RegulonDB

RegulonDB RegulonDB 10.9: Gene Form

pgrR gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	pgrR
Synonym(s):	ECK1325, G6664, b1328, ycjZ
Genome position(nucleotides):	1391991 --> 1392890 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	46.56
External database links:

ASAP:	ABE-0004457
ECHOBASE:	EB3682
ECOLIHUB:	ycjZ
OU-MICROARRAY:	b1328
STRING:	511145.b1328
COLOMBOS:	pgrR

Product

Name:

DNA-binding transcriptional repressor PgrR

Synonym(s):

PgrR, YcjZ

Sequence:

Get amino acid sequence Fasta Format

Regulator Family:

LysR

Cellular location:

cytosol

Molecular weight:

33.482

Isoelectric point:

9.458

Motif(s):

Type	Positions	Sequence
	4 -> 61	EEIADLMAFVVVAEERSFTRAAARLSMAQSALSQIVRRIEERLGLRLLTRTTRSVVPT
	21 -> 40	FTRAAARLSMAQSALSQIVR
	8 -> 65	DLMAFVVVAEERSFTRAAARLSMAQSALSQIVRRIEERLGLRLLTRTTRSVVPTEAGE
	90 -> 294	NRPSGTIRITTVEHAAKTILLPAMRTFLKSHPEIDIQLTIDYGLTDVVSERFDAGVRLGGEMDKDMIAIRIGPDIPMAIVGSPDYFSRRSVPTSVSQLIDHQAINLYLPTSGTANRWRLIRGGREVRVRMEGQLLLNTIDLIIDAAIDGHGLAYLPYDQVERAIKEKKLIRVLDKFTPDLPGYHLYYPHRRHAGSAFSLFIDRLK

Classification:

Multifun Terms (GenProtEC)
		2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
		3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.2 - activator
		3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol
	molecular_function	GO:0003677 - DNA binding GO:0003700 - DNA-binding transcription factor activity GO:0043565 - sequence-specific DNA binding
	biological_process	GO:0006351 - transcription, DNA-templated GO:0006355 - regulation of transcription, DNA-templated GO:0045892 - negative regulation of transcription, DNA-templated GO:0071978 - bacterial-type flagellum-dependent swarming motility

Note(s):

Note(s): ...[more].

Evidence:

[APPPINH] Assay of protein partially-purified from its native host
[HIFS] Human inference of function from sequence

Reference(s):

[1] Perez-Rueda E., et al., 2000
[2] Perez-Rueda E., et al., 2004
[3] Shimada T., et al., 2013

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

MODBASE:

PFAM:

PFAM:

PRIDE:

PRINTS:

PROSITE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

pgrR

Operon arrangement:

Transcription unit	Promoter
pgrR

Elements in the selected gene context region unrelated to any object in RegulonDB

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	ycjZp7	1391872	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 3.515. P-value: 5.657e-5 Read more >	[ICWHO]	[4]
promoter	TSS_1753 (cluster)	1391946	forward	For this promoter, there is a cluster of 2 transcription start sites,in the interval 1391946 to 1391947, where the highest frequency is at position 1389971. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[5]
promoter	TSS_1754	1392990	reverse	nd	[RS-EPT-CBR]	[5]
promoter	mppAp5	1393054	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 2.916. P-value: 4.450e-5 Read more >	[ICWHO]	[4]
promoter	mppAp13	1393121	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.823. P-value: 9.234e-5 Read more >	[ICWHO]	[4]
promoter	mppAp9	1393139	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.454. P-value: 4.406e-5 Read more >	[ICWHO]	[4]
promoter	mppAp4	1393204	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 2.905. P-value: 9.805e-5 Read more >	[ICWHO]	[4]

Evidence
[ICWHO] Inferred computationally without human oversight
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] Perez-Rueda E., Collado-Vides J., 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12., Nucleic Acids Res 28(8):1838-47
[2] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50
[3] Shimada T., Yamazaki K., Ishihama A., 2013, Novel regulator PgrR for switch control of peptidoglycan recycling in Escherichia coli., Genes Cells 18(2):123-34
[4] 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
[5] 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.

RegulonDB