RegulonDB RegulonDB 10.8: Gene Form
   

gmhA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

fadE yafJ gmhA ldtF ArcA FadR terminator TSS_443 (cluster) TSS_443 (cluster) TSS_442 TSS_442 TSS_441 TSS_441 TSS_440 (cluster) TSS_440 (cluster) TSS_439 TSS_439 TSS_438 TSS_438 TSS_437 TSS_437 lpcAp1 lpcAp1 fadEp fadEp

Gene      
Name: gmhA    Texpresso search in the literature
Synonym(s): ECK0223, G6106, b0222, lpcA, tfrA, yafI
Genome position(nucleotides): 243543 --> 244121 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 50.95
External database links:  
ASAP:
 ABE-0000751
ECHOBASE:
 EB2940
OU-MICROARRAY:
 b0222
PortEco:
 lpcA
STRING:
 511145.b0222
COLOMBOS: gmhA


Product      
Name: D-sedoheptulose 7-phosphate isomerase
Synonym(s): GmhA, LpcA, TfrA, YafI
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 20.815
Isoelectric point: 6.389
Motif(s):
 
Type Positions Sequence
119 -> 121 STS
37 -> 192 LADSFKAGGKVLSCGNGGSHCDAMHFAEELTGRYRENRPGYPAIAISDVSHISCVGNDFGFNDIFSRYVEAVGREGDVLLGISTSGNSANVIKAIAAAREKGMKVITLTGKDGGKMAGTADIEIRVPHFGYADRIQEIHIKVIHILIQLIEKEMVK
93 -> 94 ND
169 -> 169 D
61 -> 61 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:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0032991 - protein-containing complex
molecular_function GO:0016853 - isomerase activity
GO:0046872 - metal ion binding
GO:0008270 - zinc ion binding
GO:0008968 - D-sedoheptulose 7-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:0009244 - lipopolysaccharide core region biosynthetic process
GO:0051289 - protein homotetramerization
GO:1901135 - carbohydrate derivative metabolic process
GO:2001061 - D-glycero-D-manno-heptose 7-phosphate biosynthetic process
Note(s): Note(s): ...[more].
Reference(s): [1] Linkevicius M., et al., 2013
External database links:  
DIP:
 DIP-48179N
ECOCYC:
 G6106-MONOMER
ECOLIWIKI:
 b0222
INTERPRO:
 IPR001347
INTERPRO:
 IPR035461
INTERPRO:
 IPR004515
MODBASE:
 P63224
PDB:
 2I2W
PDB:
 2I22
PFAM:
 PF13580
PRIDE:
 P63224
PRODB:
 PRO_000022820
PROSITE:
 PS51464
REFSEQ:
 NP_414757
SMR:
 P63224
SWISSMODEL:
 P63224
UNIPROT:
 P63224


Operon      
Name: gmhA         
Operon arrangement:
Transcription unit        Promoter
 


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 lpcAp1 243468 forward Similarity to the consensus
Read more > 		[ICWHO] [2]
  promoter TSS_437 243512 forward nd [RS-EPT-CBR] [3]
  promoter TSS_438 244083 forward nd [RS-EPT-CBR] [3]
  promoter TSS_439 244089 forward nd [RS-EPT-CBR] [3]
  promoter TSS_440 (cluster) 244094 forward For this promoter, there
Read more > 		[RS-EPT-CBR] [3]
  promoter TSS_441 244103 forward nd [RS-EPT-CBR] [3]
  promoter TSS_442 244121 forward nd [RS-EPT-CBR] [3]
  promoter TSS_443 (cluster) 244123 forward For this promoter, there
Read more > 		[RS-EPT-CBR] [3]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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


Reference(s)    

 [1] Linkevicius M., Sandegren L., Andersson DI., 2013, Mechanisms and fitness costs of tigecycline resistance in Escherichia coli., J Antimicrob Chemother 68(12):2809-19

 [2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [3] 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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