RegulonDB

Gene
Name:	ushA
Synonym(s):	ECK0474, EG11060, b0480
Genome position(nucleotides):	504914 --> 506566 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	50.88
Reference(s):	[1] Burns DM., et al., 1983 [2] Burns DM., et al., 1986 [3] Cowman A., et al., 1980
External database links:

ASAP:	ABE-0001668
CGSC:	22
ECHOBASE:	EB1053
ECOLIHUB:	ushA
MIM:	211800
OU-MICROARRAY:	b0480
STRING:	511145.b0480
COLOMBOS:	ushA

Gene

Name:

ushA

Synonym(s):

ECK0474, EG11060, b0480

Genome position(nucleotides):

504914 --> 506566 Genome Browser

Strand:

forward

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

50.88

Reference(s):

[1] Burns DM., et al., 1983
[2] Burns DM., et al., 1986
[3] Cowman A., et al., 1980

External database links:

ASAP:

ABE-0001668

CGSC:

ECHOBASE:

ECOLIHUB:

MIM:

OU-MICROARRAY:

STRING:

COLOMBOS:

Type

Positions

Sequence

1 -> 25

MKLLQRGVALALLTTFTLASETALA

364 -> 509

IGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISYKNVLKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFVAKDGKLNDLKIKGEPVDPAKTYRMATLNFNATGGDGYPRL

26 -> 342

YEQDKTYKITVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEVAAEGGSVLLLSGGDINTGVPESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSANIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAKIGNPEYFTDIEFRKPADEAKLVIQELQQTEKPDIIIAATHMGHYDNGEHGSNAPGDVEMARALPAGSLAMIVGGHSQDPVCMAAENKKQVDYVPGTPCKPDQQNGIWIVQAHEWGKYVGRADFEFRNGEMKMVNYQLIPVNLKKKVTWEDGKSERVLYTPEIAEN

343 -> 361

QQMISLLSPFQNKGKAQLE

498 -> 504

FNATGGD

Type

Positions

Sequence

1 -> 25

MKLLQRGVALALLTTFTLASETALA

364 -> 509

IGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISYKNVLKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFVAKDGKLNDLKIKGEPVDPAKTYRMATLNFNATGGDGYPRL

26 -> 342

343 -> 361

QQMISLLSPFQNKGKAQLE

498 -> 504

FNATGGD

256 -> 256

35 -> 254

TVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEVAAEGGSVLLLSGGDINTGVPESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSANIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAKIGNPEYFTDIEFRKPADEAKLVIQELQQTEKPDIIIAATHMGHYDNGEHGSNAPGDVEMARALPAGSLAMIVGGHSQ

362 -> 550

VKIGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISYKNVLKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFVAKDGKLNDLKIKGEPVDPAKTYRMATLNFNATGGDGYPRLDNKPGYVNTGFIDAEVLKAYIQKSSPLDVSVYEPKGEVSWQ

375 -> 379

RDKVR

Multifun Terms (GenProtEC)

1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.10 - sugar nucleotide biosynthesis, conversions

Gene Ontology Terms (GO)

cellular_component

GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space

molecular_function

GO:0016788 - hydrolase activity, acting on ester bonds
GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0008253 - 5'-nucleotidase activity
GO:0000166 - nucleotide binding
GO:0008768 - UDP-sugar diphosphatase activity

biological_process

GO:0016311 - dephosphorylation
GO:0009166 - nucleotide catabolic process

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	fsrp8	504767	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.925. P-value: 1.809e-5 Read more >	[ICWHO]	[9]
promoter	fsrp6	504847	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.494. P-value: 8.807e-6 Read more >	[ICWHO]	[9]
promoter	fsrp5	504852	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.46. P-value: 1.288e-5 Read more >	[ICWHO]	[9]
promoter	fsrp9	504855	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 6.135. P-value: 1.371e-6 Read more >	[ICWHO]	[9]
promoter	TSS_644	504883	forward	nd	[RS-EPT-CBR]	[10]
promoter	ushAp6	504886	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.816. P-value: 8.524e-5 Read more >	[ICWHO]	[9]
promoter	TSS_645	504888	forward	nd	[RS-EPT-CBR]	[10]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

fsrp8

504767

reverse

Similarity to the consensus
Read more >

[ICWHO]

[9]

promoter

fsrp6

504847

reverse

Similarity to the consensus
Read more >

[ICWHO]

[9]

promoter

fsrp5

504852

reverse

Similarity to the consensus
Read more >

[ICWHO]

[9]

promoter

fsrp9

504855

reverse

Similarity to the consensus
Read more >

[ICWHO]

[9]

promoter

TSS_644

504883

forward

[RS-EPT-CBR]

[10]

promoter

ushAp6

504886

forward

Similarity to the consensus
Read more >

[ICWHO]

[9]

promoter

TSS_645

504888

forward

[RS-EPT-CBR]

[10]

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] Burns DM., Abraham LJ., Beacham IR., 1983, Characterization of the ush gene of Escherichia coli and its protein products., Gene 25(2-3):343-53
[2] Burns DM., Beacham IR., 1986, Nucleotide sequence and transcriptional analysis of the E. coli ushA gene, encoding periplasmic UDP-sugar hydrolase (5'-nucleotidase): regulation of the ushA gene, and the signal sequence of its encoded protein product., Nucleic Acids Res 14(10):4325-42
[3] Cowman A., Beacham IR., 1980, Molecular cloning of the gene (ush) from Escherichia coli specifying periplasmic UDP-sugar hydrolase (5'-nucleotidase)., Gene 12(3-4):281-6
[4] Edwards CJ., Innes DJ., Burns DM., Beacham IR., 1993, UDP-sugar hydrolase isozymes in Salmonella enterica and Escherichia coli: silent alleles of ushA in related strains of group I Salmonella isolates, and of ushB in wild-type and K12 strains of E. coli, indicate recent and early silencing events, respectively., FEMS Microbiol Lett 114(3):293-8
[5] Krug U., Patzschke R., Zebisch M., Balbach J., Strater N., 2013, Contribution of the two domains of E. coli 5'-nucleotidase to substrate specificity and catalysis., FEBS Lett 587(5):460-6
[6] Neu HC., 1967, The 5'-nucleotidase of Escherichia coli. II. Surface localization and purification of the Escherichia coli 5'-nucleotidase inhibitor., J Biol Chem 242(17):3905-11
[7] Taylor N., Beacham IR., 1975, Synthesis of Escherichia coli uridine diphosphate glucose hydrolase, and demonstration of an inhibitor, in Salmonella typhimurium cytoplasm., Biochem Soc Trans 3(3):386-7
[8] Taylor NS., Beacham IR., 1975, Synthesis and localisation of Escherichia coli UDP-glucose hydrolase (5'-nucleotidase), and demonstration of a cytoplasmic inhibitor of this enzyme in Salmonella typhimurium., Biochim Biophys Acta 411(2):216-21
[9] 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
[10] 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] Burns DM., Abraham LJ., Beacham IR., 1983, Characterization of the ush gene of Escherichia coli and its protein products., Gene 25(2-3):343-53

[2] Burns DM., Beacham IR., 1986, Nucleotide sequence and transcriptional analysis of the E. coli ushA gene, encoding periplasmic UDP-sugar hydrolase (5'-nucleotidase): regulation of the ushA gene, and the signal sequence of its encoded protein product., Nucleic Acids Res 14(10):4325-42

[3] Cowman A., Beacham IR., 1980, Molecular cloning of the gene (ush) from Escherichia coli specifying periplasmic UDP-sugar hydrolase (5'-nucleotidase)., Gene 12(3-4):281-6

[4] Edwards CJ., Innes DJ., Burns DM., Beacham IR., 1993, UDP-sugar hydrolase isozymes in Salmonella enterica and Escherichia coli: silent alleles of ushA in related strains of group I Salmonella isolates, and of ushB in wild-type and K12 strains of E. coli, indicate recent and early silencing events, respectively., FEMS Microbiol Lett 114(3):293-8

[5] Krug U., Patzschke R., Zebisch M., Balbach J., Strater N., 2013, Contribution of the two domains of E. coli 5'-nucleotidase to substrate specificity and catalysis., FEBS Lett 587(5):460-6

[6] Neu HC., 1967, The 5'-nucleotidase of Escherichia coli. II. Surface localization and purification of the Escherichia coli 5'-nucleotidase inhibitor., J Biol Chem 242(17):3905-11

[7] Taylor N., Beacham IR., 1975, Synthesis of Escherichia coli uridine diphosphate glucose hydrolase, and demonstration of an inhibitor, in Salmonella typhimurium cytoplasm., Biochem Soc Trans 3(3):386-7

[8] Taylor NS., Beacham IR., 1975, Synthesis and localisation of Escherichia coli UDP-glucose hydrolase (5'-nucleotidase), and demonstration of a cytoplasmic inhibitor of this enzyme in Salmonella typhimurium., Biochim Biophys Acta 411(2):216-21

[9] 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

[10] 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.