RegulonDB RegulonDB 10.7: Gene Form
   

ldtB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybiT ybiR ldtB mntR CRP AscG ybiTp ybiTp ldtBp ldtBp TSS_980 TSS_980

Gene      
Name: ldtB    Texpresso search in the literature
Synonym(s): ECK0809, G6422, b0819, ybiS
Genome position(nucleotides): 854824 <-- 855744 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.99
External database links:  
ASAP:
ABE-0002797
ECHOBASE:
EB3108
OU-MICROARRAY:
b0819
PORTECO:
ybiS
REGULONDB:
b0819
STRING:
511145.b0819
M3D: ldtB
COLOMBOS: ldtB
PortEco: b0819


Product      
Name: L,D-transpeptidase LdtB
Synonym(s): LdtB, YbiS
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space
Molecular weight: 33.325
Isoelectric point: 6.364
Motif(s):
 
Type Positions Sequence
101 -> 231 IVINSAEMRLYYYPKGTNTVIVLPIGIGQLGKDTPINWTTKVERKKAGPTWTPTAKMHAEYRAAGEPLPAVVPAGPDNPMGLYALYIGRLYAIHGTNANFGIGLRVSHGCVRLRNEDIKFLFEKVPVGTRV
210 -> 210 C
1 -> 24 MNMKLKTLFAAAFAVVGFCSTASA
25 -> 306 VTYPLPTDGSRLVGQNQVITIPEGNTQPLEYFAAEYQMGLSNMMEANPGVDTFLPKGGTVLNIPQQLILPDTVHEGIVINSAEMRLYYYPKGTNTVIVLPIGIGQLGKDTPINWTTKVERKKAGPTWTPTAKMHAEYRAAGEPLPAVVPAGPDNPMGLYALYIGRLYAIHGTNANFGIGLRVSHGCVRLRNEDIKFLFEKVPVGTRVQFIDEPVKATTEPDGSRYIEVHNPLSTTEAQFEGQEIVPITLTKSVQTVTGQPDVDQVVLDEAIKNRSGMPVRLN
194 -> 212 HGTNANFGIGLRVSHGCVR

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.6 - biosynthesis of macromolecules (cellular constituents) --> 1.6.7 - murein (peptidoglycan)
Gene Ontology Terms (GO)  
cellular_component GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space
molecular_function GO:0016757 - transferase activity, transferring glycosyl groups
GO:0016787 - hydrolase activity
GO:0016740 - transferase activity
GO:0004180 - carboxypeptidase activity
GO:0071972 - peptidoglycan L,D-transpeptidase activity
biological_process GO:0006508 - proteolysis
GO:0009252 - peptidoglycan biosynthetic process
GO:0008360 - regulation of cell shape
GO:0018104 - peptidoglycan-protein cross-linking
GO:0071555 - cell wall organization
Note(s): Note(s): ...[more].
Reference(s): [1] Zhai Y., et al., 2002
External database links:  
DIP:
DIP-48069N
ECOCYC:
G6422-MONOMER
ECOLIWIKI:
b0819
INTERPRO:
IPR005490
INTERPRO:
IPR038063
INTERPRO:
IPR041597
PFAM:
PF03734
PFAM:
PF17969
PRIDE:
P0AAX8
PROTEINMODELPORTAL:
P0AAX8
REFSEQ:
NP_415340
SMR:
P0AAX8
UNIPROT:
P0AAX8


Operon      
Name: ldtB         
Operon arrangement:
Transcription unit        Promoter
ldtB


Transcriptional Regulation      
Display Regulation             
Activated by: CRP, Rob
Repressed by: CRP


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_980 855304 reverse nd [RS-EPT-CBR] [2]


Evidence    

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



Reference(s)    

 [1] Zhai Y., Saier MH., 2002, The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes., Protein Sci 11(9):2196-207

 [2] 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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