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Product(s) |

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Standard Name	yhdE
Gene Synonym(s)	ECK3236, b3248, JW3217^[1], JW3217
Product Desc.	conserved protein^[2]^[3] Function unknown; homologous to B. subtilis maf; yceF paralog^[4]
Product Synonyms(s)	conserved protein^[1], B3248^[2]^[1], YhdE^[2]^[1] , ECK3236, JW3217, b3248
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): mreBCD-yhdE-rng^[2]
Regulation/Activity
Quick Links
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Notes

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Maf is a nucleotide-binding protein implicated in inhibition of septum formation in B. subtilis. AFMB Structural Genomics target No. 24 (http://afmb.cnrs-mrs.fr/article171.html).^[4]

Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	yhdE
Mnemonic	Systematic nomenclature
Synonyms	ECK3236, b3248, JW3217^[1], JW3217
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	73.19 minutes	MG1655: 3396400..3395807 <gbrowseImage> name=NC_000913:3395807..3396400 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3326269..3325676 <gbrowseImage> name=NC_012967:3325676..3326269 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3282955..3283548 <gbrowseImage> name=NC_012759:3282955..3283548 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3398233..3397640 <gbrowseImage> name=NC_007779:3397640..3398233 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3494145..3493552 <gbrowseImage> name=NC_010473:3493552..3494145 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Description	Reference	Availability	Comments
yhdE(del)::kan (Keio:JW3217)	deletion	deletion		CGSC10437^[5] Shigen	CGSC10437^[5] Shigen
yhdE772(del)::kan				PMID:16738554	CGSC:105144
yhdE+ overexpression			increased dTMP pool	PMID:24210219		Fig 2
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW3217	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACTTCTCTGTATTTAGCTTC Primer 2:CCGCCGTCATGTTTATCCCTTTT
3G9	Kohara Phage	Genobase	PMID:3038334
21D3	Kohara Phage	Genobase	PMID:3038334
zhc-6::Tn10	Linked marker	CAG12153 = CGSC7442^[5]	est. P1 cotransduction: 28% ^[6] Synonyms:zha-6::Tn10
acrF3083::Tn10	Linked marker	CAG12075 = CGSC7447^[5]	est. P1 cotransduction: 50% ^[6] Synonyms:zhd-3083::Tn10, zhe-3083::Tn10
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG11298	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11298	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001271	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947753	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1275	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010653	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	YhdE
Synonyms	conserved protein^[1], B3248^[2]^[1], YhdE^[2]^[1] , ECK3236, JW3217, b3248
Product description	conserved protein^[2]^[3] Function unknown; homologous to B. subtilis maf; yceF paralog^[4]
EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00528	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003697	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0047429	nucleoside-triphosphate diphosphatase activity	PMID:24210219	IDA: Inferred from Direct Assay		F	Fig. 1	complete
	GO:0036218	dTTP diphosphatase activity	PMID:24210219	IDA: Inferred from Direct Assay		F	Fig. 1	complete
	GO:0036221	UTP diphosphatase activity	PMID:24210219	IDA: Inferred from Direct Assay		F	Fig. 1	complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	References	Evidence
Protein	qseC	PMID:16606699	Experiment(s):EBI-1145294
Protein	pepD	PMID:16606699	Experiment(s):EBI-1145294
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MTSLYLASGS PRRQELLAQL GVTFERIVTG IEEQRQPQES AQQYVVRLAR EKARAGVAQT AKDLPVLGAD TIVILNGEVL EKPRDAEHAA QMLRKLSGQT HQVMTAVALA DSQHILDCLV VTDVTFRTLT DEDIAGYVAS DEPLDKAGAY GIQGLGGCFV RKINGSYHAV VGLPLVETYE LLSNFNALRE KRDKHDG
Length	197
Mol. Wt	21.514 kDa
pI	5.7 (calculated)
Extinction coefficient	8,940 - 9,190 (calc based on 6 Y, 0 W, and 2 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	Notes	References
Domain	2..192	PF02545 Maf-like protein		PMID:19920124
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=yhdE taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

The X-ray crystallographic structure of the paralogous protein YceF is available.[[1]]

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16131136	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947753	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010653	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P25536	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11298	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11298	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947753	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001271	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1275	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MG1655	699	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	184	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	555	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
mreBCD-yhdE-rng
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:3396380..3396420 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b3248 (EcoliWiki Page)	NCBI GEO profiles for yhdE
microarray	GenExpDB:b3248 (EcoliWiki Page)	Summary of data for yhdE from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to yhdE Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG11298	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1275	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3248
EcoGene	EcoGene:EG11298	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001271	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010653	Escherichia coli str. K-12 substr. MG1655
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Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Anopheles gambiae	ENSANGP00000011116 (score: 1.000; bootstrap: 92%)	From Inparanoid:20070104
Arabidopsis thaliana	AT5G42770 (score: 1.000; bootstrap: 100%) AT5G66550 (score: 0.426) AT2G25500 (score: 0.088)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000029880 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00030049 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00008316 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000018572 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-030131-2854 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040425-3858 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0189591 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0032077 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000026877 (score: 1.000; bootstrap: 100%) ENSGALP00000026872 (score: 0.087)	From Inparanoid:20070104
Homo sapiens	ENSP00000344560 (score: 1.000; bootstrap: 100%) ENSP00000305749 (score: 0.099)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000000099 (score: 1.000; bootstrap: 100%) ENSMODP00000000078 (score: 0.079)	From Inparanoid:20070104
Mus musculus	MGI:1916349 (score: 1.000; bootstrap: 100%) MGI:1913817 (score: 0.088)	From Inparanoid:20070104
Oryza gramene	Q75GV5 (score: 1.000; bootstrap: 100%) Q8GS82 (score: 0.329)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000037028 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000038215 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YOR111W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC3G63c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000139382 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000145608 (score: 0.118) NEWSINFRUP00000147317 (score: 0.099)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000051816 (score: 1.000; bootstrap: 82%)	From Inparanoid:20070104
Shigella flexneri	YHDE	From SHIGELLACYC
E. coli O157	YHDE	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF02545 Maf-like protein
Panther (EcoliWiki Page)	PTHR11746:SF53
Superfamily (EcoliWiki Page)	SUPERFAMILY:52972
EcoCyc	EcoCyc:EG11298	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11298	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001271	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1275	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010653	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 ^5.3 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

yhdE:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to yhdE Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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