lldD:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

lldD

Gene Synonym(s)

ECK3595, b3605, JW3580, lct, lctD, icdE[1][2]

Product Desc.

L- L-lactate dehydrogenase, FMN dependent[3]

Product Synonyms(s)

L-lactate dehydrogenase, FMN-linked[1], B3605[2][1], Lct[2][1], IcdE[2][1], LctD[2][1], LldD[2][1] , ECK3595, JW3580, lct, lctD, b3605

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): lldPRD[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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Arc regulon.[3]



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

lldD

Mnemonic

L-Lactose dehydrogenase

Synonyms

ECK3595, b3605, JW3580, lct, lctD, icdE[1][2]

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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

81.42 minutes, 81.42 minutes 

MG1655: 3777850..3779040
<gbrowseImage> name=NC_000913:3777850..3779040 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3720637..3721827
<gbrowseImage> name=NC_012967:3720637..3721827 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3666176..3667366
<gbrowseImage> name=NC_012759:3666176..3667366 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3860588..3859398
<gbrowseImage> name=NC_007779:3859398..3860588 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3875427..3876617
<gbrowseImage> name=NC_010473:3875427..3876617 source=DH10B preset=GeneLocation </gbrowseImage>

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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

ΔlldD (Keio:JW3580)

deletion

deletion

PMID:16738554

Shigen
CGSC10638[4]

lldD::Tn5KAN-I-SceI (FB21336)

Insertion at nt 519 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21336

contains pKD46

lldD::Tn5KAN-I-SceI (FB21337)

Insertion at nt 519 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21337

does not contain pKD46

ΔlldD::kan

deletion

Biolog:respiration

unable to respire a-Hydroxybutyrate

PMID:16095938

lldD1

CGSC:9110

lldD2

CGSC:10049

ΔlldD789::kan

PMID:16738554

CGSC:101676


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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

JW3580

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCATTATTTCCGCAGCCAGCGA

Primer 2:CCTGCCGCATTCCCTTTCGCCAT

5D2

Kohara Phage

Genobase

PMID:3038334

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[4]

est. P1 cotransduction: % [5]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[4]

est. P1 cotransduction: 10% [5]

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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:EG11963

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11963

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001889

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948121

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1906

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011784

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

LldD

Synonyms

L-lactate dehydrogenase, FMN-linked[1], B3605[2][1], Lct[2][1], IcdE[2][1], LctD[2][1], LldD[2][1] , ECK3595, JW3580, lct, lctD, b3605

Product description

L- L-lactate dehydrogenase, FMN dependent[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.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status

GO:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0004460

L-lactate dehydrogenase (cytochrome) activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01559

F

Seeded from EcoCyc (v14.0)

complete

GO:0004460

L-lactate dehydrogenase (cytochrome) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020920

F

Seeded from EcoCyc (v14.0)

complete

GO:0004460

L-lactate dehydrogenase (cytochrome) activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.1.2.3

F

Seeded from EcoCyc (v14.0)

complete

GO:0006089

lactate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020920

P

Seeded from EcoCyc (v14.0)

complete

GO:0010181

FMN binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012133

F

Seeded from EcoCyc (v14.0)

complete

GO:0010181

FMN binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020920

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008259

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012133

P

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 Notes References Evidence

Protein

glnG

PMID:16606699

Experiment(s):EBI-1146220

Protein

rpsD

PMID:16606699

Experiment(s):EBI-1146220

Protein

groL

PMID:16606699

Experiment(s):EBI-1146220

Protein

insH1

PMID:16606699

Experiment(s):EBI-1146220, EBI-1146220

Protein

glyQ

PMID:15690043

Experiment(s):EBI-892932

Protein

hldD

PMID:15690043

Experiment(s):EBI-892932

Protein

rplV

PMID:15690043

Experiment(s):EBI-892932

Protein

rpmB

PMID:15690043

Experiment(s):EBI-892932

Protein

rpsB

PMID:15690043

Experiment(s):EBI-892932

Protein

radC

PMID:15690043

Experiment(s):EBI-892932

Protein

rfaD

PMID:19402753

LCMS(ID Probability):99.0

Protein

glyQ

PMID:19402753

LCMS(ID Probability):99.0

Protein

yicR

PMID:19402753

LCMS(ID Probability):99.0

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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

plasma membrane

From EcoCyc[6]


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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 

MIISAASDYR AAAQRILPPF LFHYMDGGAY SEYTLRRNVE DLSEVALRQR ILKNMSDLSL
ETTLFNEKLS MPVALAPVGL CGMYARRGEV QAAKAADAHG IPFTLSTVSV CPIEEVAPAI
KRPMWFQLYV LRDRGFMRNA LERAKAAGCS TLVFTVDMPT PGARYRDAHS GMSGPNAAMR
RYLQAVTHPQ WAWDVGLNGR PHDLGNISAY LGKPTGLEDY IGWLGNNFDP SISWKDLEWI
RDFWDGPMVI KGILDPEDAR DAVRFGADGI VVSNHGGRQL DGVLSSARAL PAIADAVKGD
IAILADSGIR NGLDVVRMIA LGADTVLLGR AFLYALATAG QAGVANLLNL IEKEMKVAMT
LTGAKSISEI TQDSLVQGLG KELPAALAPM AKGNAA
Length

396

Mol. Wt

42.729 kDa

pI

6.9 (calculated)

Extinction coefficient

54,890 - 55,265 (calc based on 11 Y, 7 W, and 3 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

13..377

PF01070 FMN-dependent dehydrogenase

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=lldD 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:16131476

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948121

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011784

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P33232

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11963

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11963

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948121

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001889

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1906

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

Ecoli K-12

10.901+/-0.11

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

Protein

E. coli K-12 MG1655

445

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

316

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

215

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

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Notes

Transcription and Transcriptional Regulation

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<protect>

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

Transcription unit(s)

lldPRD

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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_000913:3777830..3777870 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:b3605 (EcoliWiki Page)

NCBI GEO profiles for lldD

microarray

GenExpDB:b3605 (EcoliWiki Page)

Summary of data for lldD 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 lldD Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11963

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1906

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3605

EcoGene

EcoGene:EG11963

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001889

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011784

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

  • ENSANGP00000018221 (score: 1.000; bootstrap: 100%)
  • ENSANGP00000024226 (score: 0.343)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000002303 (score: 1.000; bootstrap: 89%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT4G18360 (score: 1.000; bootstrap: 100%)
  • AT3G14420 (score: 0.820)
  • AT3G14415 (score: 0.802)
  • AT3G14130 (score: 0.447)
  • AT3G14150 (score: 0.431)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000000134 (score: 1.000; bootstrap: 100%)
  • ENSBTAP00000026392 (score: 0.253)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00024710 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00018286 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000008826 (score: 1.000; bootstrap: 100%)
  • ENSCAFP00000014763 (score: 0.204)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000003109 (score: 1.000; bootstrap: 100%)
  • ENSCINP00000004306 (score: 0.080)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-040426-1239 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-040425-2172 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0184082 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0061356 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA15579-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000023770 (score: 1.000; bootstrap: 100%)
  • ENSGALP00000014358 (score: 0.158)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000217301 (score: 1.000; bootstrap: 100%)
  • ENSP00000354314 (score: 0.233)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000012052 (score: 1.000; bootstrap: 100%)
  • ENSMMUP00000021764 (score: 0.164)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000004954 (score: 1.000; bootstrap: 100%)
  • ENSMODP00000006643 (score: 0.212)

From Inparanoid:20070104

Mus musculus

  • MGI:96011 (score: 1.000; bootstrap: 100%)
  • MGI:1860477 (score: 0.188)

From Inparanoid:20070104

Oryza gramene

  • Q7FAS1 (score: 1.000; bootstrap: 100%)
  • Q6YT73 (score: 0.790)
  • O22544 (score: 0.683)
  • Q8H3I4 (score: 0.398)
  • Q7XPR4 (score: 0.398)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000022702 (score: 1.000; bootstrap: 100%)
  • ENSPTRP00000045214 (score: 0.228)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000006330 (score: 1.000; bootstrap: 100%)
  • ENSRNOP00000026357 (score: 0.204)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YML054C (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPAPB1A113 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000131974 (score: 1.000; bootstrap: 100%)
  • NEWSINFRUP00000137123 (score: 0.259)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00026505001 (score: 1.000; bootstrap: 100%)
  • GSTENP00029148001 (score: 0.264)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000051132 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

LLDD

From SHIGELLACYC

E. coli O157

LLDD

From ECOO157CYC

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Do-It-Yourself Web Tools

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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)

PF01070 FMN-dependent dehydrogenase

Superfamily (EcoliWiki Page)

SUPERFAMILY:51395

Panther (EcoliWiki Page)

PTHR10578:SF8

EcoCyc

EcoCyc:EG11963

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11963

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001889

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1906

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011784

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 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. ↑ 3.0 3.1 3.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 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).
  6. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

Categories

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