[6] Fayat G., et al., 1983 [7] Springer M., et al., 1985
Terminator(s)
Type:	rho-independent
Sequence:	tacaaaaaaaGCCTCCACTGGGAGGCtttcaggcgc
Reference(s):	[6] Fayat G., et al., 1983

Transcription unit

Name:	pheMST-ihfA
Gene(s):	ihfA, pheT, pheS, pheM Genome Browser M3D Gene expression COLOMBOS
Note(s):	The pheMST operon, which codes for the phenylalanyl-tRNA synthetase, is the target of attenuation control (by the PheM leader peptide) Mayaux JF,1984 in response to phenylalanine availability Springer M,1985 Springer M,1983 Mayaux JF,1985; specifically, through tRNA-pnenylalanyl aminoacylation Trudel M,1984. As an extra step in regulation it has been observed that the transcription of the upstream gene, rplT (coding for the ribosomal protein L20 Fayat G,1983), passes through its own terminator and continues to the pheMST operon, but the transcription is stopped at the end of the attenuator region because of the 90% effective pheM terminator, before the pheS transcription can start Springer M,1985. In addition, the ihfA gene has been identified as part of the same pheMST transcription unit, not only because it is downstream and in the same direction, but also because there is a translational start sequence overlapping the pheT end and a Rho-independent terminator sequence downstream of ihfA Mechulam Y,1985.
Evidence:	[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s):	[6] Fayat G., et al., 1983 [8] Mayaux JF., et al., 1985 [9] Mayaux JF., et al., 1984 [4] Mechulam Y., et al., 1985 [7] Springer M., et al., 1985 [10] Springer M., et al., 1983 [11] Trudel M., et al., 1984
Promoter
Name:	pheMp
+1:	1799301
Distance from start of the gene:	31
Sequence:	tttcgtttcaacgccatcaaaacattgacttttatcgccgtagccttttcaataaaggtcTtttgaagagtaccaaaaggt
Evidence:	[COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[6] Fayat G., et al., 1983 [7] Springer M., et al., 1985
Terminator(s)
Type:	rho-independent
Sequence:	agtgaaaagaAAAAAGGCCGCAGAGCGGCCTTTTtagttagatc
Reference(s):	[4] Mechulam Y., et al., 1985

Transcription unit

Name:	rplT-pheM
Gene(s):	pheM, rplT Genome Browser M3D Gene expression COLOMBOS
Note(s):	rplT transcription can pass through its own terminator and continue with the downstream operon pheMST, but there is an efficient terminator before the pheS gene. The pheMST operon is regulated by attenuation in response to phenylalanine availability, through its peptide leader pheM and its antiterminator or terminator structures Fayat G,1983.
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s):	[6] Fayat G., et al., 1983
Promoter
Name:	rplTp
+1:	1799763
Distance from start of the gene:	14
Sequence:	cgcgtgcctgccgtacgcataagccgttaacgtttttaactttttaattagaatatagatAcaggagagcacatatggctc
Evidence:	[COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[6] Fayat G., et al., 1983 [12] Wu TH., et al., 1984
Terminator(s)
Type:	rho-independent
Sequence:	tacaaaaaaaGCCTCCACTGGGAGGCtttcaggcgc
Reference(s):	[6] Fayat G., et al., 1983

TF binding sites (TFBSs)

[FNR,-] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
nd	FNR	repressor	rplTp	nd	nd	nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[13]

Transcription factor	Function	Promoter	Binding Sites	Evidence (Confirmed, Strong, Weak)	Reference(s)
FNR	repressor	rplTp	nd	nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[13]

Transcription unit

Name:	rplT
Gene(s):	rplT Genome Browser M3D Gene expression COLOMBOS
Note(s):	The rplT gene codes for the L20 ribosomal protein. Its gene expression is corelated with the downstream operon pheMST, which codes for the phenylalanine-tRNA synthetase. Sometimes transcription stops at the end of rplT, and other times it continues downstream to the pheST attenuation control region ( composed of the pheM ORF that codes for the leader peptide and the secondary structure regions) Fayat G,1983.
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s):	[6] Fayat G., et al., 1983
Promoter
Name:	rplTp
+1:	1799763
Distance from start of the gene:	14
Sequence:	cgcgtgcctgccgtacgcataagccgttaacgtttttaactttttaattagaatatagatAcaggagagcacatatggctc
Evidence:	[COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[6] Fayat G., et al., 1983 [12] Wu TH., et al., 1984
Terminator(s)
Type:	rho-independent
Sequence:	gaaacgaaaaGAGGGAGACTAGCTCCCTCTttcaactggc
Reference(s):	[6] Fayat G., et al., 1983

TF binding sites (TFBSs)

[FNR,-] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
nd	FNR	repressor	rplTp	nd	nd	nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[13]

Transcription factor	Function	Promoter	Binding Sites	Evidence (Confirmed, Strong, Weak)	Reference(s)
FNR	repressor	rplTp	nd	nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[13]

Transcription unit

Name:	rpmI-rplT
Gene(s):	rplT, rpmI Genome Browser M3D Gene expression COLOMBOS
Note(s):	rpmI may be regulated by CRP, based on a site identified via Selex analysis Shimada T,2013.
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s):	[14] Lesage P., et al., 1990 [12] Wu TH., et al., 1984
Promoter
Name:	rpmIp
+1:	1800427
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	428
Sequence:	tagacttagtcgagatcagccctaacgccgagccgccggtttgtcgtataatggattacgGcaaattcctctatgaaaaga -35 -10 +1
Note(s):	It is probable that the three promoters localized upstream from rpmIp contribute to more than 90% of the rplT expression Lesage P,1990 The expression of the rpml and rplT genes, independently from infC, seems to be irrelevant, since the promoter of both (rpmlp) contributes to only a small fraction of rplT expression.
Evidence:	[COMP-AINF] [COMP-HINF] [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[6] Fayat G., et al., 1983 [2] Huerta AM., et al., 2003 [14] Lesage P., et al., 1990 [15] Maciag A., et al., 2011 [16] Mayaux JF., et al., 1983 [17] Wertheimer SJ., et al., 1988 [12] Wu TH., et al., 1984
Terminator(s)
Type:	rho-independent
Sequence:	gaaacgaaaaGAGGGAGACTAGCTCCCTCTttcaactggc
Reference(s):	[6] Fayat G., et al., 1983

Allosteric regulation of RNA-polymerase

	Regulator	Function	Promoter target of RNApol	Growth Conditions	Note	Evidence	Reference
	DksA-ppGpp	inhibition	rpmIp	nd		[EXP-IDA-PURIFIED-PROTEIN] [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [EXP-IMP]	[18]

Evidence:	[EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis [EXP-IMP] Inferred from mutant phenotype
Reference(s):	[18] Lemke JJ., et al., 2011

Transcription unit

Name:	infC-rpmI-rplT
Gene(s):	rplT, rpmI, infC Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s):	[14] Lesage P., et al., 1990
Promoter
Name:	infCp2
+1:	1800818
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	180
Sequence:	gcgggcattcgtgttaaagcagacttgagaaatgagaagattggctttaaaatccgcgagCacactttgcgtcgcgtccca -35 -10 +1
Note(s):	infCp2 is the major promoter for infC expression Wertheimer SJ,1988.
Evidence:	[COMP-AINF] [COMP-AINF-POSITIONAL-IDENTIFICATION] [COMP-HINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[19] Butler JS., et al., 1986 [2] Huerta AM., et al., 2003 [20] Liveris D., et al., 1991 [16] Mayaux JF., et al., 1983 [21] Pramanik A., et al., 1986 [17] Wertheimer SJ., et al., 1988
Terminator(s)
Type:	rho-independent
Sequence:	gaaacgaaaaGAGGGAGACTAGCTCCCTCTttcaactggc
Reference(s):	[6] Fayat G., et al., 1983

Allosteric regulation of RNA-polymerase

	Regulator	Function	Promoter target of RNApol	Growth Conditions	Note	Evidence	Reference
	DksA-ppGpp	inhibition	infCp2	nd		[EXP-IDA-PURIFIED-PROTEIN] [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [EXP-IMP]	[18]

Evidence:	[EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis [EXP-IMP] Inferred from mutant phenotype
Reference(s):	[18] Lemke JJ., et al., 2011

Transcription unit

Name:	infC
Gene(s):	infC Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s):	[14] Lesage P., et al., 1990
Promoter
Name:	infCp1
+1:	1801346
Distance from start of the gene:	708
Sequence:	actgaagaacaaattcgcgatgaagttaacggatgtatccgtttagtctatgatatgtacAgcacttttggcttcgagaag
Note(s):	Although there are only 3 bp in the intergenic region between thrS and infC, infC expression is independent from thrS since its expression is controlled by three promoters which depend on several physiological conditions Wertheimer SJ,1988.
Evidence:	[COMP-AINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR]
Reference(s):	[19] Butler JS., et al., 1986 [20] Liveris D., et al., 1991 [16] Mayaux JF., et al., 1983 [22] Salgado H, et al., 2012 [17] Wertheimer SJ., et al., 1988
Terminator(s)
Type:	rho-independent
Sequence:	taataaacgaAACAAAGGCGAACAAAGCCTGTGAAGCCCGAAGGCTCCACAGACAGTGCTACTTGAAggccttactg
Reference(s):	[23] Feng CQ., et al., 2019 [24] Lesnik EA., et al., 2001

Allosteric regulation of RNA-polymerase

	Regulator	Function	Promoter target of RNApol	Growth Conditions	Note	Evidence	Reference
	DksA-ppGpp	inhibition	infCp1	nd		[EXP-IDA-PURIFIED-PROTEIN] [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [EXP-IMP]	[18]

Evidence:	[EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis [EXP-IMP] Inferred from mutant phenotype
Reference(s):	[18] Lemke JJ., et al., 2011

Transcription unit

Name:	thrS-infC
Gene(s):	infC, thrS Genome Browser M3D Gene expression COLOMBOS
Note(s):	A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for thrS. This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence:	[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s):	[14] Lesage P., et al., 1990 [25] Springer M., et al., 1986
Promoter
Name:	thrSp
+1:	1802733
Distance from start of the gene:	163
Sequence:	aatcgaatcaatgtgaaacggaaaggtacaatctccctttttttagtgttaacatcgctcAaccgggtggaaggtgagagg
Evidence:	[EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR]
Reference(s):	[14] Lesage P., et al., 1990 [16] Mayaux JF., et al., 1983 [22] Salgado H, et al., 2012 [25] Springer M., et al., 1986 [17] Wertheimer SJ., et al., 1988
Terminator(s)
Type:	rho-independent
Sequence:	taataaacgaAACAAAGGCGAACAAAGCCTGTGAAGCCCGAAGGCTCCACAGACAGTGCTACTTGAAggccttactg
Reference(s):	[23] Feng CQ., et al., 2019 [24] Lesnik EA., et al., 2001

TF binding sites (TFBSs)

[NsrR,-] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
remote	NsrR	repressor	thrSp	1802649	1802660	80.0	catttgttggCTAGATGGTTTCgcaatgaact	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[26]

Allosteric regulation of RNA-polymerase

	Regulator	Function	Promoter target of RNApol	Growth Conditions	Note	Evidence	Reference
	DksA-ppGpp	inhibition	thrSp	nd		[EXP-IDA-PURIFIED-PROTEIN] [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [EXP-IMP]	[18]

Evidence:	[EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis [EXP-IMP] Inferred from mutant phenotype
Reference(s):	[18] Lemke JJ., et al., 2011

Transcription unit

Name:	thrS-infC-rpmI-rplT-pheMST-ihfA
Gene(s):	ihfA, pheT, pheS, pheM, rplT, rpmI, infC, thrS Genome Browser M3D Gene expression COLOMBOS
Note(s):	The transcription pattern in the thrS-infC-rpmI-rplT-pheMST-infA cluster is highly complex and the mRNA level for each gene is determined by a variety of factors, including multiple promoters, cotranscription, and readthrough of transcription termination signals. Although there is no experimental evidence of a transcript that comprises the whole cluster of genes Wertheimer SJ,1988, we would not like Fayat G,1983 to discard the possibility that these genes form an operon. In addition, there are at least six regions upstream thrS that could serve as promoters, based on homology to the Escherichia coli σ⁷⁰ consensus sequence Wertheimer SJ,1988.
Evidence:	[IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process
Reference(s):	[6] Fayat G., et al., 1983 [17] Wertheimer SJ., et al., 1988
Promoter
Name:	thrSp
+1:	1802733
Distance from start of the gene:	163
Sequence:	aatcgaatcaatgtgaaacggaaaggtacaatctccctttttttagtgttaacatcgctcAaccgggtggaaggtgagagg
Evidence:	[EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR]
Reference(s):	[14] Lesage P., et al., 1990 [16] Mayaux JF., et al., 1983 [22] Salgado H, et al., 2012 [25] Springer M., et al., 1986 [17] Wertheimer SJ., et al., 1988

TF binding sites (TFBSs)

[NsrR,-] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
remote	NsrR	repressor	thrSp	1802649	1802660	80.0	catttgttggCTAGATGGTTTCgcaatgaact	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS]	W	[26]

Allosteric regulation of RNA-polymerase

	Regulator	Function	Promoter target of RNApol	Growth Conditions	Note	Evidence	Reference
	DksA-ppGpp	inhibition	thrSp	nd		[EXP-IDA-PURIFIED-PROTEIN] [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [EXP-IMP]	[18]

Evidence:	[EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis [EXP-IMP] Inferred from mutant phenotype
Reference(s):	[18] Lemke JJ., et al., 2011

RNA cis-regulatory element

Regulation, transcriptional elongation
Attenuator type:	Transcriptional
Strand:	reverse

Structure type	Energy	LeftPos	RightPos	Sequence (RNA-strand)
terminator	-13.1	1799152	1799179	acagcgcctgAAAGCCTCCCAGTGGAGGCTTTTTTTGtatgcgcgtt
terminator	-6.0	1799359	1799379	agttgaaagaGGGAGCTAGTCTCCCTCTTTtcgtttcaac
terminator	-23.3	1800034	1800078	aagtagcactGTCTGTGGAGCCTTCGGGCTTCACAGGCTTTGTTCGCCTTTGTTtcgtttatta
terminator	-8.3	1802585	1802617	aatttttcttTGTATGTGATCTTTCGTGTGGGTCACCACTGCaaataaggat
anti-terminator	-5.13	1799175	1799216	aatccaggagGCTAGCGCGTGAGAAGAGAAACGGAAAACAGCGCCTGAAAGcctcccagtg
anti-terminator	-8.7	1799373	1799405	aagcgaaagcAGCTCTGGCATAAGCCAGTTGAAAGAGGGAGCtagtctccct
anti-terminator	-8.2	1800065	1800097	aagaaacagtAAGGCCTTCAAGTAGCACTGTCTGTGGAGCCTtcgggcttca
anti-anti-terminator	-6.13	1799194	1799243	ccgcttctttTTTTACTTTAGCACCTGAATCCAGGAGGCTAGCGCGTGAGAAGAGAAACggaaaacagc
anti-anti-terminator	-3.5	1800082	1800116	catggtgctcGCTCCTAAGAAGAAACAGTAAGGCCTTCAAGTAGcactgtctgt

Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"

REGULATION, RNA cis-regulatory element:
Rfam type:	Cis-reg; leader
Strand:	reverse

	Description	Rfam score	Left Pos	Right Pos	Sequence (RNA-strand)
	Phenylalanine leader peptide	77.4	1799152	1799276	aaagguaacgCAAGCAAUGAAUGCUGCUAUUUUCCGCUUCUUUUUUUACUUUAGCACCUGAAUCCAGGAGGCUAGCGCGUGAGAAGAGAAACGGAAAACAGCGCCUGAAAGCCUCCCAGUGGAGGCUUUUUUUGUaugcgcguuu

Notes: "The provied "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appears as the reverse complement of the sequence delimited by LeftPos-RightPos"

Evidence
[COMP-AINF] Inferred computationally without human oversight
[COMP-HINF] Inferred by a human based on computational evidence
[COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping
[COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping
[COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] Aviv M., Giladi H., Schreiber G., Oppenheim AB., Glaser G., 1994, Expression of the genes coding for the Escherichia coli integration host factor are controlled by growth phase, rpoS, ppGpp and by autoregulation., Mol Microbiol 14(5):1021-31
[2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78
[3] Mechulam Y., Blanquet S., Fayat G., 1987, Dual level control of the Escherichia coli pheST-himA operon expression. tRNA(Phe)-dependent attenuation and transcriptional operator-repressor control by himA and the SOS network., J Mol Biol 197(3):453-70
[4] Mechulam Y., Fayat G., Blanquet S., 1985, Sequence of the Escherichia coli pheST operon and identification of the himA gene., J Bacteriol 163(2):787-91
[5] Bykowski T., Sirko A., 1998, Selected phenotypes of ihf mutants of Escherichia coli., Biochimie 80(12):987-1001
[6] Fayat G., Mayaux JF., Sacerdot C., Fromant M., Springer M., Grunberg-Manago M., Blanquet S., 1983, Escherichia coli phenylalanyl-tRNA synthetase operon region. Evidence for an attenuation mechanism. Identification of the gene for the ribosomal protein L20., J Mol Biol 171(3):239-61
[7] Springer M., Mayaux JF., Fayat G., Plumbridge JA., Graffe M., Blanquet S., Grunberg-Manago M., 1985, Attenuation control of the Escherichia coli phenylalanyl-tRNA synthetase operon., J Mol Biol 181(4):467-78
[8] Mayaux JF., Fayat G., Panvert M., Springer M., Grunberg-Manago M., Blanquet S., 1985, Control of phenylalanyl-tRNA synthetase genetic expression. Site-directed mutagenesis of the pheS, T operon regulatory region in vitro., J Mol Biol 184(1):31-44
[9] Mayaux JF., Springer M., Graffe M., Fromant M., Fayat G., 1984, IS4 transposition in the attenuator region of the Escherichia coli pheS,T operon., Gene 30(1-3):137-46
[10] Springer M., Trudel M., Graffe M., Plumbridge J., Fayat G., Mayaux JF., Sacerdot C., Blanquet S., Grunberg-Manago M., 1983, Escherichia coli phenylalanyl-tRNA synthetase operon is controlled by attenuation in vivo., J Mol Biol 171(3):263-79
[11] Trudel M., Springer M., Graffe M., Fayat G., Blanquet S., Grunberg-Manago M., 1984, Regulation of E.coli phenylalanyl-tRNA synthetase operon in vivo., Biochim Biophys Acta 782(1):10-7
[12] Wu TH., Wood DL., Stein PL., Comer MM., 1984, Transcription of a gene cluster coding for two aminoacyl-tRNA synthetases and an initiation factor in Escherichia coli., J Mol Biol 173(2):177-209
[13] Salmon K., Hung SP., Mekjian K., Baldi P., Hatfield GW., Gunsalus RP., 2003, Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR., J Biol Chem 278(32):29837-55
[14] Lesage P., Truong HN., Graffe M., Dondon J., Springer M., 1990, Translated translational operator in Escherichia coli. Auto-regulation in the infC-rpmI-rplT operon., J Mol Biol 213(3):465-75
[15] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55
[16] Mayaux JF., Fayat G., Fromant M., Springer M., Grunberg-Manago M., Blanquet S., 1983, Structural and transcriptional evidence for related thrS and infC expression., Proc Natl Acad Sci U S A 80(20):6152-6
[17] Wertheimer SJ., Klotsky RA., Schwartz I., 1988, Transcriptional patterns for the thrS-infC-rplT operon of Escherichia coli., Gene 63(2):309-20
[18] Lemke JJ., Sanchez-Vazquez P., Burgos HL., Hedberg G., Ross W., Gourse RL., 2011, Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA., Proc Natl Acad Sci U S A 108(14):5712-7
[19] Butler JS., Springer M., Dondon J., Graffe M., Grunberg-Manago M., 1986, Escherichia coli protein synthesis initiation factor IF3 controls its own gene expression at the translational level in vivo., J Mol Biol 192(4):767-80
[20] Liveris D., Klotsky RA., Schwartz I., 1991, Growth rate regulation of translation initiation factor IF3 biosynthesis in Escherichia coli., J Bacteriol 173(12):3888-93
[21] Pramanik A., Wertheimer SJ., Schwartz JJ., Schwartz I., 1986, Expression of Escherichia coli infC: identification of a promoter in an upstream thrS coding sequence., J Bacteriol 168(2):746-51
[22] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.
[23] Feng CQ., Zhang ZY., Zhu XJ., Lin Y., Chen W., Tang H., Lin H., 2019, iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators., Bioinformatics 35(9):1469-1477
[24] Lesnik EA., Sampath R., Levene HB., Henderson TJ., McNeil JA., Ecker DJ., 2001, Prediction of rho-independent transcriptional terminators in Escherichia coli., Nucleic Acids Res 29(17):3583-94
[25] Springer M., Graffe M., Butler JS., Grunberg-Manago M., 1986, Genetic definition of the translational operator of the threonine-tRNA ligase gene in Escherichia coli., Proc Natl Acad Sci U S A 83(12):4384-8
[26] Partridge JD., Bodenmiller DM., Humphrys MS., Spiro S., 2009, NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility., Mol Microbiol 73(4):680-94

RegulonDB