ebgA: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

ebgA

Gene Synonym(s)

ECK3066, b3076, JW5511[1], JW5511

Product Desc.

evolved β-D-galactosidase, α subunit; cryptic gene[2][3];

Component of evolved β-D-galactosidase[3]

Evolved beta-galactosidase, alpha subunit; normal substrate and function unknown; alpha(4)beta(4) holoenzyme[4]

Product Synonyms(s)

cryptic beta-D-galactosidase, alpha subunit[1], B3076[2][1], EbgA[2][1] , ECK3066, JW5511, b3076

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ebgAC[2], OP00170

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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Wildtype EbgA can be mutated to hydrolyze lactose. EbgA has an Ig-like domain: pfam PF00703 aligns to residues 209-318. ebgA, uidA and lacZ are paralogs.[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

ebgA

Mnemonic

Evolved beta-galactosidase

Synonyms

ECK3066, b3076, JW5511[1], JW5511

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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

69.42 minutes 

MG1655: 3220655..3223747
<gbrowseImage> name=NC_000913:3220655..3223747 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3155450..3158542
<gbrowseImage> name=NC_012967:3155450..3158542 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3107803..3110895
<gbrowseImage> name=NC_012759:3107803..3110895 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3221289..3224381
<gbrowseImage> name=NC_007779:3221289..3224381 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3318400..3321492
<gbrowseImage> name=NC_010473:3318400..3321492 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

ebgAW976C

W976C

(improve activity)

Strain variation; seeded from UniProt:P06864

ebgAS978G

S978G

(improve activity)

Strain variation; seeded from UniProt:P06864

ebgAE93K

E93K

(improve activity)

Strain variation; seeded from UniProt:P06864

ebgAD92N

D92N

(improve activity)

Strain variation; seeded from UniProt:P06864

ΔebgA (Keio:JW5511)

deletion

deletion

PMID:16738554

Shigen

ebgA::Tn5KAN-I-SceI (FB21020)

Insertion at nt 2366 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21020

contains pKD46

ebgA::Tn5KAN-I-SceI (FB21021)

Insertion at nt 2925 in Minus orientation

PMID:15262929

E. coli Genome Project:FB21021

does not contain pKD46

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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

JW5511

Plasmid clone

Shigen

PMID:16769691

Status:cloned as old JW

Primer 1:GCCAATCGCTGGGAAAACATTCA

Primer 2:CCTTGCTTATTCTCGCTGTGCAA

19F2

Kohara Phage

Genobase

PMID:3038334

17E4

Kohara Phage

Genobase

PMID:3038334

4A1

Kohara Phage

Genobase

PMID:3038334

aer-3075::Tn10

Linked marker

CAG12152 = CGSC7438[5]

est. P1 cotransduction: 84% [6]
Synonyms:zgh-3075::Tn10, zgj-3075::Tn10

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[5]

est. P1 cotransduction: % [6]
Synonyms:zgj-203::Tn10, zha-203::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:EG10252

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10252

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000246

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947583

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0248

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010104

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

EbgA

Synonyms

cryptic beta-D-galactosidase, alpha subunit[1], B3076[2][1], EbgA[2][1] , ECK3066, JW5511, b3076

Product description

evolved β-D-galactosidase, α subunit; cryptic gene[2][3];

Component of evolved β-D-galactosidase[3]

Evolved beta-galactosidase, alpha subunit; normal substrate and function unknown; alpha(4)beta(4) holoenzyme[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:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011013

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013781

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014718

F

Seeded from EcoCyc (v14.0)

complete

GO:0004553

hydrolase activity, hydrolyzing O-glycosyl compounds

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006101

F

Seeded from EcoCyc (v14.0)

complete

GO:0004553

hydrolase activity, hydrolyzing O-glycosyl compounds

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006102

F

Seeded from EcoCyc (v14.0)

complete

GO:0004553

hydrolase activity, hydrolyzing O-glycosyl compounds

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006103

F

Seeded from EcoCyc (v14.0)

complete

GO:0004553

hydrolase activity, hydrolyzing O-glycosyl compounds

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006104

F

Seeded from EcoCyc (v14.0)

complete

GO:0004553

hydrolase activity, hydrolyzing O-glycosyl compounds

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013812

F

Seeded from EcoCyc (v14.0)

complete

GO:0004565

beta-galactosidase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004199

F

Seeded from EcoCyc (v14.0)

complete

GO:0004565

beta-galactosidase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.2.1.23

F

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004199

P

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006101

P

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006102

P

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006103

P

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006104

P

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011013

P

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013781

P

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013812

P

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014718

P

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0326

P

Seeded from EcoCyc (v14.0)

complete

GO:0009341

beta-galactosidase complex

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004199

C

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:0016798

hydrolase activity, acting on glycosyl bonds

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0326

F

Seeded from EcoCyc (v14.0)

complete

GO:0030246

carbohydrate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011013

F

Seeded from EcoCyc (v14.0)

complete

GO:0030246

carbohydrate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014718

F

Seeded from EcoCyc (v14.0)

complete

GO:0043169

cation binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013781

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

Subunits of evolved β-D-galactosidase

could be indirect


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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 

MNRWENIQLT HENRLAPRAY FFSYDSVAQA RTFARETSSL FLPLSGQWNF HFFDHPLQVP
EAFTSELMAD WGHITVPAMW QMEGHGKLQY TDEGFPFPID VPFVPSDNPT GAYQRIFTLS
DGWQGKQTLI KFDGVETYFE VYVNGQYVGF SKGSRLTAEF DISAMVKTGD NLLCVRVMQW
ADSTYVEDQD MWWSAGIFRD VYLVGKHLTH INDFTVRTDF DEAYCDATLS CEVVLENLAA
SPVVTTLEYT LFDGERVVHS SAIDHLAIEK LTSASFAFTV EQPQQWSAES PYLYHLVMTL
KDANGNVLEV VPQRVGFRDI KVRDGLFWIN NRYVMLHGVN RHDNDHRKGR AVGMDRVEKD
LQLMKQHNIN SVRTAHYPND PRFYELCDIY GLFVMAETDV ESHGFANVGD ISRITDDPQW
EKVYVERIVR HIHAQKNHPS IIIWSLGNES GYGCNIRAMY HAAKALDDTR LVHYEEDRDA
EVVDIISTMY TRVPLMNEFG EYPHPKPRII CEYAHAMGNG PGGLTEYQNV FYKHDCIQGH
YVWEWCDHGI QAQDDHGNVW YKFGGDYGDY PNNYNFCLDG LIYSDQTPGP GLKEYKQVIA
PVKIHARDLT RGELKVENKL WFTTLDDYTL HAEVRAEGET LATQQIKLRD VAPNSEAPLQ
ITLPQLDARE AFLNITVTKD SRTRYSEAGH PIATYQFPLK ENTAQPVPFA PNNARPLTLE
DDRLSCTVRG YNFAITFSKM SGKPTSWQVN GESLLTREPK INFFKPMIDN HKQEYEGLWQ
PNHLQIMQEH LRDFAVEQSD GEVLIISRTV IAPPVFDFGM RCTYIWRIAA DGQVNVALSG
ERYGDYPHII PCIGFTMGIN GEYDQVAYYG RGPGENYADS QQANIIDIWR STVDAMFENY
PFPQNNGNRQ HVRWTALTNR HGNGLLVVPQ RPINFSAWHY TQENIHAAQH CNELQRSDDI
TLNLDHQLLG LGSNSWGSEV LDSWRVWFRD FSYGFTLLPV SGGEATAQSL ASYEFGAGFF
STNLHSENKQ
Length

1,030

Mol. Wt

117.878 kDa

pI

5.3 (calculated)

Extinction coefficient

210,510 - 212,135 (calc based on 49 Y, 25 W, and 13 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

727..998

PF02929 Beta galactosidase small chain

PMID:19920124

Domain

209..318

PF00703 domain

PMID:19920124

Domain

320..604

PF02836 Glycosyl hydrolases family 2, TIM barrel domain

PMID:19920124

Domain

38..207

PF02837 Glycosyl hydrolases family 2, sugar binding domain

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=ebgA 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:49176308

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947583

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010104

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P06864

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10252

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10252

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947583

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000246

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0248

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

3a

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

Low confidence in the sequencing data set.

PMID: 24766808

Protein

E. coli K-12 MG1655

1a

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

Low confidence in the sequencing data set.

PMID: 24766808

Protein

E. coli K-12 MG1655

0a

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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<protect>

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

Transcription unit(s)

ebgAC

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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_000913:3220635..3220675 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:b3076 (EcoliWiki Page)

NCBI GEO profiles for ebgA

microarray

GenExpDB:b3076 (EcoliWiki Page)

Summary of data for ebgA 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
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Notes

Accessions Related to ebgA Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10252

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0248

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3076

EcoGene

EcoGene:EG10252

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000246

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010104

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

Shigella flexneri

EBGA

From SHIGELLACYC

E. coli O157

EBGA

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)

PF02929 Beta galactosidase small chain

Pfam (EcoliWiki Page)

PF00703 domain

Pfam (EcoliWiki Page)

PF02836 Glycosyl hydrolases family 2, TIM barrel domain

Pfam (EcoliWiki Page)

PF02837 Glycosyl hydrolases family 2, sugar binding domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:49303

Superfamily (EcoliWiki Page)

SUPERFAMILY:49303

Superfamily (EcoliWiki Page)

SUPERFAMILY:49785

Superfamily (EcoliWiki Page)

SUPERFAMILY:51445

Superfamily (EcoliWiki Page)

SUPERFAMILY:74650

EcoCyc

EcoCyc:EG10252

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10252

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000246

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0248

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010104

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 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. ↑ 3.0 3.1 3.2 3.3 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).

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