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Standard Name	agaB
Gene Synonym(s)	ECK3126, b3138, JW3107, yraD^[1], yraD
Product Desc.	AgaB^[2]^[3]; Component of EIIAga^[2]^[3] Putative PTS system N-acetylgalactosamine-specific enzyme IIB component ^[4]
Product Synonyms(s)	N-acetylgalactosamine-specific enzyme IIB component of PTS^[1], B3138^[2]^[1], YraD^[2]^[1], AgaB^[2]^[1] , ECK3126, JW3107, yraD, b3138
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): agaSYBCDI^[2], agaSkbaYagaBCDI
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	agaB
Mnemonic	Acetylgalactosamine
Synonyms	ECK3126, b3138, JW3107, yraD^[1], yraD
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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	70.74 minutes	MG1655: 3282192..3282668 <gbrowseImage> name=NC_000913:3282192..3282668 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3219403..3219879 <gbrowseImage> name=NC_012967:3219403..3219879 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3169340..3169816 <gbrowseImage> name=NC_012759:3169340..3169816 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3284025..3284501 <gbrowseImage> name=NC_007779:3284025..3284501 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3379937..3380413 <gbrowseImage> name=NC_010473:3379937..3380413 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
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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	Comments
ΔagaB (Keio:JW3107)	deletion	deletion	PMID:16738554	Shigen CGSC10366^[5]
agaB::Tn5KAN-I-SceI (FB21040)	Insertion at nt 304 in Minus orientation		PMID:15262929	E. coli Genome Project:FB21040	contains pKD46
agaB::Tn5KAN-I-SceI (FB21041)	Insertion at nt 304 in Minus orientation		PMID:15262929	E. coli Genome Project:FB21041	does not contain pKD46
ΔagaB752::kan			PMID:16738554	CGSC:99936
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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
JW3107	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACCAGTCCAAATATTCTCTT Primer 2:CCGTCAGGGATTTGTTCTTTTTG
20F4	Kohara Phage	Genobase	PMID:3038334
16C4	Kohara Phage	Genobase	PMID:3038334
aer-3075::Tn10	Linked marker	CAG12152 = CGSC7438^[5]	est. P1 cotransduction: 2% ^[6] Synonyms:zgh-3075::Tn10, zgj-3075::Tn10
sfsB203::Tn10	Linked marker	CAG12072 = CGSC7440^[5]	est. P1 cotransduction: 10% ^[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:EG12769	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12769	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002382	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947653	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2622	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010310	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	AgaB
Synonyms	N-acetylgalactosamine-specific enzyme IIB component of PTS^[1], B3138^[2]^[1], YraD^[2]^[1], AgaB^[2]^[1] , ECK3126, JW3107, yraD, b3138
Product description	AgaB^[2]^[3]; Component of EIIAga^[2]^[3] Putative PTS system N-acetylgalactosamine-specific enzyme IIB component ^[4]
EC number (for enzymes)	2.7.1.69^[1]
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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:0005575	cellular component	127.0.0.1 15:00, 17 February 2015 (CST)	ND: No biological Data available		C		Missing: reference
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018455	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006810	transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0813	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008643	carbohydrate transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0762	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008982	protein-N(PI)-phosphohistidine-sugar phosphotransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004720	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008982	protein-N(PI)-phosphohistidine-sugar phosphotransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018455	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008982	protein-N(PI)-phosphohistidine-sugar phosphotransferase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.7.1.69	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009401	phosphoenolpyruvate-dependent sugar phosphotransferase system	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004720	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009401	phosphoenolpyruvate-dependent sugar phosphotransferase system	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018455	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009401	phosphoenolpyruvate-dependent sugar phosphotransferase system	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0598	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016301	kinase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0418	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0808	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004720	C	Seeded from EcoCyc (v14.0)	complete
	GO:0003674	molecular function	127.0.0.1 15:00, 17 February 2015 (CST)	ND: No biological Data available		F	Function (IIB-gam) determined by homology to unannotated genes of both E. coli and B. sub, PMID:8932697 could be as ISA with the PTS homologs if they become valididated.	Missing: reference
	GO:0008150	biological process	127.0.0.1 15:00, 17 February 2015 (CST)	ND: No biological Data available		P	Only existing information determined by homology to unannotated genes of both E. coli and B. sub, PMID:8932697 could be as ISA with the PTS homologs if they become valididated.	Missing: reference
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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 EIIAga	could be indirect
Protein	atpD		PMID:16606699	Experiment(s):EBI-1144893
Protein	rfaH		PMID:16606699	Experiment(s):EBI-1144893
Protein	umuC		PMID:16606699	Experiment(s):EBI-1144893
Protein	purC		PMID:16606699	Experiment(s):EBI-1144893
Protein	sucB		PMID:16606699	Experiment(s):EBI-1144893
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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
plasma membrane			From EcoCyc^[3]
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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 MTSPNILLTR IDNRLVHGQV GVTWTSTIGA NLLVVVDDVV ANDDIQQKLM GITAETYGFG IRFFTIEKTI NVIGKAAPHQ KIFLICRTPQ TVRKLVEGGI DLKDVNVGNM HFSEGKKQIS SKVYVDDQDL TDLRFIKQRG VNVFIQDVPG DQKEQIPD
Length	158
Mol. Wt	17.621 kDa
pI	6.7 (calculated)
Extinction coefficient	8,480 - 8,605 (calc based on 2 Y, 1 W, and 1 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	5..155	PF03830 PTS system sorbose subfamily IIB component		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=agaB 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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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:16131030	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947653	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010310	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P42909	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12769	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12769	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947653	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002382	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2622	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	E. coli K-12 MG1655	7^a	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	6^a	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	5^a	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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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
agaSYBCDI
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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_000913:3282172..3282212 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:b3138 (EcoliWiki Page)	NCBI GEO profiles for agaB
microarray	GenExpDB:b3138 (EcoliWiki Page)	Summary of data for agaB 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 agaB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12769	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2622	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3138
EcoGene	EcoGene:EG12769	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002382	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010310	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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<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
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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
Superfamily (EcoliWiki Page)	SUPERFAMILY:52728
Pfam (EcoliWiki Page)	PF03830 PTS system sorbose subfamily IIB component
EcoCyc	EcoCyc:EG12769	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12769	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002382	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2622	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010310	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.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^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
↑ ^3.0 ^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
↑ ^4.0 ^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).

agaB: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 agaB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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