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Gene |

Product(s) |

Expression|

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Standard Name	ytfM
Gene Synonym(s)	ECK4216, b4220, JW4179^[1], JW4179, yftM
Product Desc.	outer membrane protein^[2]^[3] Outer membrane protein, function unknown; has a C-terminal beta-barrel OM protein domain and an N-terminal periplasmic domain^[4]
Product Synonyms(s)	predicted outer membrane protein and surface antigen^[1], B4220^[2]^[1], YtfM^[2]^[1] , ECK4216, JW4179, yftM, b4220
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ytfM^[2]
Regulation/Activity
Quick Links
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Notes

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Predicted 21 aa signal peptide is consistent with an observed secB-dependent precursor cleavage that is blocked by azide (Marani, 2006). Putative ytfMNP operon. yftM added as synonym as a common mispelling. ytfM and bamA are paralogs. Null ytfM mutants do not have OM composition or integrity defects, but they do grow slowly (Stegmeier, 2007).^[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	ytfM
Mnemonic	Systematic nomenclature
Synonyms	ECK4216, b4220, JW4179^[1], JW4179, yftM
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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	95.71 minutes, 95.71 minutes	MG1655: 4440405..4442138 <gbrowseImage> name=NC_000913:4440405..4442138 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4426139..4427872 <gbrowseImage> name=NC_012967:4426139..4427872 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4379140..4380873 <gbrowseImage> name=NC_012759:4379140..4380873 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4447062..4448795 <gbrowseImage> name=NC_007779:4447062..4448795 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4540767..4542500 <gbrowseImage> name=NC_010473:4540767..4542500 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)	Reference	Availability
ΔytfM (Keio:JW4179)	deletion	deletion	PMID:16738554	Shigen CGSC11009^[5]
ΔytfM769::kan			PMID:16738554	CGSC:106084
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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
JW4179	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCGCTATATCCGACAGTTATG Primer 2:CCTAATTCTGGCCCCAGACCGAT
5B5	Kohara Phage	Genobase	PMID:3038334
E1H3	Kohara Phage	Genobase	PMID:3038334
cycA30::Tn10	Linked marker	CAG12073 = CGSC7482^[5]	est. P1 cotransduction: 61% ^[6]
zjf-920::Tn10	Linked marker	CAG12019 = CGSC7484^[5]	est. P1 cotransduction: 86% ^[6] Synonyms:zjh-901::Tn10, zjg-920::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
NCBI (EcoliWiki Page)	GeneID:948733	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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	YtfM
Synonyms	predicted outer membrane protein and surface antigen^[1], B4220^[2]^[1], YtfM^[2]^[1] , ECK4216, JW4179, yftM, b4220
Product description	outer membrane protein^[2]^[3] Outer membrane protein, function unknown; has a C-terminal beta-barrel OM protein domain and an N-terminal periplasmic domain^[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:0019867	outer membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000184	C	Seeded from EcoCyc (v14.0)	complete
	GO:0019867	outer membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010827	C	Seeded from EcoCyc (v14.0)	complete
	GO:0045203	integral to cell outer membrane	PMID:17214547	IDA: Inferred from Direct Assay		C		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	groL		PMID:16606699	Experiment(s):EBI-1147695
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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
outer membrane
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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 MRYIRQLCCV SLLCLSGSAV AANVRLQVEG LSGQLEKNVR AQLSTIESDE VTPDRRFRAR VDDAIREGLK ALGYYQPTIE FDLRPPPKKG RQVLIAKVTP GVPVLIGGTD VVLRGGARTD KDYLKLLDTR PAIGTVLNQG DYENFKKSLT SIALRKGYFD SEFTKAQLGI ALGLHKAFWD IDYNSGERYR FGHVTFEGSQ IRDEYLQNLV PFKEGDEYES KDLAELNRRL SATGWFNSVV VAPQFDKARE TKVLPLTGVV SPRTENTIET GVGYSTDVGP RVKATWKKPW MNSYGHSLTT STSISAPEQT LDFSYKMPLL KNPLEQYYLV QGGFKRTDLN DTESDSTTLV ASRYWDLSSG WQRAINLRWS LDHFTQGEIT NTTMLFYPGV MISRTRSRGG LMPTWGDSQR YSIDYSNTAW GSDVDFSVFQ AQNVWIRTLY DRHRFVTRGT LGWIETGDFD KVPPDLRFFA GGDRSIRGYK YKSIAPKYAN GDLKGASKLI TGSLEYQYNV TGKWWGAVFV DSGEAVSDIR RSDFKTGTGV GVRWESPVGP IKLDFAVPVA DKDEHGLQFY IGLGPEL
Length	577
Mol. Wt	64.797 kDa
pI	9.0 (calculated)
Extinction coefficient	115,740 - 116,115 (calc based on 26 Y, 14 W, and 3 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	1-21	UniProt Manual:Signal Peptides	UniProt:P0ADE4
Domain	290..577	PF01103 Surface antigen		PMID:19920124
Domain	189..263	PF07244 Surface antigen variable number repeat		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=ytfM 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:16132042	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948733	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ADE4	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948733	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	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	195	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	115	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	109	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)
ytfM
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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_000913:4440385..4440425 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:b4220 (EcoliWiki Page)	NCBI GEO profiles for ytfM
microarray	GenExpDB:b4220 (EcoliWiki Page)	Summary of data for ytfM 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 (4439684..4440038) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ08; Well:H10^[7]
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Notes

Accessions Related to ytfM Expression

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

Database	Accession	Notes
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4220
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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
Shigella flexneri	YTFM	From SHIGELLACYC
E. coli O157	YTFM	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)	PF01103 Surface antigen
Panther (EcoliWiki Page)	PTHR12815:SF6
Pfam (EcoliWiki Page)	PF07244 Surface antigen variable number repeat
EcoCyc	EcoCyc:	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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 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

ytfM: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 ytfM Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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