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Expression|

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Standard Name	ybgI
Gene Synonym(s)	ECK0699, b0710, JW0700^[1], JW0700
Product Desc.	conserved metal-binding protein^[2]^[3]; Component of conserved metal-binding protein^[3] Function unknown^[4]
Product Synonyms(s)	conserved metal-binding protein^[1], B0710^[2]^[1], YbgI^[2]^[1] , ECK0699, JW0700, b0710
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ybgIJKL-nei^[2]
Regulation/Activity
Quick Links
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Notes

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YbgI is a member of the widely conserved protein family UPF0135. YbgI has a dinuclear metal site. HT_Cmplx40_Cyt: YbgI+YqhD.^[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	ybgI
Mnemonic	Systematic nomenclature
Synonyms	ECK0699, b0710, JW0700^[1], JW0700
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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	15.99 minutes	MG1655: 742050..742793 <gbrowseImage> name=NC_000913:742050..742793 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 723612..724355 <gbrowseImage> name=NC_012967:723612..724355 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 644810..645553 <gbrowseImage> name=NC_012759:644810..645553 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 743249..743992 <gbrowseImage> name=NC_007779:743249..743992 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 794642..795385 <gbrowseImage> name=NC_010473:794642..795385 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: Type	Phenotype: Description	Reference	Availability	Comments
ΔybgI (Keio:JW0700)	deletion	deletion			PMID:16738554	Shigen
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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
JW0700	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAAAACACCGAACTGGAACA Primer 2:CCTGCAGGATTAGGAATATCAAT
25C10S	Kohara Phage	Genobase	PMID:3038334
asnB3057::Tn10	Linked marker	CAG18433 = CGSC7349^[5]	est. P1 cotransduction: 17% ^[6] Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.
nadA57::Tn10	Linked marker	CAG12147 = CGSC7351^[5]	est. P1 cotransduction: 21% ^[6]
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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:G6379	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13305	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002979	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945824	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3089	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002424	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	YbgI
Synonyms	conserved metal-binding protein^[1], B0710^[2]^[1], YbgI^[2]^[1] , ECK0699, JW0700, b0710
Product description	conserved metal-binding protein^[2]^[3]; Component of conserved metal-binding protein^[3] Function unknown^[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:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	F	Seeded from EcoCyc (v14.0)	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	Notes	References	Evidence
Protein	Subunits of conserved metal-binding protein	could be indirect
Protein	zapA		PMID:16606699	Experiment(s):EBI-1137753
Protein	arcA		PMID:16606699	Experiment(s):EBI-1137753
Protein	yqeI		PMID:16606699	Experiment(s):EBI-1137753
Protein	stpA		PMID:16606699	Experiment(s):EBI-1137753
Protein	skp		PMID:19402753	LCMS(ID Probability):99.6
Protein	uvrD		PMID:19402753	LCMS(ID Probability):99.4
Protein	slyD		PMID:19402753	LCMS(ID Probability):99.6
Protein	rplA		PMID:19402753	LCMS(ID Probability):99.6
Protein	lon		PMID:19402753	LCMS(ID Probability):99.6
Protein	ompA		PMID:19402753	LCMS(ID Probability):99.6
Protein	fusA		PMID:19402753	LCMS(ID Probability):99.6
Protein	gyrB		PMID:19402753	LCMS(ID Probability):99.6
Protein	tig		PMID:19402753	LCMS(ID Probability):99.6
Protein	glyQ		PMID:19402753	LCMS(ID Probability):99.6
Protein	infB		PMID:19402753	LCMS(ID Probability):99.6
Protein	ibpA		PMID:19402753	LCMS(ID Probability):99.6
Protein	ndh		PMID:19402753	LCMS(ID Probability):99.6
Protein	groS		PMID:19402753	LCMS(ID Probability):99.6
Protein	narG		PMID:19402753	LCMS(ID Probability):99.6
Protein	recA		PMID:19402753	LCMS(ID Probability):99.6
Protein	ftsY		PMID:19402753	LCMS(ID Probability):99.6
Protein	mreB		PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):22.511434
Protein	gyrA		PMID:19402753	LCMS(ID Probability):99.6
Protein	mukE		PMID:19402753	LCMS(ID Probability):99.6
Protein	pstB		PMID:19402753	LCMS(ID Probability):99.6
Protein	dnaJ		PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):17.823912
Protein	phoE		PMID:19402753	LCMS(ID Probability):99.6
Protein	miaB		PMID:19402753	LCMS(ID Probability):99.6
Protein	ybiB		PMID:19402753	LCMS(ID Probability):99.5 MALDI(Z-score):17.984699
Protein	ompC		PMID:19402753	LCMS(ID Probability):99.6
Protein	ruvB		PMID:19402753	LCMS(ID Probability):99.6
Protein	yehX		PMID:19402753	LCMS(ID Probability):99.6
Protein	udk		PMID:19402753	LCMS(ID Probability):99.4
Protein	ycgG		PMID:19402753	LCMS(ID Probability):99.6
Protein	pdxB		PMID:19402753	LCMS(ID Probability):99.6
Protein	malK		PMID:19402753	LCMS(ID Probability):99.6
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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 MKNTELEQLI NEKLNSAAIS DYAPNGLQVE GKETVQKIVT GVTASQALLD EAVRLGADAV IVHHGYFWKG ESPVIRGMKR NRLKTLLAND INLYGWHLPL DAHPELGNNA QLAALLGITV MGEIEPLVPW GELTMPVPGL ELASWIEARL GRKPLWCGDT GPEVVQRVAW CTGGGQSFID SAARFGVDAF ITGEVSEQTI HSAREQGLHF YAAGHHATER GGIRALSEWL NENTDLDVTF IDIPNPA
Length	247
Mol. Wt	26.892 kDa
pI	5.0 (calculated)
Extinction coefficient	44,460 - 44,710 (calc based on 4 Y, 7 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	5..238	PF01784 NIF3 (NGG1p interacting factor 3)		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=ybgI taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

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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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:16128685	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945824	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002424	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AFP6	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6379	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13305	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945824	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002979	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3089	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 MC4100	5.04E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI	PMID:18304323
Protein	E. coli K-12 MG1655	1665	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	1725	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	2004	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)
ybgIJKL-nei
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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_000913:742030..742070 source=MG1655 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:b0710 (EcoliWiki Page)	NCBI GEO profiles for ybgI
microarray	GenExpDB:b0710 (EcoliWiki Page)	Summary of data for ybgI 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
	GFP Fusion	Intergenic region (741694..742130) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ12; Well:D1^[7]
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Notes

Accessions Related to ybgI Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6379	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3089	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0710
EcoGene	EcoGene:EG13305	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002979	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002424	Escherichia coli str. K-12 substr. MG1655
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Notes

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	ENSANGP00000029599 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000044888 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YBGI	From SHIGELLACYC
E. coli O157	YBGI	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)	PF01784 NIF3 (NGG1p interacting factor 3)
Panther (EcoliWiki Page)	PTHR13799:SF13
Superfamily (EcoliWiki Page)	SUPERFAMILY:102705
EcoCyc	EcoCyc:G6379	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13305	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002979	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3089	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002424	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 ^3.2 ^3.3 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 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

ybgI: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 ybgI Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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