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trxB:On One Page

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Gene Name	trxB (synonyms: ECK0879, b0888, JW0871, trxR)^[1]^[2]
Product(s)	TrxB product^[1]: thioredoxin reductase, FAD/NAD(P)-binding product, B0888 product, thioredoxin reductase (NADPH) product, NADPH:oxidized thioredoxin oxidoreductase product, TrxR product
Description	thioredoxin reductase monomer^[2]^[3] Component of thioredoxin reductase^[2]
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): trxB^[2]
Regulation/Activity
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Notes

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Gene

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Nomenclature

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Standard name	trxB
Mnemonic
Synonyms	ECK0879, b0888, JW0871, trxR^[1]^[2]
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Notes

Location(s) and DNA Sequence

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Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	20.05 minutes	MG1655: 931273..930308	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 932472..931507	GBrowse(W3110)	FASTA Dump
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Strain

Map location

Genome coordinates

Genome browsers

Sequence links

MG1655

20.05 minutes

MG1655: 931273..930308
gbrowse_img.php?coord=929308..932273&genome=ecoli&name=MG1655&trackset=0&width=300&.png

EcoCyc

GBrowse(MG1655)

W3110

W3110: 932472..931507
gbrowse_img.php?coord=930507..933472&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

GBrowse(W3110)

FASTA Dump

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Notes

Sequence Features

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Feature type	Location	Description
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Alleles and Phenotypes

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Allele	Nt change(s)	AA change(s)	Reference	Availability
ΔtrxB (Keio:JW0871)	deletion	deletion	PMID:16738554^[4]	Shigen CGSC8900^[5]
trxB20				CGSC:10949
trxB15::kan				CGSC:10952
ΔtrxB786::kan			PMID:16738554^[4]	CGSC:103242
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Notes

Genetic Resources

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Resource	Resource Type	Source	Notes/Reference
JW0871	Plasmid clone	Shigen	PMID:16769691^[6] Status:Clone OK Primer 1:GCCGGCACGACCAAACACAGTAA Primer 2:CCTTTTGCGTCAGCTAAACCATC
zbh-29::Tn10	Linked marker	CAG18493 = CGSC7353^[5]	est. P1 cotransduction: % ^[7] Synonyms:zbi-29::Tn10
zca-1230::Tn10	Linked marker	CAG18478 = CGSC7356^[5]	est. P1 cotransduction: 56% ^[7] Synonyms:zbj-1230::Tn10
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Notes

Accessions in Other Databases

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG11032
EchoBASE (EcoliWiki Page)	EchoBASE:EB1025
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0888
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C1025
EcoGene (EcoliWiki Page)	EcoGene:EG11032
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:TRXB
CGSC (EcoliWiki Page)	CGSC:17569
ASAP (EcoliWikiPage)	ASAP:ABE-0003018
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Links

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Name	URL	Comments
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Product(s)

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Nomenclature

Standard name	TrxB product
Synonyms	thioredoxin reductase, FAD/NAD(P)-binding product^[1], B0888 product^[2]^[1], TrxB product^[2]^[1], thioredoxin reductase (NADPH) product^[2]^[1], NADPH:oxidized thioredoxin oxidoreductase product^[2]^[1], TrxR product^[2]^[1]
Product description	thioredoxin reductase monomer^[2]^[3]; Component of ; thioredoxin reductase^[2]^[3]
EC number (for enzymes)	1.8.1.9^[1]
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Notes

Function

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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(s)	Evidence Code	with/from	Aspect	Notes	Status
	GO:0050660	FAD binding	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001327	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0019430	removal of superoxide radicals	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005982	P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0016491	oxidoreductase activity	GO_REF:0000002 GO_REF:0000002 GO_REF:0000002 GO_REF:0000004	IEA: Inferred from Electronic Annotation	InterPro:IPR000103 InterPro:IPR001327 InterPro:IPR008255 SP_KW:KW-0560	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0005737	cytoplasm	GO_REF:0000002 GO_REF:0000004	IEA: Inferred from Electronic Annotation	InterPro:IPR005982 SP_KW:KW-0963	C	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0004791	thioredoxin-disulfide reductase activity	GO_REF:0000002 GO_REF:0000003	IEA: Inferred from Electronic Annotation	InterPro:IPR005982 EC:1.8.1.9	F	Seeded from EcoCyc 12.5 ^[8]	complete
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Interactions

Partner Type	Partner	Notes	References
Protein	Subunits of thioredoxin reductase	could be indirect
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Notes

Localization

Compartment	Description	Evidence	Notes
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Structure and Physical Properties

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Physical Properties

Sequence	at EcoCyc MGTTKHSKLL ILGSGPAGYT AAVYAARANL QPVLITGMEK GGQLTTTTEV ENWPGDPNDL TGPLLMERMH EHATKFETEI IFDHINKVDL QNRPFRLNGD NGEYTCDALI IATGASARYL GLPSEEAFKG RGVSACATCD GFFYRNQKVA VIGGGNTAVE EALYLSNIAS EVHLIHRRDG FRAEKILIKR LMDKVENGNI ILHTNRTLEE VTGDQMGVTG VRLRDTQNSD NIESLDVAGL FVAIGHSPNT AIFEGQLELE NGYIKVQSGI HGNATQTSIP GVFAAGDVMD HIYRQAITSA GTGCMAALDA ERYLDGLADA K
Mol. Wt	34.62 kDa (calc) ^[2]
pI	5.55^[2]
Extinction coefficient	18910 - 19410 (calc based on 9 Y, 1 W, and 4 C residues)
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Domains/Motifs/Modification Sites

Type	Residues	Description	Notes
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Structure

Structures	Representative Escherichia coli structure: 1TDE\|A 2-316 of 321 residues (E-value: 1.5e-168) (Percent Identity: 100.00) Representative homolog: 1EBD\|A (Geobacillus stearothermophilus) 124-310 of 321 residues (E-value: 1.0e-07) (Percent Identity: 25.87) View all other structures.
Models	View models at: EcoliPredict ModBase PSI-PRED Protein Quaternary Structure (PQS) Genomes TO Protein (GTOP)
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Structures

Representative Escherichia coli structure:
1TDE|A
2-316 of 321 residues (E-value: 1.5e-168) (Percent Identity: 100.00)
Representative homolog:
1EBD|A (Geobacillus stearothermophilus)
124-310 of 321 residues (E-value: 1.0e-07) (Percent Identity: 25.87)
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Models

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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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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:THIOREDOXIN-REDUCT-NADPH-MONOMER
UniProt (EcoliWiki Page)	UniProt:P0A9P4
PFAM (EcoliWiki Page)	PFAM:PF00070
RefSeq (EcoliWiki Page)	RefSeq:NP_415408
ModBase (EcoliWiki Page)	ModBase:P0A9P4
PDB (EcoliWiki Page)	PDB:1TDE
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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.

Transcription and Transcriptional Regulation

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Transcription unit(s)
trxB
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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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gbrowse_img.php?coord=931253..931293&genome=ecoli&name=MG1655&trackset=Genes_unlabeled+DNA_unlabeled+flip&width=400&.png
This picture shows the sequence around the N-terminus.

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

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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Mutations Affecting Expression

Allele Name	Mutation	Phenotype	Reference
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Expression Studies

Type	Reference	Notes
microarray	EcoliGenExpDB:b0888 (EcoliWiki Page)	Summary of data for trxB from multiple microarray studies
microarray	GEO Profiles:b0888 (EcoliWiki Page)	NCBI GEO profiles for trxB
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Expression Resources

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to trxB Expression

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG11032
EchoBASE (EcoliWiki Page)	EchoBASE:EB1025
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0888
EcoGene (EcoliWiki Page)	EcoGene:EG11032
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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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Organism	Homologs (Statistics)	Comments
Anopheles gambiae	ENSANGP00000016322 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000019899 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT2G41680 (score: 1.000; bootstrap: 100%) AT2G17420 (score: 0.076) AT4G35460 (score: 0.066)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0231235 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q70G58 (score: 1.000; bootstrap: 100%) Q8VX47 (score: 0.079) Q69PS6 (score: 0.079) Q6ZFU6 (score: 0.063)	From Inparanoid:20070104
Saccharomyces cerevisiae	YDR353W (score: 1.000; bootstrap: 100%) YHR106W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBC3F63 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	TRXB	From SHIGELLACYC
E. coli O157	TRXB	From ECOO157CYC
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Notes

Families

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Database	Accession	Notes
PFAM (EcoliWiki Page)	PFAM:PF00070
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Links

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Name	URL	Comments
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References

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↑ ^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 ^2.11 ^2.12 ^2.13 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 Baba T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008 PubMed EcoliWiki page
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ Kitagawa M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (A Complete Set of E. coli K-12 ORF Archive): Unique Resources for Biological Research. DNA Res 12: 291-9 PubMed EcoliWiki page
↑ ^7.0 ^7.1 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).
↑ ^8.0 ^8.1 ^8.2 ^8.3 ^8.4 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

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Retrieved from "http://ecoliwiki.net/colipedia/index.php/trxB:On_One_Page"

trxB:On One Page

From EcoliWiki

Quickview

Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Categories

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Categories

Expression

Overview

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to trxB Expression

Notes

Links

Categories

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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