RegulonDB RegulonDB 10.8: Gene Form
   

ldtF gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yafJ ldtF gmhA yafQ terminator TSS_444 TSS_444 yafKp6 yafKp6 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

Gene      
Name: ldtF    Texpresso search in the literature
Synonym(s): ECK0225, G6108, b0224, yafK
Genome position(nucleotides): 245065 <-- 245805 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.45
External database links:  
ASAP:
ABE-0000757
ECHOBASE:
EB2942
OU-MICROARRAY:
b0224
PortEco:
yafK
STRING:
511145.b0224
COLOMBOS: ldtF


Product      
Name: L,D-transpeptidase domain-containing protein LdtF
Synonym(s): LdtF, YafK
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 28.021
Isoelectric point: 9.37
Motif(s):
 
Type Positions Sequence
1 -> 19 MRKIALILAMLLIPCVSFA
20 -> 246 GLLGSSSSTTPVSKEYKQQLMGSPVYIQIFKEERTLDLYVKMGEQYQLLDSYKICKYSGGLGPKQRQGDFKSPEGFYSVQRNQLKPDSRYYKAINIGFPNAYDRAHGYEGKYLMIHGDCVSIGCYAMTNQGIDEIFQFVTGALVFGQPSVQVSIYPFRMTDANMKRHKYSNFKDFWEQLKPGYDYFEQTRKPPTVSVVNGRYVVSKPLSHEVVQPQLASNYTLPEAK
45 -> 159 YIQIFKEERTLDLYVKMGEQYQLLDSYKICKYSGGLGPKQRQGDFKSPEGFYSVQRNQLKPDSRYYKAINIGFPNAYDRAHGYEGKYLMIHGDCVSIGCYAMTNQGIDEIFQFVT

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
molecular_function GO:0016757 - transferase activity, transferring glycosyl groups
GO:0016787 - hydrolase activity
GO:0016740 - transferase activity
biological_process GO:0009252 - peptidoglycan biosynthetic process
GO:0008360 - regulation of cell shape
GO:0071555 - cell wall organization
Note(s): Note(s): ...[more].
Evidence: [IHBCE] Inferred by a human based on computational evidence
Reference(s): [1] Kuru E., et al., 2019
[2] Monton Silva A., et al., 2018
[3] Peters K., et al., 2018
[4] Sheikh J., et al., 2001
External database links:  
ECOCYC:
G6108-MONOMER
ECOLIWIKI:
b0224
INTERPRO:
IPR005490
INTERPRO:
IPR038063
PFAM:
PF03734
PRIDE:
P0AA99
REFSEQ:
NP_414759
SMR:
P0AA99
UNIPROT:
P0AA99


Operon      
Name: ldtF         
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 TSS_438 244083 forward nd [RS-EPT-CBR] [5]
  promoter TSS_439 244089 forward nd [RS-EPT-CBR] [5]
  promoter TSS_440 (cluster) 244094 forward For this promoter, there
Read more >
[RS-EPT-CBR] [5]
  promoter TSS_441 244103 forward nd [RS-EPT-CBR] [5]
  promoter TSS_442 244121 forward nd [RS-EPT-CBR] [5]
  promoter TSS_443 (cluster) 244123 forward For this promoter, there
Read more >
[RS-EPT-CBR] [5]
  promoter yafKp6 245993 reverse Similarity to the consensus
Read more >
[ICWHO] [6]
  promoter TSS_444 246205 reverse nd [RS-EPT-CBR] [5]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Kuru E., Radkov A., Meng X., Egan A., Alvarez L., Dowson A., Booher G., Breukink E., Roper DI., Cava F., Vollmer W., Brun Y., VanNieuwenhze MS., 2019, Mechanisms of Incorporation for D-Amino Acid Probes That Target Peptidoglycan Biosynthesis., ACS Chem Biol 14(12):2745-2756

 [2] Monton Silva A., Otten C., Biboy J., Breukink E., VanNieuwenhze M., Vollmer W., den Blaauwen T., 2018, The Fluorescent D-Amino Acid NADA as a Tool to Study the Conditional Activity of Transpeptidases in Escherichia coli., Front Microbiol 9:2101

 [3] Peters K., Pazos M., Edoo Z., Hugonnet JE., Martorana AM., Polissi A., VanNieuwenhze MS., Arthur M., Vollmer W., 2018, Copper inhibits peptidoglycan LD-transpeptidases suppressing β-lactam resistance due to bypass of penicillin-binding proteins., Proc Natl Acad Sci U S A 115(42):10786-10791

 [4] Sheikh J., Hicks S., Dall'Agnol M., Phillips AD., Nataro JP., 2001, Roles for Fis and YafK in biofilm formation by enteroaggregative Escherichia coli., Mol Microbiol 41(5):983-97

 [5] 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.

 [6] 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


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