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On One Page

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Gene |

Product(s) |

Expression|

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Standard Name	arnD
Gene Synonym(s)	ECK2249, b2256, JW2250, pmrJ, yfbH^[1]^[2], pbgP4, pmrJ, yfbH
Product Desc.	conserved protein^[2]^[3]
Product Synonyms(s)	conserved protein^[1], B2256^[2]^[1], YfbH^[2]^[1], PmrJ^[2]^[1] , ECK2249, JW2250, pbgP4, pmrJ, yfbH, b2256
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression
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	arnD
Mnemonic	ara4N (4-amino-4-deoxy-L-arabinose)
Synonyms	ECK2249, b2256, JW2250, pmrJ, yfbH^[1]^[2], pbgP4, pmrJ, yfbH
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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	51.04 minutes	MG1655: 2368040..2368930 <gbrowseImage> name=NC_000913:2368040..2368930 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2316531..2317421 <gbrowseImage> name=NC_012967:2316531..2317421 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2253845..2254735 <gbrowseImage> name=NC_012759:2253845..2254735 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2374688..2375578 <gbrowseImage> name=NC_007779:2374688..2375578 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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
ΔyfbH (Keio:JW2250)	deletion	deletion	PMID:16738554	Shigen CGSC9814^[4]
ΔyfbH737::kan			PMID:16738554	CGSC:104642
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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
JW2250	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACCAAAGTAGGCTTACGCAT Primer 2:CCGCGACTACCCGCAATTTGTTG
zfa-723::Tn10	Linked marker	CAG12178 gyrA+ = CGSC7526^[4]	est. P1 cotransduction: 39% ^[5] Synonyms:zei-723::Tn10, zfa-723::Tn10 nnnThe original CAG12178 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).
zfb-223::Tn10	Linked marker	CAG18484 = CGSC7406^[4]	est. P1 cotransduction: 46% ^[5] Synonyms:zej-223::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:G7169	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14092	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003745	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945334	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3845	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007462	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	YfbH
Synonyms	conserved protein^[1], B2256^[2]^[1], YfbH^[2]^[1], PmrJ^[2]^[1] , ECK2249, JW2250, pbgP4, pmrJ, yfbH, b2256
Product description	conserved protein^[2]^[3]
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. 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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011330	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005975	carbohydrate metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002509	P	Seeded from EcoCyc (v14.0)	complete
	GO:0005975	carbohydrate metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011330	P	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:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01870	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: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:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002509	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016811	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01870	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016811	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:3.5.1	F	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
Protein	groL		PMID:16606699	Experiment(s):EBI-1142351
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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 MTKVGLRIDV DTFRGTREGV PRLLEILSKH NIQASIFFSV GPDNMGRHLW RLVKPQFLWK MLRSNAASLY GWDILLAGTA WPGKEIGHAN ADIIREAAKH HEVGLHAWDH HAWQARSGNW DRQTMIDDIA RGLRTLEEII GQPVTCSAAA GWRADQKVIE AKEAFHLRYN SDCRGAMPFR PLLESGNPGT AQIPVTLPTW DEVIGRDVKA EDFNGWLLNR ILRDKGTPVY TIHAEVEGCA YQHNFVDLLK RAAQEGVTFC PLSELLSETL PLGQVVRGNI AGREGWLGCQ QIAGSR
Length	296
Mol. Wt	33.111 kDa
pI	7.6 (calculated)
Extinction coefficient	66,460 - 67,085 (calc based on 4 Y, 11 W, and 5 C residues)
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See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

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	6..170	PF01522 Polysaccharide deacetylase		PMID:19920124
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See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

<motif_map/>

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

Structures

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

Models

View models at:

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

</protect>

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:16130191	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945334	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007462	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P76472	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7169	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14092	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945334	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003745	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3845	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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See Help:Links_table for how to enter or edit information in this section of EcoliWiki.

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	39	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	0^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_000913:2368020..2368060 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:b2256 (EcoliWiki Page)	NCBI GEO profiles for yfbH
microarray	GenExpDB:b2256 (EcoliWiki Page)	Summary of data for yfbH 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 arnD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7169	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3845	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2256
EcoGene	EcoGene:EG14092	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003745	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007462	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
Shigella flexneri	S2468	From SHIGELLACYC
E. coli O157	Z3514	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)	PF01522 Polysaccharide deacetylase
Superfamily (EcoliWiki Page)	SUPERFAMILY:88713
EcoCyc	EcoCyc:G7169	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14092	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003745	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3845	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007462	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.

↑ ^1.0 ^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)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 ^2.9 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 CGSC: The Coli Genetics Stock Center
↑ ^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).

arnD: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 arnD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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