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On One Page

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Gene |

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Expression|

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Standard Name	bhsA
Gene Synonym(s)	ycfR, ECK1098, b1112, JW1098^[1]^[2], JW1098
Product Desc.	conserved hypothetical protein^[3]; protein involved in stress resistance and biofilm formation^[2] Biofilm, cell surface and signaling defects, member of YhcN Family; molecular and physiological function unknown^[4]
Product Synonyms(s)	predicted protein^[1], B1112^[3]^[1], YcfR^[3]^[1], BhsA^[2]^[1] , ECK1098, JW1098, ycfR, b1112
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ycfR^[3]
Regulation/Activity
Quick Links
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Notes

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Complex mutant phenotype includes sensitivity to acid, heat, hydrogen peroxide, and cadmium, as well as 5-fold increased biofilm in the presence of glucose, increased cell surface hydrophobicity, and increased aggregation; the mutant phenotype of enhanced biofilm formation upon stress is suppressed by exogenous indole or by a tnaA mutation (Zhang, 2007). Induced during biofilm formation. Crp regulon. Probable periplasmic protein. The first 22 aa are predicted to be a type I signal peptide.^[4]

BhsA (YcfR) is a member of the YhcN_Family of 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	bhsA
Mnemonic	influencing Biofilm through Hydrophobicity and Stress response
Synonyms	ycfR, ECK1098, b1112, JW1098^[1]^[2], JW1098
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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	25.18 minutes	MG1655: 1168296..1168553 <gbrowseImage> name=NC_000913:1168296..1168553 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1183667..1183924 <gbrowseImage> name=NC_012967:1183667..1183924 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1072221..1072478 <gbrowseImage> name=NC_012759:1072221..1072478 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1170650..1170907 <gbrowseImage> name=NC_007779:1170650..1170907 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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
ΔbhsA774::kan					PMID:16738554	CGSC:104008
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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
	Plasmid clone	Shigen	PMID:16769691 Status: Primer 1: Primer 2:
15A8	Kohara Phage	Genobase	PMID:3038334
E4C2	Kohara Phage	Genobase	PMID:3038334
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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:G6570	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13436	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003166	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945492	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3210	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003758	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	YcfR
Synonyms	predicted protein^[1], B1112^[3]^[1], YcfR^[3]^[1], BhsA^[2]^[1] , ECK1098, JW1098, ycfR, b1112
Product description	conserved hypothetical protein^[3]; protein involved in stress resistance and biofilm formation^[2] Biofilm, cell surface and signaling defects, member of YhcN Family; molecular and physiological 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:0006950	response to stress	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0346	P	Seeded from EcoCyc (v14.0)	complete
	GO:0042597	periplasmic space	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0574	C	Seeded from EcoCyc (v14.0)	complete
	GO:0042597	periplasmic space	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0200	C	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	References	Evidence
Protein	ydfG	PMID:19402753	LCMS(ID Probability):99.6
Protein	ydhX	PMID:19402753	LCMS(ID Probability):99.4
Protein	ydjF	PMID:19402753	LCMS(ID Probability):97.9
Protein	ycdY	PMID:19402753	LCMS(ID Probability):99.6
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Notes

Localization

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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 MKNVKTLIAA AILSSMSFAS FAAVEVQSTP EGQQKVGTIS ANAGTNLGSL EEQLAQKADE MGAKSFRITS VTGPNTLHGT AVIYK
Length	85
Mol. Wt	8.814 kDa
pI	9.6 (calculated)
Extinction coefficient	1,490 (calc based on 1 Y, 0 W, and 0 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
motif	1-22	UniProt Manual:Signal Peptides	UniProt:P0AB40
Domain	22..85	PF07338 Protein of unknown function (DUF1471)		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=bhsA taxon=562,83333 </beststructure>

Models

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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:16129075	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945492	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003758	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AB40	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6570	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13436	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945492	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003166	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3210	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	1.134+/-0.924	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.017509728	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	2282	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	1039	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	1967	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)
ycfR
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File:.jpg

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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_000913:1168276..1168316 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:b1112 (EcoliWiki Page)	NCBI GEO profiles for bhsA
microarray	GenExpDB:b1112 (EcoliWiki Page)	Summary of data for bhsA 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 (1168047..1168322) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ15; Well:G9^[6]
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Notes

Accessions Related to bhsA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6570	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3210	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1112
EcoGene	EcoGene:EG13436	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003166	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003758	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	YCFR	From SHIGELLACYC
E. coli O157	YCFR	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)	PF07338 Protein of unknown function (DUF1471)
EcoCyc	EcoCyc:G6570	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13436	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003166	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3210	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003758	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 ^1.8 ^1.9 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 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 ^3.6 EcoCyc (release 10.6; 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.
↑ Rudd, KE et al. (1998) Low molecular weight proteins: a challenge for post-genomic research. Electrophoresis 19 536-44 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

bhsA: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 bhsA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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