RegulonDB RegulonDB 10.9: Gene Form
   

kdsD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

kdsD yrbG kdsC lptC kdsCp1 kdsCp1 TSS_3508 TSS_3508 kdsCp2 kdsCp2 kdsCp3 kdsCp3 TSS_3506 TSS_3506 TSS_3505 TSS_3505

Gene      
Name: kdsD    Texpresso search in the literature
Synonym(s): ECK3186, G7662, b3197, yrbH
Genome position(nucleotides): 3341266 --> 3342252 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
51.87
External database links:  
ASAP:
ABE-0010504
ECHOBASE:
EB2655
ECOLIHUB:
kdsD
OU-MICROARRAY:
b3197
STRING:
511145.b3197
COLOMBOS: kdsD


Product      
Name: D-arabinose 5-phosphate isomerase KdsD
Synonym(s): KdsD, YrbH
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 35.196
Isoelectric point: 6.693
Motif(s):
 
Type Positions Sequence
45 -> 177 MFWCKGKVVVMGMGKSGHIGRKMAATFASTGTPSFFVHPGEAAHGDLGMVTPQDVVIAISNSGESSEITALIPVLKRLHVPLICITGRPESSMARAADVHLCVKVAKEACPLGLAPTSSTTATLVMGDALAVA
152 -> 152 E
193 -> 193 H
75 -> 76 GT
88 -> 88 H

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.6 - biosynthesis of macromolecules (cellular constituents) --> 1.6.3 - lipopolysaccharide --> 1.6.3.2 - core region
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0016853 - isomerase activity
GO:0046872 - metal ion binding
GO:0019146 - arabinose-5-phosphate isomerase activity
GO:0042802 - identical protein binding
GO:0097367 - carbohydrate derivative binding
biological_process GO:0005975 - carbohydrate metabolic process
GO:0009103 - lipopolysaccharide biosynthetic process
GO:0019294 - keto-3-deoxy-D-manno-octulosonic acid biosynthetic process
GO:0051289 - protein homotetramerization
GO:1901135 - carbohydrate derivative metabolic process
Note(s): Note(s): ...[more].
External database links:  
DIP:
DIP-12910N
ECOCYC:
G7662-MONOMER
ECOLIWIKI:
b3197
INTERPRO:
IPR004800
INTERPRO:
IPR035474
INTERPRO:
IPR000644
INTERPRO:
IPR001347
MODBASE:
P45395
PDB:
2XHZ
PFAM:
PF00571
PFAM:
PF01380
PRIDE:
P45395
PRODB:
PRO_000023057
PROSITE:
PS51464
PROSITE:
PS51371
REFSEQ:
NP_417664
SMR:
P45395
UNIPROT:
P45395


Operon      
Name: yrbG-kdsDC-lptCAB-rpoN-hpf-ptsN-rapZ-npr         
Operon arrangement:
Transcription unit        Promoter
yrbG-kdsD
yrbG-kdsDC-lptCAB
kdsC-lptCAB
kdsC-lptCAB
kdsC-lptCAB
lptAB
lptAB
lptB-rpoN-hpf-ptsN-yhbJ
rpoN-hpf-ptsN-yhbJ-npr


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_3505 3341124 forward nd [RS-EPT-CBR] [1]
  promoter TSS_3506 3341718 forward nd [RS-EPT-CBR] [1]
  promoter TSS_3508 3342094 forward nd [RS-EPT-CBR] [1]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates



Reference(s)    

 [1] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.


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