RegulonDB

Gene
Name:	pdeR
Synonym(s):	ECK1280, G6639, b1285, gmr, yciR
Genome position(nucleotides):	1344757 <-- 1346742 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	48.49
External database links:

ASAP:	ABE-0004317
ECHOBASE:	EB3191
OU-MICROARRAY:	b1285
PortEco:	gmr
STRING:	511145.b1285
COLOMBOS:	pdeR

Gene

Name:

pdeR

Synonym(s):

ECK1280, G6639, b1285, gmr, yciR

Genome position(nucleotides):

1344757 <-- 1346742 Genome Browser

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

48.49

External database links:

ASAP:

ECHOBASE:

OU-MICROARRAY:

PortEco:

STRING:

COLOMBOS:

Type

Positions

Sequence

175 -> 175

256 -> 256

123 -> 225

AIVILDSRGNIQRFNRLCEDYTGLKEHDVIGQSVFKLFMSRREAAASRRNNRVFFRSGNAYEVELWIPTCKGQRLFLFRNKFVHSGSGKNEIFLICSGTDITE

344 -> 344

412 -> 644

NLRKALENDQLVIHYQPKITWRGEVRSLEALVRWQSPERGLIPPLDFISYAEESGLIVPLGRWVILDVVRQVAKWRDKGINLRVAVNISARQLADQTIFTALKQVLQELNFEYCPIDVELTESCLIENDELALSVIQQFSQLGAQVHLDDFGTGYSSLSQLARFPIDAIKLDQVFVRDIHKQPVSQSLVRAIVAVAQALNLQVIAEGVESAKEDAFLTKNGINERQGFLFAKP

Type

Positions

Sequence

175 -> 175

256 -> 256

123 -> 225

AIVILDSRGNIQRFNRLCEDYTGLKEHDVIGQSVFKLFMSRREAAASRRNNRVFFRSGNAYEVELWIPTCKGQRLFLFRNKFVHSGSGKNEIFLICSGTDITE

344 -> 344

412 -> 644

4 -> 4

406 -> 658

YLWLDTNLRKALENDQLVIHYQPKITWRGEVRSLEALVRWQSPERGLIPPLDFISYAEESGLIVPLGRWVILDVVRQVAKWRDKGINLRVAVNISARQLADQTIFTALKQVLQELNFEYCPIDVELTESCLIENDELALSVIQQFSQLGAQVHLDDFGTGYSSLSQLARFPIDAIKLDQVFVRDIHKQPVSQSLVRAIVAVAQALNLQVIAEGVESAKEDAFLTKNGINERQGFLFAKPMPAVAFERWYKRYL

109 -> 179

GLSFAEQVVSEAHSAIVILDSRGNIQRFNRLCEDYTGLKEHDVIGQSVFKLFMSRREAAASRRNNRVFFRS

113 -> 113

237 -> 390

ANTDSITGLPNRNAMQDLIDHAINHADNNKVGVVYLDLDNFKKVNDAYGHLFGDQLLRDVSLAILSCLEHDQVLARPGGDEFLVLASNTSQSALEAMASRILTRLRLPFRIGLIEVYTSCSVGIALSPEHGSDSTAIIRHADTAMYTAKEGGRG

265 -> 397

NKVGVVYLDLDNFKKVNDAYGHLFGDQLLRDVSLAILSCLEHDQVLARPGGDEFLVLASNTSQSALEAMASRILTRLRLPFRIGLIEVYTSCSVGIALSPEHGSDSTAIIRHADTAMYTAKEGGRGQFCVFTP

Multifun Terms (GenProtEC)

2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related

5 - cell processes --> 5.5 - adaptations

Gene Ontology Terms (GO)

molecular_function

GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0005525 - GTP binding
GO:0071111 - cyclic-guanylate-specific phosphodiesterase activity

biological_process

GO:0010608 - posttranscriptional regulation of gene expression
GO:0019935 - cyclic-nucleotide-mediated signaling
GO:0031280 - negative regulation of cyclase activity

Transcriptional Regulation
	Display Regulation
Repressed by:	FliZ, RutR

Transcriptional Regulation

Display Regulation

Repressed by:

FliZ, RutR

RNA cis-regulatory element

Attenuation:	Transcriptional

RNA cis-regulatory element

Attenuation:

Transcriptional

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	yciTp1	1344544	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: -3.36. P-value: 8.190e-5 Read more >	[ICWHO]	[3]
promoter	TSS_1730	1344637	reverse	nd	[RS-EPT-CBR]	[4]
promoter	TSS_1731	1346842	reverse	nd	[RS-EPT-CBR]	[4]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

yciTp1

1344544

reverse

Similarity to the consensus
Read more >

[ICWHO]

[3]

promoter

TSS_1730

1344637

reverse

[RS-EPT-CBR]

[4]

promoter

TSS_1731

1346842

reverse

[RS-EPT-CBR]

[4]

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

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] Cimdins A., Simm R., Li F., Luthje P., Thorell K., Sjoling Å., Brauner A., Romling U., 2017, Alterations of c-di-GMP turnover proteins modulate semi-constitutive rdar biofilm formation in commensal and uropathogenic Escherichia coli., Microbiologyopen 6(5)
[2] Somorin YM., Vollmerhausen T., Waters N., Pritchard L., Abram F., Brennan F., O'Byrne C., 2018, Absence of Curli in Soil-Persistent Escherichia coli Is Mediated by a C-di-GMP Signaling Defect and Suggests Evidence of Biofilm-Independent Niche Specialization., Front Microbiol 9:1340
[3] 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
[4] 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.

Reference(s)

[1] Cimdins A., Simm R., Li F., Luthje P., Thorell K., Sjoling Å., Brauner A., Romling U., 2017, Alterations of c-di-GMP turnover proteins modulate semi-constitutive rdar biofilm formation in commensal and uropathogenic Escherichia coli., Microbiologyopen 6(5)

[2] Somorin YM., Vollmerhausen T., Waters N., Pritchard L., Abram F., Brennan F., O'Byrne C., 2018, Absence of Curli in Soil-Persistent Escherichia coli Is Mediated by a C-di-GMP Signaling Defect and Suggests Evidence of Biofilm-Independent Niche Specialization., Front Microbiol 9:1340

[3] 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

[4] 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.