serB: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

serB

Gene Synonym(s)

ECK4380, b4388, JW4351[1], JW4351

Product Desc.

PSERPHOSPHA- Phosphoserine phosphatase; HAD9[2]

Product Synonyms(s)

3-phosphoserine phosphatase[1], B4388[3][1], SerB[3][1] , ECK4380, JW4351, b4388

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): serB[3], serB-radA[3]

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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HAD superfamily.[2]



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

serB

Mnemonic

Serine

Synonyms

ECK4380, b4388, JW4351[1], JW4351

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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

99.64 minutes, 99.64 minutes 

MG1655: 4622918..4623886
<gbrowseImage> name=NC_000913:4622918..4623886 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4613109..4614077
<gbrowseImage> name=NC_012967:4613109..4614077 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4561402..4562370
<gbrowseImage> name=NC_012759:4561402..4562370 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4629575..4630543
<gbrowseImage> name=NC_007779:4629575..4630543 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4669380..4670348
<gbrowseImage> name=NC_010473:4669380..4670348 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
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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

ΔserB (Keio:JW4351)

deletion

deletion

PMID:16738554

Shigen
CGSC11106[4]

serB28

CGSC:8563

serB22

CGSC:11493

[serB32]

CGSC:44247

null allele

ΔserB784::kan

PMID:16738554

CGSC:102916


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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

JW4351

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCCTAACATTACCTGGTGCGA

Primer 2:CCtTTCTGATTCAGGCTGCCTGA

15C9

Kohara Phage

Genobase

PMID:3038334

12A4

Kohara Phage

Genobase

PMID:3038334

mdoB202::Tn10

Linked marker

CAG18430 = CGSC7488[4]

est. P1 cotransduction: 32% [5]
Synonyms:zjj-202::Tn10, zji-202::Tn10

thrA34::Tn10

Linked marker

CAG18442 = CGSC7320[4]

est. P1 cotransduction: 55% [5]
Synonyms:thr-34::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:EG10945

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10945

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000934

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948913

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0938

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014393

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

SerB

Synonyms

3-phosphoserine phosphatase[1], B4388[3][1], SerB[3][1] , ECK4380, JW4351, b4388

Product description

PSERPHOSPHA- Phosphoserine phosphatase; HAD9[2]

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:0006545

glycine biosynthetic process

P

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0004647

phosphoserine phosphatase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004469

F

Seeded from EcoCyc (v14.0)

complete

GO:0004647

phosphoserine phosphatase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.1.3.3

F

Seeded from EcoCyc (v14.0)

complete

GO:0006564

L-serine biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004469

P

Seeded from EcoCyc (v14.0)

complete

GO:0006564

L-serine biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0718

P

Seeded from EcoCyc (v14.0)

complete

GO:0006564

L-serine biosynthetic process

PMID:14086727

IDA: Inferred from Direct Assay

P

complete

GO:0004647

phosphoserine phosphatase activity

PMID:14086727

IDA: Inferred from Direct Assay

F

complete

GO:0005737

cytoplasm

PMID:14086727

IDA: Inferred from Direct Assay

C

complete

GO:0008652

cellular amino acid biosynthetic process

PMID:14086727

IDA: Inferred from Direct Assay

P

complete

GO:0016791

phosphatase activity

PMID:14086727

IDA: Inferred from Direct Assay

F

complete

GO:0000287

magnesium ion binding

PMID:14086727

IDA: Inferred from Direct Assay

F

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

nadE

PMID:16606699

Experiment(s):EBI-1147974

Protein

rpsJ

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsP

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsT

PMID:19402753

LCMS(ID Probability):99.6

Protein

fimA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmA

PMID:19402753

LCMS(ID Probability):99.6

Protein

hdeA

PMID:19402753

LCMS(ID Probability):99.2

Protein

atpC

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmC

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplW

PMID:19402753

LCMS(ID Probability):99.6

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 

MPNITWCDLP EDVSLWPGLP LSLSGDEVMP LDYHAGRSGW LLYGRGLDKQ RLTQYQSKLG
AAMVIVAAWC VEDYQVIRLA GSLTARATRL AHEAQLDVAP LGKIPHLRTP GLLVMDMDST
AIQIECIDEI AKLAGTGEMV AEVTERAMRG ELDFTASLRS RVATLKGADA NILQQVRENL
PLMPGLTQLV LKLETLGWKV AIASGGFTFF AEYLRDKLRL TAVVANELEI MDGKFTGNVI
GDIVDAQYKA KTLTRLAQEY EIPLAQTVAI GDGANDLPMI KAAGLGIAYH AKPKVNEKAE
VTIRHADLMG VFCILSGSLN QK
Length

322

Mol. Wt

35.043 kDa

pI

5.6 (calculated)

Extinction coefficient

39,420 - 39,920 (calc based on 8 Y, 5 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

111..284

PF00702 haloacid dehalogenase-like hydrolase

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=serB 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:16132205

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948913

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014393

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AGB0

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10945

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10945

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948913

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000934

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0938

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 MG1655

790

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

242

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

565

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)

serB

serB-radA

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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_000913:4622898..4622938 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:b4388 (EcoliWiki Page)

NCBI GEO profiles for serB

microarray

GenExpDB:b4388 (EcoliWiki Page)

Summary of data for serB 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 (4622275..4622499) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ01; Well:C8[6]

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Notes

Accessions Related to serB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10945

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0938

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4388

EcoGene

EcoGene:EG10945

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000934

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014393

Escherichia coli str. K-12 substr. MG1655

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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

  • ENSANGP00000016587 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000033488 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT1G18640 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000017392 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00024962 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00013379 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000014881 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000019825 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-050809-127 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-050809-29 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0230054 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0023129 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA17627-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000003767 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000275605 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000005752 (score: 1.000; bootstrap: 100%)
  • ENSMMUP00000007982 (score: 0.366)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000008168 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:97788 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000032819 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000001228 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YGR208W (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPBC3H77c (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000162591 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000022202 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

SERB

From SHIGELLACYC

E. coli O157

SERB

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)

PF00702 haloacid dehalogenase-like hydrolase

Superfamily (EcoliWiki Page)

SUPERFAMILY:56784

EcoCyc

EcoCyc:EG10945

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10945

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000934

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0938

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014393

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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

  1. ↑ 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. ↑ 2.0 2.1 2.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 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).
  6. ↑ 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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