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Standard Name	arnB
Gene Synonym(s)	yfbE, ECK2246, b2253, JW5372, pmrH^[1]^[2], pgbP1, pmrH
Product Desc.	G7166^[2]^[3] UDP-4-amino-4-deoxy-L-arabinose synthase; UDP-4"-ketopentose aminotransferase; L-glutamate is the amine donor^[4]
Product Synonyms(s)	uridine 5'-(beta-1-threo-pentapyranosyl-4-ulose diphosphate) aminotransferase, PLP-dependent^[1], B2253^[2]^[1], YfbE^[2]^[1], PmrH^[2]^[1], ArnB^[2]^[1] , ECK2246, JW5372, pgbP1, pmrH, yfbE, b2253
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yfbE^[2]
Regulation/Activity
Quick Links
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Notes

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Involved in a lipid A modification required for polymyxin B and cationic antimicrobial peptide resistance. basRS regulon. AFMB Structural Genomics target No. 36 (http://afmb.cnrs-mrs.fr/article171.html). otherPDB (S. typhimurium): 1MDO, 1MDX, 1MDZ.^[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	arnB
Mnemonic	ara4N (4-amino-4-deoxy-L-arabinose)
Synonyms	yfbE, ECK2246, b2253, JW5372, pmrH^[1]^[2], pgbP1, pmrH
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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	50.95 minutes	MG1655: 2363932..2365089 <gbrowseImage> name=NC_000913:2363932..2365089 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 2249755..2250894 <gbrowseImage> name=NC_012759:2249755..2250894 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2370580..2371737 <gbrowseImage> name=NC_007779:2370580..2371737 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2454938..2456077 <gbrowseImage> name=NC_010473:2454938..2456077 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)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
ΔarnB734::kan					PMID:16738554	CGSC:106132
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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
	Plasmid clone	Shigen	PMID:16769691 Status: Primer 1: Primer 2:
4B4	Kohara Phage	Genobase	PMID:3038334
5H12	Kohara Phage	Genobase	PMID:3038334
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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:G7166	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14089	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003742	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947375	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3842	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007456	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	YfbE
Synonyms	uridine 5'-(beta-1-threo-pentapyranosyl-4-ulose diphosphate) aminotransferase, PLP-dependent^[1], B2253^[2]^[1], YfbE^[2]^[1], PmrH^[2]^[1], ArnB^[2]^[1] , ECK2246, JW5372, pgbP1, pmrH, yfbE, b2253
Product description	G7166^[2]^[3] UDP-4-amino-4-deoxy-L-arabinose synthase; UDP-4"-ketopentose aminotransferase; L-glutamate is the amine donor^[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:0008483	transaminase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01167	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008483	transaminase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.6.1	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008483	transaminase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0032	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008610	lipid biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0444	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009103	lipopolysaccharide biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0448	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009245	lipid A biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0441	P	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015421	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015422	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046493	lipid A metabolic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01167	P	Seeded from EcoCyc (v14.0)	complete
	GO:0046677	response to antibiotic	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0046	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
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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
cytoplasm			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 MDRYSMAEGK AMSEFLPFSR PAMGVEELAA VKEVLESGWI TTGPKNQALE QAFCQLTGNQ HAIAVSSATA GMHITLMALK IGKGDEVITP SLTWVSTLNM ISLLGATPVM VDVDRDTLMV TPEAIESAIT PRTKAIIPVH YAGAPADIDA IRAIGERYGI AVIEDAAHAV GTYYKGRHIG AKGTAIFSFH AIKNITCAEG GLIVTDNENL ARQLRMLKFH GLGVDAYDRQ TWGRAPQAEV LTPGYKYNLT DINAAIALTQ LVKLEHLNTR RREIAQQYQQ ALAALPFQPL SLPAWPHVHA WHLFIIRVDE QRCGISRDAL MEALKERGIG TGLHFRAAHT QKYYRERFPT LSLPNTEWNS ERICSLPLFP DMTTADADHV ITALQQLAGQ
Length	390
Mol. Wt	42.89 kDa
pI	6.8 (calculated)
Extinction coefficient	49,390 - 49,890 (calc based on 11 Y, 6 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	10..374	PF01041 DegT/DnrJ/EryC1/StrS aminotransferase 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=arnB 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:145698288	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947375	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007456	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77690	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7166	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14089	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947375	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003742	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3842	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	105	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	389	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	12^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)
yfbE
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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_000913:2363912..2363952 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:b2253 (EcoliWiki Page)	NCBI GEO profiles for arnB
microarray	GenExpDB:b2253 (EcoliWiki Page)	Summary of data for arnB 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 (2363553..2363958) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ11; Well:H6^[5]
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Notes

Accessions Related to arnB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7166	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3842	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2253
EcoGene	EcoGene:EG14089	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003742	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007456	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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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Anopheles gambiae	ENSANGP00000028500 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000030930 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000020782 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	S2465	From SHIGELLACYC
E. coli O157	Z3511	From ECOO157CYC
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Do-It-Yourself Web Tools

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)	PF01041 DegT/DnrJ/EryC1/StrS aminotransferase family
Superfamily (EcoliWiki Page)	SUPERFAMILY:53383
Panther (EcoliWiki Page)	PTHR11751:SF186
EcoCyc	EcoCyc:G7166	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14089	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003742	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3842	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007456	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 ^1.11 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 ^2.11 ^2.12 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^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.
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

arnB: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 arnB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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