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On One Page

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Gene |

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Expression|

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Standard Name	yciF
Gene Synonym(s)	ECK1252, b1258, JW1250^[1], JW1250
Product Desc.	conserved protein^[2]; putative structural protein^[3]; Component of putative structural protein^[3] Function unknown, H-NS repressed^[4]; dimeric; rubrerythrin/ferritin-like putative metal-binding protein^[5]
Product Synonyms(s)	conserved protein^[1], B1258^[2]^[1], YciF^[2]^[1] , ECK1252, JW1250, b1258
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yciGFE^[2]
Regulation/Activity
Quick Links
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Notes

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Protein sequencing reveals ATG at codon 3 is also utilized as a start. YciF homolog from X. axonopodis pv. passiflorae is upregulated by host plant leaf extract. Salmonella ortholog regulated by RpoS. yciF and yciE are paralogs.^[5]

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	yciF
Mnemonic	Systematic nomenclature
Synonyms	ECK1252, b1258, JW1250^[1], JW1250
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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	28.31 minutes	MG1655: 1313794..1313294 <gbrowseImage> name=NC_000913:1313294..1313794 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1313364..1312864 <gbrowseImage> name=NC_012967:1312864..1313364 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1204143..1204643 <gbrowseImage> name=NC_012759:1204143..1204643 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1317484..1316984 <gbrowseImage> name=NC_007779:1316984..1317484 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1403190..1402690 <gbrowseImage> name=NC_010473:1402690..1403190 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
Coding Start (SO:0000323)	MG1655	1313294	Edman degradation	PMID:8455549
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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)	Reference	Availability
ΔyciF (Keio:JW1250)	deletion	deletion	PMID:16738554	Shigen CGSC9127^[6]
ΔyciF766::kan			PMID:16738554	CGSC:104056
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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
JW1250	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAATATGAAGACCATTGAAGA Primer 2:CCGGCTTTATTTTCGGCTTTCTT
14C4	Kohara Phage	Genobase	PMID:3038334
oppC506::Tn10	Linked marker	CAG12169 = CGSC7369^[6]	est. P1 cotransduction: 72% ^[7] Synonyms:zch-506::Tn10, zci-506::Tn10
trpC83::Tn10	Linked marker	CAG18455 = CGSC7371^[6]	est. P1 cotransduction: 87% ^[7] Synonyms:trpB83::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:EG11126	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11126	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001110	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947133	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1116	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004222	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	YciF
Synonyms	conserved protein^[1], B1258^[2]^[1], YciF^[2]^[1] , ECK1252, JW1250, b1258
Product description	conserved protein^[2]; putative structural protein^[3]; Component of putative structural protein^[3] Function unknown, H-NS repressed^[4]; dimeric; rubrerythrin/ferritin-like putative metal-binding protein^[5]
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:0006974	response to DNA damage stimulus	PMID:11967071	IEP: Inferred from Expression Pattern		P		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 putative structural protein	could be indirect
Protein	mdtC		PMID:16606699	Experiment(s):EBI-1139331
Protein	polB		PMID:16606699	Experiment(s):EBI-1139331
Protein	kdpD		PMID:16606699	Experiment(s):EBI-1139331
Protein	trpA		PMID:16606699	Experiment(s):EBI-1139331, EBI-1139344
Protein	fabI		PMID:16606699	Experiment(s):EBI-1139331
Protein	rpmB		PMID:19402753	LCMS(ID Probability):99.6
Protein	ybgI		PMID:19402753	LCMS(ID Probability):99.6
Protein	pfkA		PMID:19402753	MALDI(Z-score):27.964914
Protein	talA		PMID:19402753	MALDI(Z-score):38.865437
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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 MNMKTIEDVF IHLLSDTYSA EKQLTRALAK LARATSNEKL SQAFHAHLEE THGQIERIDQ VVESESNLKI KRMKCVAMEG LIEEANEVIE STEKNEVRDA ALIAAAQKVE HYEIASYGTL ATLAEQLGYR KAAKLLKETL EEEKATDIKL TDLAINNVNK KAENKA
Length	166
Mol. Wt	18.597 kDa
pI	5.5 (calculated)
Extinction coefficient	5,960 - 6,085 (calc based on 4 Y, 0 W, and 1 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..163	PF05974 Domain of unknown function (DUF892)		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=yciF 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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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:16129219	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947133	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004222	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P21362	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11126	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11126	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947133	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001110	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1116	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	Notes	Reference(s)
Protein	Ecoli K-12	62.672+/-0.662	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.02	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	3^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	164	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	0^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	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)
yciGFE
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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.

YciF is repressed by H-NS.^[4]

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:1313774..1313814 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:b1258 (EcoliWiki Page)	NCBI GEO profiles for yciF
microarray	GenExpDB:b1258 (EcoliWiki Page)	Summary of data for yciF 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 yciF Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11126	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1116	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1258
EcoGene	EcoGene:EG11126	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001110	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004222	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
Shigella flexneri	YCIF	From SHIGELLACYC
E. coli O157	YCIF	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
Superfamily (EcoliWiki Page)	SUPERFAMILY:47240
Pfam (EcoliWiki Page)	PF05974 Domain of unknown function (DUF892)
EcoCyc	EcoCyc:EG11126	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11126	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001110	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1116	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004222	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 Yoshida, T et al. (1993) Function of the Escherichia coli nucleoid protein, H-NS: molecular analysis of a subset of proteins whose expression is enhanced in a hns deletion mutant. Mol. Gen. Genet. 237 113-22 PubMed
↑ ^5.0 ^5.1 ^5.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^6.0 ^6.1 ^6.2 CGSC: The Coli Genetics Stock Center
↑ ^7.0 ^7.1 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).

yciF: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 yciF Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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