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Gene |

Product(s) |

Expression|

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Quickview

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Standard Name	syd
Gene Synonym(s)	ECK2788, b2793, JW2764, ydr^[1], ydr
Product Desc.	predicted protein^[2]^[3] Interacts with secY^[4]
Product Synonyms(s)	predicted protein^[1], B2793^[2]^[1], Ydr^[2]^[1], Syd^[2]^[1] , ECK2788, JW2764, ydr, b2793
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): syd^[2]
Regulation/Activity
Quick Links
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Notes

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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	syd
Mnemonic	secY-d1 suppression
Synonyms	ECK2788, b2793, JW2764, ydr^[1], ydr
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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	62.99 minutes	MG1655: 2923302..2922757 <gbrowseImage> name=NC_000913:2922757..2923302 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2814209..2813664 <gbrowseImage> name=NC_012967:2813664..2814209 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2809905..2810450 <gbrowseImage> name=NC_012759:2809905..2810450 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2923936..2923391 <gbrowseImage> name=NC_007779:2923391..2923936 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3017180..3016635 <gbrowseImage> name=NC_010473:3016635..3017180 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	2922757	Edman degradation	PMID:7890670
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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
Δsyd (Keio:JW2764)	deletion	deletion	PMID:16738554	Shigen CGSC10167^[5]
Δsyd-720::kan			PMID:16738554	CGSC:103076
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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
JW2764	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGACGATTTGACCGCACAAGC Primer 2:CCaAGAAGAGGCTTAAGTTGATT
10B5	Kohara Phage	Genobase	PMID:3038334
8C5	Kohara Phage	Genobase	PMID:3038334
cysI95::Tn10	Linked marker	CAG12173 = CGSC7425^[5]	est. P1 cotransduction: 22% ^[6] Synonyms:cysC95::Tn10
fucP3072::Tn10	Linked marker	CAG12079 = CGSC7427^[5]	est. P1 cotransduction: 72% ^[6] Synonyms:fuc-3072::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:G7451	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12959	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004014	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947271	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2792	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009154	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	Syd
Synonyms	predicted protein^[1], B2793^[2]^[1], Ydr^[2]^[1], Syd^[2]^[1] , ECK2788, JW2764, ydr, b2793
Product description	predicted protein^[2]^[3] Interacts with secY^[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:0005515	protein binding	PMID:19139097	IPI: Inferred from Physical Interaction	UniProtKB:P0AGA2	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	yccS		PMID:19402753	LCMS(ID Probability):99.4
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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 MDDLTAQALK DFTARYCDAW HEEHKSWPLS EELYGVPSPC IISTTEDAVY WQPQPFTGEQ NVNAVERAFD IVIQPTIHTF YTTQFAGDMH AQFGDIKLTL LQTWSEDDFR RVQENLIGHL VTQKRLKLPP TLFIATLEEE LEVISVCNLS GEVCKETLGT RKRTHLASNL AEFLNQLKPL L
Length	181
Mol. Wt	20.708 kDa
pI	4.8 (calculated)
Extinction coefficient	27,960 - 28,460 (calc based on 4 Y, 4 W, and 4 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	8..181	PF07348 Syd protein		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=syd 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:16130700	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947271	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009154	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A8U0	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7451	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12959	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947271	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004014	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2792	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	11.303+/-0.085	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.039449541	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	982	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	268	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	527	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)
syd
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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_000913:2923282..2923322 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:b2793 (EcoliWiki Page)	NCBI GEO profiles for syd
microarray	GenExpDB:b2793 (EcoliWiki Page)	Summary of data for syd 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 (2923219..2923443) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ14; Well:A1^[7]
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Notes

Accessions Related to syd Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7451	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2792	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2793
EcoGene	EcoGene:EG12959	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004014	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009154	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	SYD	From SHIGELLACYC
E. coli O157	SYD	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)	PF07348 Syd protein
EcoCyc	EcoCyc:G7451	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12959	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004014	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2792	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009154	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 ^2.6 ^2.7 ^2.8 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 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

syd: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 syd Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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