RegulonDB

Gene
Name:	dgcN
Synonym(s):	ECK2601, EG12880, b2604, yfiN
Genome position(nucleotides):	2742383 --> 2743609 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	48.33
External database links:

ASAP:	ABE-0008570
ECHOBASE:	EB2718
OU-MICROARRAY:	b2604
PORTECO:	yfiN
REGULONDB:	b2604
STRING:	511145.b2604
M3D:	dgcN
COLOMBOS:	dgcN
PortEco:	b2604

Gene

Name:

dgcN

Synonym(s):

ECK2601, EG12880, b2604, yfiN

Genome position(nucleotides):

2742383 --> 2743609 Genome Browser

Strand:

forward

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

48.33

External database links:

ASAP:

ECHOBASE:

OU-MICROARRAY:

PORTECO:

REGULONDB:

STRING:

M3D:

COLOMBOS:

PortEco:

Type

Positions

Sequence

278 -> 408

KTSALLFLDGDNFKYINDTWGHATGDRVLIEIAKRLAEFGGLRHKAYRLGGDEFAMVLYDVQSESEVQQICSALTQIFNLPFDLHNGHQTTMTLSIGYAMTIEHASAEKLQELADHNMYQAKHQRAEKLVR

45 -> 145

LKQYAQKNLALTAATMTYSLEAAVVFADGPAATETLAALGQQGQFSTAEVRDKQQNILASWHYTRKDPGDTFSNFISHWLFPAPIIQPIRHNGETIGEVRL

53 -> 73

LALTAATMTYSLEAAVVFADG

329 -> 330

113 -> 133

GDTFSNFISHWLFPAPIIQPI

Type

Positions

Sequence

278 -> 408

KTSALLFLDGDNFKYINDTWGHATGDRVLIEIAKRLAEFGGLRHKAYRLGGDEFAMVLYDVQSESEVQQICSALTQIFNLPFDLHNGHQTTMTLSIGYAMTIEHASAEKLQELADHNMYQAKHQRAEKLVR

45 -> 145

LKQYAQKNLALTAATMTYSLEAAVVFADGPAATETLAALGQQGQFSTAEVRDKQQNILASWHYTRKDPGDTFSNFISHWLFPAPIIQPIRHNGETIGEVRL

53 -> 73

LALTAATMTYSLEAAVVFADG

329 -> 330

113 -> 133

GDTFSNFISHWLFPAPIIQPI

155 -> 175

FIWFSLAVLTGCILLASGIAI

25 -> 45

SIFITMMLIWLLLSVTSVLTL

183 -> 236

NGLVEALKNITDVVHDVRSNRNFSRRVSEERIAEFHRFALDFNSLLDEMEEWQL

249 -> 403

ALHDPLTGLANRAAFRSGINTLMNNSDARKTSALLFLDGDNFKYINDTWGHATGDRVLIEIAKRLAEFGGLRHKAYRLGGDEFAMVLYDVQSESEVQQICSALTQIFNLPFDLHNGHQTTMTLSIGYAMTIEHASAEKLQELADHNMYQAKHQRA

Multifun Terms (GenProtEC)

5 - cell processes --> 5.3 - motility, chemotaxis, energytaxis (aerotaxis, redoxtaxis etc)

Gene Ontology Terms (GO)

cellular_component

GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0016021 - integral component of membrane
GO:0032153 - cell division site

molecular_function

GO:0005515 - protein binding
GO:0016740 - transferase activity
GO:0046872 - metal ion binding
GO:0000166 - nucleotide binding
GO:0005525 - GTP binding
GO:0042802 - identical protein binding
GO:0052621 - diguanylate cyclase activity

biological_process

GO:0007165 - signal transduction
GO:0043709 - cell adhesion involved in single-species biofilm formation
GO:1902201 - negative regulation of bacterial-type flagellum-dependent cell motility
GO:0036460 - cellular response to cell envelope stress

Transcriptional Regulation
	Display Regulation
Repressed by:	YjjQ

Transcriptional Regulation

Display Regulation

Repressed by:

YjjQ

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	yfiRp7	2741677	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 5.215. P-value: 2.931e-6 Read more >	[ICWHO]	[3]
promoter	yfiRp8	2741702	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 9.849. P-value: 1.456e-6 Read more >	[ICWHO]	[3]
promoter	yfiRp6	2741751	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.328. P-value: 8.440e-5 Read more >	[ICWHO]	[3]
promoter	yfiRp5	2741762	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.784. P-value: 5.888e-5 Read more >	[ICWHO]	[3]
promoter	yfiRp3	2741822	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.584. P-value: 6.979e-5 Read more >	[ICWHO]	[3]
promoter	TSS_2945	2743141	forward	nd	[RS-EPT-CBR]	[4]
promoter	TSS_2946	2743327	forward	nd	[RS-EPT-CBR]	[4]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

yfiRp7

2741677

forward

Similarity to the consensus
Read more >

[ICWHO]

[3]

promoter

yfiRp8

2741702

forward

Similarity to the consensus
Read more >

[ICWHO]

[3]

promoter

yfiRp6

2741751

forward

Similarity to the consensus
Read more >

[ICWHO]

[3]

promoter

yfiRp5

2741762

forward

Similarity to the consensus
Read more >

[ICWHO]

[3]

promoter

yfiRp3

2741822

forward

Similarity to the consensus
Read more >

[ICWHO]

[3]

promoter

TSS_2945

2743141

forward

[RS-EPT-CBR]

[4]

promoter

TSS_2946

2743327

forward

[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] Boehm A., Kaiser M., Li H., Spangler C., Kasper CA., Ackermann M., Kaever V., Sourjik V., Roth V., Jenal U., 2010, Second messenger-mediated adjustment of bacterial swimming velocity., Cell 141(1):107-16
[2] Steiner S., Lori C., Boehm A., Jenal U., 2013, Allosteric activation of exopolysaccharide synthesis through cyclic di-GMP-stimulated protein-protein interaction., EMBO J 32(3):354-68
[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] Boehm A., Kaiser M., Li H., Spangler C., Kasper CA., Ackermann M., Kaever V., Sourjik V., Roth V., Jenal U., 2010, Second messenger-mediated adjustment of bacterial swimming velocity., Cell 141(1):107-16

[2] Steiner S., Lori C., Boehm A., Jenal U., 2013, Allosteric activation of exopolysaccharide synthesis through cyclic di-GMP-stimulated protein-protein interaction., EMBO J 32(3):354-68

[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.