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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	ypjA
Gene Synonym(s)	ECK2644, b2647, JW5422^[1], JW5422
Product Desc.	adhesin-like autotransporter^[2]^[3] Overexpression increases adhesion, function unknown; OM autotransporter homolog^[4]
Product Synonyms(s)	adhesin-like autotransporter^[1], B2647^[2]^[1], YpjA^[2]^[1] , ECK2644, JW5422, b2647
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ypjA^[2]
Regulation/Activity
Quick Links
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Notes

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Mutants have reduced OM vesiculation (McBroom, 2006).^[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	ypjA
Mnemonic	Systematic nomenclature
Synonyms	ECK2644, b2647, JW5422^[1], JW5422
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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	59.84 minutes	MG1655: 2780748..2776168 <gbrowseImage> name=NC_000913:2776168..2780748 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 2661980..2666560 <gbrowseImage> name=NC_012759:2661980..2666560 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2781382..2776802 <gbrowseImage> name=NC_007779:2776802..2781382 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)	Reference	Availability
ΔypjA (Keio:JW5422)	deletion	deletion	PMID:16738554	Shigen CGSC11380^[5]
ΔypjA732::kan			PMID:16738554	CGSC:105936
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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
JW5422	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAACAGGACCAGTCCCTATTA Primer 2:CCGAACGACCAGTTCACACCAGC
4C9	Kohara Phage	Genobase	PMID:3038334
2D4	Kohara Phage	Genobase	PMID:3038334
12G12	Kohara Phage	Genobase	PMID:3038334
pheA18::Tn10	Linked marker	CAG12158 = CGSC7421^[5]	est. P1 cotransduction: 20% ^[6]
srlD3131::Tn10	Linked marker	CAG18642 = CGSC7423^[5]	est. P1 cotransduction: 10% ^[6] Synonyms:zfh-3131::Tn10, zfi-3131::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:G7382	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13213	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003950	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948630	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3005	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008713	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	YpjA
Synonyms	adhesin-like autotransporter^[1], B2647^[2]^[1], YpjA^[2]^[1] , ECK2644, JW5422, b2647
Product description	adhesin-like autotransporter^[2]^[3] Overexpression increases adhesion, function unknown; OM autotransporter homolog^[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:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0007155	cell adhesion	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003991	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009279	cell outer membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0998	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0019867	outer membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006315	C	Seeded from EcoCyc (v14.0)	complete
	GO:0019898	extrinsic to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9903	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	Notes	References	Evidence
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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 MNTIHLRCLF RMNPLVWCLW ADVAAKLRSL KRYSVFTFQR MKFMNRTSPY YCRRSVLSLL ISALIYAPPG MAAFTTNVIG VVNDETVDGN QKVDERGTTN NTHIINHGQQ NVHGGVSNGS LIESGGYQDI GSHNNFVGQA NNTTINGGRQ SIHDGGISTG TTIESGNQDV YKGGISNGTT IKGGASRVEG GSANGILIDG GSQIVKVQGH ADGTTINKSG SQDVVQGSLA TNTTINGGRQ YVEQSTVETT TIKNGGEQRV YESRALDTTI EGGTQSLNSK STAKNTHIYS GGTQIVDNTS TSDVIEVYSG GVLDVRGGTA TNVTQHDGAI LKTNTNGTTV SGTNSEGAFS IHNHVADNVL LENGGHLDIN AYGSANKTII KDKGTMSVLT NAKADATRID NGGVMDVAGN ATNTIINGGT QNINNYGIAT GTNINSGTQN IKSGGKADTT IISSGSRQVV EKDGTAIGSN ISAGGSLIVY TGGIAHGVNQ ETGSALVANT GAGTDIEGYN KLSHFTITGG EANYVVLENT GELTVVAKTS AKNTTIDTGG KLIVQKEAKT DSTRLNNGGV LEVQDGGEAK HVEQQSGGAL IASTTSGTLI EGTNSYGDAF YIRNSEAKNV VLENAGSLTV VTGSRAVDTI INANGKMDVY GKDVGTVLNS AGTQTIYASA TSDKANIKGG KQTVYGLATE ANIESGEQIV DGGSTEKTHI NGGTQTVQNY GKAINTDIVS GLQQIMANGT AEGSIINGGS QVVNEGGLAE NSVLNDGGTL DVREKGSATG IQQSSQGALV ATTRATRVTG TRADGVAFSI EQGAANNILL ANGGVLTVES DTSSDKTQVN MGGREIVKTK ATATGTTLTG GEQIVEGVAN ETTINDGGIQ TVSANGEAIK TKINEGGTLT VNDNGKATDI VQNSGAALQT STANGIEISG THQYGTFSIS GNLATNMLLE NGGNLLVLAG TEARDSTVGK GGAMQNLGQD SATKVNSGGQ YTLGRSKDEF QALARAEDLQ VAGGTAIVYA GTLADASVSG ATGSLSLMTP RDNVTPVKLE GAVRITDSAT LTLGNGVDTT LADLTAASRG SVWLNSNNSC AGTSNCEYRV NSLLLNDGDV YLSAQTAAPA TTNGIYNTLT TNELSGSGNF YLHTNVAGSR GDQLVVNNNA TGNFKIFVQD TGVSPQSDDA MTLVKTGGGD ASFTLGNTGG FVDLGTYEYV LKSDGNSNWN LTNDVKPNPD PIPNPKPDPK PDPKPDPNPK PDPTPDPTPT PVPEKRITPS TAAVLNMAAT LPLVFDAELN SIRERLNIMK ASPHNNNVWG ATYNTRNNVT TDAGAGFEQT LTGMTVGIDS RNDIPEGITT LGAFMGYSHS HIGFDRGGHG SVGSYSLGGY ASWEHESGFY LDGVVKLNRF KSNVAGKMSS GGAANGSYHS NGLGGHIETG MRFTDGNWNL TPYASLTGFT ADNPEYHLSN GMKSKSVDTR SIYRELGATL SYNMRLGNGM EVEPWLKAAV RKEFVDDNRV KVNSDGNFVN YLSGRRGIYQ AGIKASFSST LSGHLGVGYS HSAGVESPWN AVAGVNWSF
Length	1,569
Mol. Wt	162.773 kDa
pI	5.5 (calculated)
Extinction coefficient	119,070 - 119,695 (calc based on 43 Y, 10 W, and 5 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	1-29	UniProt Manual:Signal Peptides	UniProt:P52143
Domain	1259..1512	PF03797 Autotransporter beta-domain		PMID:19920124
Domain	1057..1180	PF03212 Pertactin		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=ypjA 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:90111474	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948630	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008713	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P52143	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7382	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13213	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948630	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003950	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3005	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	E. coli K-12 MG1655	2	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	4	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)
ypjA
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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_000913:2780728..2780768 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:b2647 (EcoliWiki Page)	NCBI GEO profiles for ypjA
microarray	GenExpDB:b2647 (EcoliWiki Page)	Summary of data for ypjA 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 (2780805..2781122) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ10; Well:A7^[7]
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Notes

Accessions Related to ypjA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7382	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3005	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2647
EcoGene	EcoGene:EG13213	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003950	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008713	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
Apis mellifera	ENSAPMP00000010996 (score: 1.000; bootstrap: 100%) ENSAPMP00000031667 (score: 0.060)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000038104 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	YP_026164 (score: 0.092) WBGene00041562 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00019146 (score: 1.000; bootstrap: 80%) WBGene00021761 (score: 0.097) WBGene00019273 (score: 0.080) WBGene00019085 (score: 0.075) WBGene00003058 (score: 0.074) WBGene00020576 (score: 0.060) WBGene00011522 (score: 0.052)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000022582 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000015132 (score: 1.000; bootstrap: 100%) ENSCINP00000006485 (score: 0.101) ENSCINP00000006407 (score: 0.099) YP_026164 (score: 1.000; bootstrap: 50%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0215928 (score: 1.000; bootstrap: 100%) DDB0188625 (score: 0.055)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000001188 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1929709 (score: 1.000; bootstrap: 55%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAPB2C81 (score: 1.000; bootstrap: 100%) SPBC12895 (score: 0.330) SPCC1889c (score: 0.301) SPBC9474 (score: 0.220) SPBC13488c (score: 0.141) SPAC9777c (score: 0.141) SPCC17421 (score: 0.128) SPAP11E102c (score: 0.127) SPAC1F86 (score: 0.100) SPBC21D106c (score: 0.054)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000023419 (score: 1.000; bootstrap: 71%) ENSXETP00000050976 (score: 0.169) YP_026164 (score: 1.000; bootstrap: 65%)	From Inparanoid:20070104
E. coli O157	YPJA	From ECOO157CYC
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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)	PF03797 Autotransporter beta-domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:51126
Superfamily (EcoliWiki Page)	SUPERFAMILY:103515
Pfam (EcoliWiki Page)	PF03212 Pertactin
EcoCyc	EcoCyc:G7382	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13213	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003950	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3005	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008713	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

ypjA: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 ypjA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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