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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	rutA
Gene Synonym(s)	ycdM, ECK1003, b1012, JW0997^[1]^[2], JW0997
Product Desc.	predicted coenzyme F₄₂₀-dependent N⁵,N¹⁰-methylenetetrahydromethanopterin reductase^[2]^[3] Gene in rut operon for pyrimidine nitrogen catabolism; putative luciferase-like monooxygenase^[4]
Product Synonyms(s)	predicted monooxygenase^[1], YcdM^[2]^[1], B1012^[2]^[1], RutA^[2]^[1] , ECK1003, JW0997, ycdM, b1012
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rutABCDEFG^[2]
Regulation/Activity
Quick Links
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Notes

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NtrC regulon. The rut operon is required for the utilization of thymidine, uridine and cytidine as nitrogen sources at 37C, but not at room temperature.^[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	rutA
Mnemonic	PyRimidine UTilization
Synonyms	ycdM, ECK1003, b1012, JW0997^[1]^[2], JW0997
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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	23.11 minutes	MG1655: 1073234..1072086 <gbrowseImage> name=NC_000913:1072086..1073234 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1089147..1090295 <gbrowseImage> name=NC_012967:1089147..1090295 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 975054..976202 <gbrowseImage> name=NC_012759:975054..976202 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1074433..1073285 <gbrowseImage> name=NC_007779:1073285..1074433 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1127162..1126014 <gbrowseImage> name=NC_010473:1126014..1127162 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
ΔrutA756::kan					PMID:16738554	CGSC:106332
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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:

7B5

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:G6523	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13859	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003123	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945643	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3619	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003416	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	YcdM
Synonyms	predicted monooxygenase^[1], YcdM^[2]^[1], B1012^[2]^[1], RutA^[2]^[1] , ECK1003, JW0997, ycdM, b1012
Product description	predicted coenzyme F₄₂₀-dependent N⁵,N¹⁰-methylenetetrahydromethanopterin reductase^[2]^[3] Gene in rut operon for pyrimidine nitrogen catabolism; putative luciferase-like monooxygenase^[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:0004497	monooxygenase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0503	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	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	References	Evidence
Protein	ompL	PMID:16606699	Experiment(s):EBI-1138614
Protein	yodC	PMID:16606699	Experiment(s):EBI-1138614
Protein	ymfG	PMID:16606699	Experiment(s):EBI-1138614
Protein	dnaK	PMID:16606699	Experiment(s):EBI-1138614
Protein	yghW	PMID:16606699	Experiment(s):EBI-1138614
Protein	nadE	PMID:16606699	Experiment(s):EBI-1138614
Protein	rplB	PMID:16606699	Experiment(s):EBI-1138614
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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 MQDAAPRLTF TLRDEERLMM KIGVFVPIGN NGWLISTHAP QYMPTFELNK AIVQKAEHYH FDFALSMIKL RGFGGKTEFW DHNLESFTLM AGLAAVTSRI QIYATAATLT LPPAIVARMA ATIDSISGGR FGVNLVTGWQ KPEYEQMGIW PGDDYFSRRY DYLTEYVQVL RDLWGTGKSD FKGDFFTMND CRVSPQPSVP MKVICAGQSD AGMAFSARYA DFNFCFGKGV NTPTAFAPTA ARMKQAAEQT GRDVGSYVLF MVIADETDDA ARAKWEHYKA GADEEALSWL TEQSQKDTRS GTDTNVRQMA DPTSAVNINM GTLVGSYASV ARMLDEVASV PGAEGVLLTF DDFLSGIETF GERIQPLMQC RAHLPALTQE VA
Length	382
Mol. Wt	42.219 kDa
pI	5.0 (calculated)
Extinction coefficient	56,380 - 56,880 (calc based on 12 Y, 7 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	20..344	PF00296 Luciferase-like monooxygenase		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=rutA 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:49176071	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945643	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003416	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P75898	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6523	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13859	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945643	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003123	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3619	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	0^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	4	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)
rutABCDEFG
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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_000913:1073214..1073254 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:b1012 (EcoliWiki Page)	NCBI GEO profiles for rutA
microarray	GenExpDB:b1012 (EcoliWiki Page)	Summary of data for rutA 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 (1073137..1073536) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ16; Well:C4^[5]
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Notes

Accessions Related to rutA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6523	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3619	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1012
EcoGene	EcoGene:EG13859	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003123	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003416	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
Xenopus tropicalis	ENSXETP00000008934 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	S1085	From SHIGELLACYC
E. coli O157	Z1511	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)	PF00296 Luciferase-like monooxygenase
Superfamily (EcoliWiki Page)	SUPERFAMILY:51679
EcoCyc	EcoCyc:G6523	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13859	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003123	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3619	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003416	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)
↑ ^2.00 ^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 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

rutA: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 rutA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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