RegulonDB

Gene
Name:	ldtF
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:

ECOLIWIKI:

INTERPRO:

INTERPRO:

PFAM:

PRIDE:

REFSEQ:

SMR:

UNIPROT:

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	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 is a cluster of 2 transcription start sites,in the interval 244094 to 244095, where the highest frequency is at position 244095. The most upstream position of this cluster is assigned as TSS position in the promoter. 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 is a cluster of 2 transcription start sites,in the interval 244123 to 244124, where the highest frequency is at position 244124. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[5]
promoter	yafKp6	245993	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.148. P-value: 9.805e-5 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