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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	rhmD
Gene Synonym(s)	ECK2240, b2247, JW2241, yfaW^[1], JW2241, yfaW
Product Desc.	predicted enolase^[2]^[3] Putative dehydratase, function unknown^[4]
Product Synonyms(s)	predicted enolase^[1], B2247^[2]^[1], RhmD^[2]^[1] , ECK2240, JW2241, yfaW, b2247
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rhmD^[2]
Regulation/Activity
Quick Links
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Notes

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YfaW functions as a L-rhamnonate dehydratate (B.K. Hubbard, J.A. Gerlt, unpublished observations, as cited in Gerlt. 2005). Uses L-lyxonate as substrate.^[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	rhmD
Mnemonic
Synonyms	ECK2240, b2247, JW2241, yfaW^[1], JW2241, yfaW
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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	50.83 minutes, 50.83 minutes	MG1655: 2359448..2358231 <gbrowseImage> name=NC_000913:2358231..2359448 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2307939..2306722 <gbrowseImage> name=NC_012967:2306722..2307939 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2244036..2245253 <gbrowseImage> name=NC_012759:2244036..2245253 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2366096..2364879 <gbrowseImage> name=NC_007779:2364879..2366096 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2450436..2449219 <gbrowseImage> name=NC_010473:2449219..2450436 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: Description	Reference	Availability	Comments
ΔyfaW (Keio:JW2241)	deletion	deletion		PMID:16738554	Shigen CGSC9807^[5]
yfaWH29N		H29N	Loss of activity due to absence of substrate binding			seeded from UniProt:P77215
yfaWH277N		H277N	35-fold decrease in activity. 59- fold decrease in substrate affinity			seeded from UniProt:P77215
yfaWH325N		H325N	Loss of activity. 2-fold decrease in substrate affinity			seeded from UniProt:P77215
ΔyfaW728::kan				PMID:16738554	CGSC:104632
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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
JW2241	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGAGAACATCATGACCCTACC Primer 2:CCGTGGCTGTAGGGGCGTTTCAA
22C4	Kohara Phage	Genobase	PMID:3038334
4B4	Kohara Phage	Genobase	PMID:3038334
zfa-723::Tn10	Linked marker	CAG12178 gyrA+ = CGSC7526^[5]	est. P1 cotransduction: 58% ^[6] 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^[5]	est. P1 cotransduction: 29% ^[6] 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:G7160	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3838	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2247
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C2789
EcoGene	EcoGene:EG14085	Escherichia coli str. K-12 substr. MG1655
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:Z3505
ASAP	ASAP:ABE-0007436	Escherichia coli str. K-12 substr. MG1655
EcoCyc (EcoliWiki Page)	ECOCYC:G7160	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945881	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003736	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	RhmD
Synonyms	predicted enolase^[1], B2247^[2]^[1], RhmD^[2]^[1] , ECK2240, JW2241, yfaW, b2247
Product description	predicted enolase^[2]^[3] Putative dehydratase, function unknown^[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:0000287	magnesium ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0460	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001354	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009063	cellular amino acid catabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018110	P	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050032	L-rhamnonate dehydratase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01288	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050032	L-rhamnonate dehydratase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.2.1.90	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	References	Evidence
Protein	groL	PMID:16606699	Experiment(s):EBI-1142317
Protein	modA	PMID:16606699	Experiment(s):EBI-1142317
Protein	rplQ	PMID:16606699	Experiment(s):EBI-1142317
Protein	tatE	PMID:16606699	Experiment(s):EBI-1142317
Protein	rpsI	PMID:16606699	Experiment(s):EBI-1142317
Protein	yfgC	PMID:16606699	Experiment(s):EBI-1142317
Protein	rplO	PMID:16606699	Experiment(s):EBI-1142317
Protein	fur	PMID:16606699	Experiment(s):EBI-1142317
Protein	nadE	PMID:16606699	Experiment(s):EBI-1142317
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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 MENIMTLPKI KQVRAWFTGG ATAEKGAGGG DYHDQGANHW IDDHIATPMS KYRDYEQSRQ SFGINVLGTL VVEVEAENGQ TGFAVSTAGE MGCFIVEKHL NRFIEGKCVS DIKLIHDQML SATLYYSGSG GLVMNTISCV DLALWDLFGK VVGLPVYKLL GGAVRDEIQF YATGARPDLA KEMGFIGGKM PTHWGPHDGD AGIRKDAAMV ADMREKCGED FWLMLDCWMS QDVNYATKLA HACAPYNLKW IEECLPPQQY ESYRELKRNA PVGMMVTSGE HHGTLQSFRT LSETGIDIMQ PDVGWCGGLT TLVEIAAIAK SRGQLVVPHG SSVYSHHAVI TFTNTPFSEF LMTSPDCSTM RPQFDPILLN EPVPVNGRIH KSVLDKPGFG VELNRDCNLK RPYSH
Length	405
Mol. Wt	44.713 kDa
pI	5.7 (calculated)
Extinction coefficient	63,370 - 64,620 (calc based on 13 Y, 8 W, and 10 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	References
Domain	175..273	PF01188 Mandelate racemase / muconate lactonizing enzyme, C-terminal domain	PMID:19920124
Domain	58..161	PF02746 Mandelate racemase / muconate lactonizing enzyme, N-terminal 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=yfaW 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:226524733	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945881	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007436	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77215	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7160	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14085	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945881	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003736	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3838	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	1^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	1^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	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)
yfaW
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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_000913:2359428..2359468 source=MG1655 flip=1 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:b2247 (EcoliWiki Page)	NCBI GEO profiles for yfaW
microarray	GenExpDB:b2247 (EcoliWiki Page)	Summary of data for yfaW 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 rhmD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7160	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3838	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2247
EcoGene	EcoGene:EG14085	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003736	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007436	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
Bos taurus	ENSBTAP00000031013 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000026835 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000021880 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
E. coli O157	Z3505	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)	PF01188 Mandelate racemase / muconate lactonizing enzyme, C-terminal domain
Pfam (EcoliWiki Page)	PF02746 Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:51604
Panther (EcoliWiki Page)	PTHR13794:SF28
Superfamily (EcoliWiki Page)	SUPERFAMILY:54826
EcoCyc	EcoCyc:G7160	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14085	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003736	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3838	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007436	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 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 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 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).

rhmD: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 rhmD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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