ssb:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

ssb

Gene Synonym(s)

ECK4051, b4059, JW4020, exrB, lexC[1], lexC

Product Desc.

ssDNA-binding protein[2][3]

Single-stranded DNA-binding protein; alkali-inducible; homotetramer[4]

Product Synonyms(s)

Single-stranded DNA-binding protein[1], B4059[2][1], LexC[2][1], ExrB[2][1], Ssb[2][1] , ECK4051, exrB, JW4020, lexC, b4059

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ssb[2], OP00091

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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SSB binds to RecQ and stimulates DNA unwinding (Shereda, 2007). Secondary structure of DNA does not effect binding of SSB. SSB increases the binding of RecA in DNA with secondary structure. LexA regulon.[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

ssb

Mnemonic

Single-strand binding

Synonyms

ECK4051, b4059, JW4020, exrB, lexC[1], lexC

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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

92.08 minutes, 92.08 minutes 

MG1655: 4272148..4272684
<gbrowseImage> name=NC_000913:4272148..4272684 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4253058..4253594
<gbrowseImage> name=NC_012967:4253058..4253594 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4210993..4211529
<gbrowseImage> name=NC_012759:4210993..4211529 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4277715..4278251
<gbrowseImage> name=NC_007779:4277715..4278251 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4371844..4372380
<gbrowseImage> name=NC_010473:4371844..4372380 source=DH10B preset=GeneLocation </gbrowseImage>

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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

4272151

Edman degradation

PMID:6270666
PMID:7042342


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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

ssbH56L

H56L

Reduces DNA-binding affinity

seeded from UniProt:P0AGE0

ssbL11F

L11F

Increased frequency of precise excision of transposon Tn10 derivatives (mutant SSB-202)

seeded from UniProt:P0AGE0

ssbP25S

P25S

Increased frequency of precise excision of transposon Tn10 derivatives (mutant SSB-202)

seeded from UniProt:P0AGE0

ssbG5D

G5D

Increased frequency of precise excision of transposon Tn10 derivatives (mutant SSB-200)

seeded from UniProt:P0AGE0

ssbH56Y

H56Y

Destabilizes the tetramer (mutant SSB-1)

seeded from UniProt:P0AGE0

ssbF61A

F61A

Reduces DNA-binding affinity

seeded from UniProt:P0AGE0

ssbV103M

V103M

Increased frequency of precise excision of transposon Tn10 derivatives (mutant SSB-201)

seeded from UniProt:P0AGE0

ssb-113(ts)

temperature sensitive

PMID:340916

CGSC:12155

ssb-1(ts)

temperature sensitive

PMID:3884590

CGSC:8613


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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

JW4020

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCCAGCAGAGGCGTAAACAA

Primer 2:CCGAACGGAATGTCATCATCAAA

12D1

Kohara Phage

Genobase

PMID:3038334

3F12

Kohara Phage

Genobase

PMID:3038334

malF3089::Tn10

Linked marker

CAG12164 = CGSC7476[5]

est. P1 cotransduction: 29% [6]

zje-2241::Tn10

Linked marker

CAG18427 = CGSC7481[5]

est. P1 cotransduction: 26% [6]

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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:EG10976

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10976

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000965

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948570

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0969

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013298

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

Ssb

Synonyms

Single-stranded DNA-binding protein[1], B4059[2][1], LexC[2][1], ExrB[2][1], Ssb[2][1] , ECK4051, exrB, JW4020, lexC, b4059

Product description

ssDNA-binding protein[2][3]

Single-stranded DNA-binding protein; alkali-inducible; homotetramer[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:0000725

recombinational repair

PMID:2087220

TAS: Traceable Author Statement

P

Seeded from EcoCyc (v14.0)

complete

GO:0003697

single-stranded DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000424

F

Seeded from EcoCyc (v14.0)

complete

GO:0003697

single-stranded DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011344

F

Seeded from EcoCyc (v14.0)

complete

GO:0003697

single-stranded DNA binding

PMID:4566449

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011344

P

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0235

P

Seeded from EcoCyc (v14.0)

complete

GO:0006298

mismatch repair

PMID:2087220

TAS: Traceable Author Statement

P

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

dnaK

PMID:15690043

Experiment(s):EBI-885071

Protein

gyrA

PMID:15690043

Experiment(s):EBI-885071

Protein

malP

PMID:15690043

Experiment(s):EBI-885071

Protein

mtgA

PMID:15690043

Experiment(s):EBI-885071

Protein

nohA

PMID:15690043

Experiment(s):EBI-885071

Protein

parC

PMID:15690043

Experiment(s):EBI-885071

Protein

priA

PMID:15690043

Experiment(s):EBI-885071

Protein

recG

PMID:15690043

Experiment(s):EBI-885071

Protein

recJ

PMID:15690043

Experiment(s):EBI-885071, EBI-881943, EBI-889451

Protein

rplB

PMID:15690043

Experiment(s):EBI-885071

Protein

rplC

PMID:15690043

Experiment(s):EBI-885071, EBI-891913

Protein

rpoB

PMID:15690043

Experiment(s):EBI-885071

Protein

rpoC

PMID:15690043

Experiment(s):EBI-885071

Protein

rpsD

PMID:15690043

Experiment(s):EBI-885071

Protein

sbcB

PMID:15690043

Experiment(s):EBI-885071, EBI-891913

Protein

secA

PMID:15690043

Experiment(s):EBI-885071

Protein

mnmE

PMID:15690043

Experiment(s):EBI-885071

Protein

topB

PMID:15690043

Experiment(s):EBI-885071, EBI-888082, EBI-893650

Protein

tufA

PMID:15690043

Experiment(s):EBI-885071, EBI-891913

Protein

arnA

PMID:15690043

Experiment(s):EBI-885071

Protein

yfiF

PMID:15690043

Experiment(s):EBI-885071

Protein

hupA

PMID:15690043

Experiment(s):EBI-891913

Protein

rplD

PMID:15690043

Experiment(s):EBI-891913

Protein

rplL

PMID:15690043

Experiment(s):EBI-891913

Protein

rplS

PMID:15690043

Experiment(s):EBI-891913

Protein

rplV

PMID:15690043

Experiment(s):EBI-891913

Protein

rplX

PMID:15690043

Experiment(s):EBI-891913

Protein

rpmB

PMID:15690043

Experiment(s):EBI-891913

Protein

rpmG

PMID:15690043

Experiment(s):EBI-891913

Protein

rpoA

PMID:15690043

Experiment(s):EBI-891913

Protein

rpsJ

PMID:15690043

Experiment(s):EBI-891913

Protein

rpsU

PMID:15690043

Experiment(s):EBI-891913

Protein

slyD

PMID:15690043

Experiment(s):EBI-891913

Protein

rhlE

PMID:16606699

Experiment(s):EBI-1147361

Protein

pepD

PMID:16606699

Experiment(s):EBI-1147361

Protein

yaiX

PMID:15690043

Experiment(s):EBI-885071

Protein

slyD

PMID:19402753

LCMS(ID Probability):99.4

Protein

rpsD

PMID:19402753

MALDI(Z-score):33.548330

Protein

rplX

PMID:19402753

LCMS(ID Probability):99.6

Protein

gyrA

PMID:19402753

MALDI(Z-score):28.202049

Protein

rplS

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmG

PMID:19402753

LCMS(ID Probability):99.6

Protein

malP

PMID:19402753

MALDI(Z-score):24.997072

Protein

tufB

PMID:19402753

MALDI(Z-score):23.296361

Protein

rplB

PMID:19402753

MALDI(Z-score):37.104445

Protein

rpmB

PMID:19402753

LCMS(ID Probability):99.4

Protein

secA

PMID:19402753

MALDI(Z-score):19.878648

Protein

hupA

PMID:19402753

LCMS(ID Probability):99.6

Protein

yfiF

PMID:19402753

MALDI(Z-score):38.597137

Protein

rpoA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):2.164891

Protein

rplD

PMID:19402753

LCMS(ID Probability):99.6

Protein

mnmE

PMID:19402753

MALDI(Z-score):35.041849

Protein

parC

PMID:19402753

MALDI(Z-score):25.319264

Protein

recG

PMID:19402753

MALDI(Z-score):26.866939

Protein

priA

PMID:19402753

MALDI(Z-score):27.249047

Protein

sbcB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):28.217789

Protein

rplL

PMID:19402753

LCMS(ID Probability):99.6

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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 

MASRGVNKVI LVGNLGQDPE VRYMPNGGAV ANITLATSES WRDKATGEMK EQTEWHRVVL
FGKLAEVASE YLRKGSQVYI EGQLRTRKWT DQSGQDRYTT EVVVNVGGTM QMLGGRQGGG
APAGGNIGGG QPQGGWGQPQ QPQGGNQFSG GAQSRPQQSA PAAPSNEPPM DFDDDIPF
Length

178

Mol. Wt

18.973 kDa

pI

5.4 (calculated)

Extinction coefficient

27,960 (calc based on 4 Y, 4 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

Initiator Methionine

1

Removed

UniProt:P0AGE0

Domain

6..113

PF00436 Single-strand binding protein family

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=ssb 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:16131885

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013298

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AGE0

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10976

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10976

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948570

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000965

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948570

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0969

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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 MC4100

1.28E+03

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

E. coli K-12 MG1655

14444

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

2329

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

6777

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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<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

ssb

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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_000913:4272128..4272168 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:b4059 (EcoliWiki Page)

NCBI GEO profiles for ssb

microarray

GenExpDB:b4059 (EcoliWiki Page)

Summary of data for ssb 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 (4271368..4271753) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ20; Well:H12[7]

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Notes

Accessions Related to ssb Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10976

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0969

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4059

EcoGene

EcoGene:EG10976

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000965

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013298

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

Anopheles gambiae

  • ENSANGP00000003047 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000022197 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT4G11060 (score: 1.000; bootstrap: 100%)
  • AT3G18580 (score: 0.125)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000014520 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000005789 (score: 1.000; bootstrap: 100%)
  • ENSCAFP00000003810 (score: 0.291)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-050417-340 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-050417-341 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0010438 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA18119-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000020973 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000265304 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000029533 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000017014 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:1920040 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q6L4W0 (score: 1.000; bootstrap: 100%)
  • Q5VP75 (score: 0.146)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000033880 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000016217 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000161163 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000030466 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Shigella flexneri

SSB

From SHIGELLACYC

E. coli O157

SSB

From ECOO157CYC

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Do-It-Yourself Web Tools

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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)

PF00436 Single-strand binding protein family

Superfamily (EcoliWiki Page)

SUPERFAMILY:50249

Panther (EcoliWiki Page)

PTHR10302:SF0

EcoCyc

EcoCyc:EG10976

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10976

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000965

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0969

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013298

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 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).
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

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