ssuB:On One Page

From EcoliWiki
Jump to: navigation, search

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

Quickview

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

<protect>

Standard Name

ssuB

Gene Synonym(s)

ECK0924, b0933, JW0916, ycbE[1], ycbE

Product Desc.

SsuB[2][3];

Component of YcbE/YcbM ABC transporter[2]; aliphatic sulfonate ABC transporter[3]

Putative aliphatic sulphonate transport ATP-binding protein; sulfur starvation inducible; Cbl regulon[4]

Product Synonyms(s)

alkanesulfonate transporter subunit[1], ATP-binding component of ABC superfamily[1], B0933[2][1], YcbE[2][1], SsuB[2][1] , ECK0924, JW0916, ycbE, b0933

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ssuEADCB[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

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

edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]





Gene

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

ssuB

Mnemonic

Sulfonate-sulfur utilization

Synonyms

ECK0924, b0933, JW0916, ycbE[1], ycbE

edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]


<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

21.39 minutes 

MG1655: 993267..992500
<gbrowseImage> name=NC_000913:992500..993267 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1011135..1010368
<gbrowseImage> name=NC_012967:1010368..1011135 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 895468..896235
<gbrowseImage> name=NC_012759:895468..896235 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 994466..993699
<gbrowseImage> name=NC_007779:993699..994466 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1047195..1046428
<gbrowseImage> name=NC_010473:1046428..1047195 source=DH10B preset=GeneLocation </gbrowseImage>

edit table

</protect>

Notes

Sequence Features

[back to top]


See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes
edit table

<protect></protect>

Notes

Alleles and Phenotypes

[back to top]


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

ΔssuB (Keio:JW0916)

deletion

deletion

PMID:16738554

Shigen
CGSC8928[5]

ΔssuB749::kan

PMID:16738554

CGSC:103036


edit table

<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table

</protect>

Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW0916

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAATACTGCTCGTCTGAACCA

Primer 2:CCCCCCTGTTTTCTCAGGCGAGT

11F5

Kohara Phage

Genobase

PMID:3038334

7F5

Kohara Phage

Genobase

PMID:3038334

9E9

Kohara Phage

Genobase

PMID:3038334

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[5]

est. P1 cotransduction: 13% [6]
Synonyms:zbj-1230::Tn10

zcb-3059::Tn10

Linked marker

CAG12094 = CGSC7358[5]

est. P1 cotransduction: 72% [6]

edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG12358

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12358

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002226

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947220

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2261

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003173

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



Product(s)

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

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

Standard name

SsuB

Synonyms

alkanesulfonate transporter subunit[1], ATP-binding component of ABC superfamily[1], B0933[2][1], YcbE[2][1], SsuB[2][1] , ECK0924, JW0916, ycbE, b0933

Product description

SsuB[2][3];

Component of YcbE/YcbM ABC transporter[2]; aliphatic sulfonate ABC transporter[3]

Putative aliphatic sulphonate transport ATP-binding protein; sulfur starvation inducible; Cbl regulon[4]

EC number (for enzymes)


edit table

<protect></protect>

Notes

Function

[back to top]


<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:0000166

nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0005215

transporter activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01724

F

Seeded from EcoCyc (v14.0)

complete

GO:0005215

transporter activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017875

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003439

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017871

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017875

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

PMID:10506196

ISS: Inferred from Sequence or Structural Similarity

F

Seeded from EcoCyc (v14.0)

Missing: with/from

GO:0005886

plasma membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017875

C

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0997

C

Seeded from EcoCyc (v14.0)

complete

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:0006790

sulfur metabolic process

PMID:10506196

IGI: Inferred from Genetic Interaction

P

Seeded from EcoCyc (v14.0)

Missing: with/from

GO:0006790

sulfur metabolic process

PMID:10506196

IGI: Inferred from Genetic Interaction

EcoliWiki:ssuE
EcoliWiki:ssuD
EcoliWiki:ssuC
EcoliWiki:ssuA

P

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:0016787

hydrolase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017875

F

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc (v14.0)

complete

GO:0016887

ATPase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003439

F

Seeded from EcoCyc (v14.0)

complete

GO:0016887

ATPase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017871

F

Seeded from EcoCyc (v14.0)

complete

GO:0017111

nucleoside-triphosphatase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

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

GO:0042626

ATPase activity, coupled to transmembrane movement of substances

PMID:10506196

ISS: Inferred from Sequence or Structural Similarity

F

Seeded from EcoCyc (v14.0)

Missing: with/from

GO:0042918

alkanesulfonate transport

PMID:10506196

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc (v14.0)

complete

GO:0043190

ATP-binding cassette (ABC) transporter complex

PMID:10506196

ISS: Inferred from Sequence or Structural Similarity

C

Seeded from EcoCyc (v14.0)

Missing: with/from

edit table

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

Subunits of YcbE/YcbM ABC transporter

could be indirect

Protein

ydhK

PMID:16606699

Experiment(s):EBI-1138421

Protein

groL

PMID:16606699

Experiment(s):EBI-1138421

Protein

dnaK

PMID:16606699

Experiment(s):EBI-1138421

Protein

pncB

PMID:16606699

Experiment(s):EBI-1138421
edit table

</protect>

Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes

cytoplasm

From EcoCyc[3]


edit table

<protect></protect>

Notes

Structure and Physical Properties

[back to top]


<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 

MNTARLNQGT PLLLNAVSKH YAENIVLNQL DLHIPAGQFV AVVGRSGGGK STLLRLLAGL
ETPTAGDVLA GTTPLAEIQE DTRMMFQDAR LLPWKSVIDN VGLGLKGQWR DAARRALAAV
GLENRAGEWP AALSGGQKQR VALARALIHR PGLLLLDEPL GALDALTRLE MQDLIVSLWQ
EHGFTVLLVT HDVSEAVAMA DRVLLIEEGK IGLDLTVDIP RPRRLGSVRL AELEAEVLQR
VMQRGESETR LRKQG
Length

255

Mol. Wt

27.738 kDa

pI

7.1 (calculated)

Extinction coefficient

23,490 (calc based on 1 Y, 4 W, and 0 C residues)

edit table


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

51..161

PF00005 ABC transporter

PMID:19920124

edit table

<motif_map/>

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

Structures

<beststructure> gene=ssuB taxon=562,83333 </beststructure>

Models

View models at:

edit table
</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

[back to top]


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

Resource type Source Notes/Reference
edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16128900

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947220

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003173

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AAI1

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12358

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12358

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947220

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002226

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2261

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]




Expression

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]


See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

Ecoli K-12

0.256+/-0.035

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

Protein

E. coli K-12 MG1655

7

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

12

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

12a

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

edit table

Notes

Transcription and Transcriptional Regulation

[back to top]


<protect>

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

Transcription unit(s)

ssuEADCB

edit table
Figure courtesy of RegulonDB

</protect>

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

[back to top]


<protect><gbrowseImage> name=NC_000913:993247..993287 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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

</protect>

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

[back to top]


<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
edit table


Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b0933 (EcoliWiki Page)

NCBI GEO profiles for ssuB

microarray

GenExpDB:b0933 (EcoliWiki Page)

Summary of data for ssuB from multiple microarray studies

edit table


Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes
edit table

<protect></protect>

Notes

Accessions Related to ssuB Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG12358

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2261

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0933

EcoGene

EcoGene:EG12358

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002226

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003173

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



Evolution

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]


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

Organism Homologs (Statistics) Comments

Drosophila melanogaster

  • FBgn0031362 (score: 1.000; bootstrap: 69%)
  • FBgn0032167 (score: 0.229)
  • FBgn0025683 (score: 0.225)
  • FBgn0020762 (score: 0.211)
  • FBgn0031516 (score: 0.208)
  • FBgn0031220 (score: 0.184)
  • FBgn0052091 (score: 0.175)
  • FBgn0031449 (score: 0.159)
  • FBgn0031515 (score: 0.153)
  • FBgn0003996 (score: 0.077)
  • FBgn0003515 (score: 0.074)
  • FBgn0020445 (score: 0.059)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA14594-PA (score: 1.000; bootstrap: 57%)
  • GA16356-PA (score: 0.236)
  • GA15545-PA (score: 0.235)
  • GA19180-PA (score: 0.225)
  • GA18458-PA (score: 0.185)
  • GA16671-PA (score: 0.176)
  • GA16397-PA (score: 0.154)
  • GA15454-PA (score: 0.057)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000130824 (score: 1.000; bootstrap: 57%)
  • NEWSINFRUP00000130826 (score: 0.180)
  • NEWSINFRUP00000167567 (score: 0.137)
  • NEWSINFRUP00000182359 (score: 0.125)
  • NEWSINFRUP00000177047 (score: 0.125)
  • NEWSINFRUP00000168237 (score: 0.097)
  • NEWSINFRUP00000171182 (score: 0.092)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00014344001 (score: 1.000; bootstrap: 57%)
  • GSTENP00014343001 (score: 0.105)
  • GSTENP00020877001 (score: 0.101)
  • GSTENP00038511001 (score: 0.091)
  • GSTENP00014937001 (score: 0.051)

From Inparanoid:20070104

Shigella flexneri

YCBE

From SHIGELLACYC

E. coli O157

YCBE

From ECOO157CYC

edit table


Do-It-Yourself Web Tools

<protect></protect>

Notes

Families

[back to top]


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

Database Accession Notes

Pfam (EcoliWiki Page)

PF00005 ABC transporter

Panther (EcoliWiki Page)

PTHR24220:SF204

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

EcoCyc

EcoCyc:EG12358

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12358

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002226

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2261

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003173

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



References

[back to top]


See Help:References for how to manage references in EcoliWiki.

  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 3.2 3.3 3.4 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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. ↑ 5.0 5.1 5.2 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).

Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=ssuB:On_One_Page&oldid=219324"