RegulonDB

Gene
Name:	dtpD
Synonym(s):	ECK0698, G6378, b0709, ybgH
Genome position(nucleotides):	741075 <-- 742556 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	52.43
External database links:

ASAP:	ABE-0002420
ECHOBASE:	EB3088
OU-MICROARRAY:	b0709
PortEco:	dtpD
STRING:	511145.b0709
COLOMBOS:	dtpD

Gene

Name:

dtpD

Synonym(s):

ECK0698, G6378, b0709, ybgH

Genome position(nucleotides):

741075 <-- 742556 Genome Browser

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

52.43

External database links:

ASAP:

ECHOBASE:

OU-MICROARRAY:

PortEco:

STRING:

COLOMBOS:

Type

Positions

Sequence

14 -> 34

VVALQIWEYFSFYGMRALLIL

49 -> 69

ELFSAYCSLVYVTPILGGFLA

101 -> 121

SFLYLSLAIIVCGYGLFKSNV

235 -> 255

WSVYALIVATIIGLGVLAKIY

344 -> 364

IWGKFALGLGLMSAGFCILTL

Type

Positions

Sequence

14 -> 34

VVALQIWEYFSFYGMRALLIL

49 -> 69

ELFSAYCSLVYVTPILGGFLA

101 -> 121

SFLYLSLAIIVCGYGLFKSNV

235 -> 255

WSVYALIVATIIGLGVLAKIY

344 -> 364

IWGKFALGLGLMSAGFCILTL

379 -> 399

LMVLGLAVMGFAELFIDPVAM

77 -> 443

MAVMLGALLMAIGHVVLGASEIHPSFLYLSLAIIVCGYGLFKSNVSCLLGELYEPTDPRRDGGFSLMYAAGNVGSIIAPIACGYAQEEYSWAMGFGLAAVGMIAGLVIFLCGNRHFTHTRGVNKKVLRATNFLLPNWGWLLVLLVATPALITILFWKEWSVYALIVATIIGLGVLAKIYRKAENQKQRKELGLIVTLTFFSMLFWAFAQQGGSSISLYIDRFVNRDMFGYTVPTAMFQSINAFAVMLCGVFLAWVVKESVAGNRTVRIWGKFALGLGLMSAGFCILTLSARWSAMYGHSSLPLMVLGLAVMGFAELFIDPVAMSQITRIEIPGVTGVLTGIYMLLSGAIANYLAGVIADQTSQASFD

78 -> 98

AVMLGALLMAIGHVVLGASEI

138 -> 158

GGFSLMYAAGNVGSIIAPIAC

163 -> 163

413 -> 433

VLTGIYMLLSGAIANYLAGVI

18 -> 18

22 -> 22

267 -> 287

LGLIVTLTFFSMLFWAFAQQG

297 -> 297

312 -> 332

MFQSINAFAVMLCGVFLAWVV

212 -> 232

NWGWLLVLLVATPALITILFW

21 -> 21

167 -> 187

WAMGFGLAAVGMIAGLVIFLC

395 -> 395

462 -> 482

ITWGALACVGLVLMIWLYQAL

Multifun Terms (GenProtEC)

1 - metabolism --> 1.1 - carbon utilization --> 1.1.3 - amino acids

4 - transport --> 4.2 - Electrochemical potential driven transporters --> 4.2.A - Porters (Uni-, Sym- and Antiporters)

6 - cell structure --> 6.1 - membrane

Gene Ontology Terms (GO)

cellular_component

GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane

molecular_function

GO:0022857 - transmembrane transporter activity
GO:0015333 - peptide:proton symporter activity
GO:0042937 - tripeptide transmembrane transporter activity
GO:0035673 - oligopeptide transmembrane transporter activity
GO:0071916 - dipeptide transmembrane transporter activity
GO:1904680 - peptide transmembrane transporter activity

biological_process

GO:0015031 - protein transport
GO:0006857 - oligopeptide transport
GO:0015833 - peptide transport
GO:0042938 - dipeptide transport
GO:0042939 - tripeptide transport
GO:0055085 - transmembrane transport
GO:0035672 - oligopeptide transmembrane transport
GO:1902600 - proton transmembrane transport
GO:0035442 - dipeptide transmembrane transport

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	dtpDp5	742622	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.418. P-value: 9.327e-5 Read more >	[ICWHO]	[3]
promoter	dtpDp6	742623	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.55. P-value: 6.979e-5 Read more >	[ICWHO]	[3]
promoter	TSS_833	742669	reverse	nd	[RS-EPT-CBR]	[4]
promoter	dtpDp8	742670	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.894. P-value: 4.586e-5 Read more >	[ICWHO]	[3]
promoter	TSS_835 (cluster)	743357	forward	For this promoter, there is a cluster of 2 transcription start sites,in the interval 743357 to 743358, where the highest frequency is at position 742580. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[4]
promoter	TSS_836	743410	forward	nd	[RS-EPT-CBR]	[4]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

dtpDp5

742622

reverse

Similarity to the consensus
Read more >

[ICWHO]

[3]

promoter

dtpDp6

742623

reverse

Similarity to the consensus
Read more >

[ICWHO]

[3]

promoter

TSS_833

742669

reverse

[RS-EPT-CBR]

[4]

promoter

dtpDp8

742670

reverse

Similarity to the consensus
Read more >

[ICWHO]

[3]

promoter

TSS_835 (cluster)

743357

forward

For this promoter, there
Read more >

[RS-EPT-CBR]

[4]

promoter

TSS_836

743410

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] Jindal S., Yang L., Day PJ., Kell DB., 2019, Involvement of multiple influx and efflux transporters in the accumulation of cationic fluorescent dyes by Escherichia coli., BMC Microbiol 19(1):195
[2] Kitamura K., Kinsui EZ., Abe F., 2017, Critical role of the proton-dependent oligopeptide transporter (POT) in the cellular uptake of the peptidyl nucleoside antibiotic, blasticidin S., Biochim Biophys Acta 1864(2):393-398
[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] Jindal S., Yang L., Day PJ., Kell DB., 2019, Involvement of multiple influx and efflux transporters in the accumulation of cationic fluorescent dyes by Escherichia coli., BMC Microbiol 19(1):195

[2] Kitamura K., Kinsui EZ., Abe F., 2017, Critical role of the proton-dependent oligopeptide transporter (POT) in the cellular uptake of the peptidyl nucleoside antibiotic, blasticidin S., Biochim Biophys Acta 1864(2):393-398

[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.