RegulonDB RegulonDB 11.1: Gene Form
   

ydcZ gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

curA mnaT ydcZ ydcY TSS_1824 TSS_1824 yncBp4 yncBp4 TSS_1823 TSS_1823 TSS_1822 TSS_1822 TSS_1821 TSS_1821 TSS_1820 TSS_1820 TSS_1819 TSS_1819 ydcZp1 ydcZp1

Gene      
Name: ydcZ    Texpresso search in the literature
Synonym(s): ECK1441, G6758, b1447
Genome position(nucleotides): 1517882 <-- 1518331
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.78
External database links:  
ASAP:
 ABE-0004823
ECHOBASE:
 EB3532
ECOLIHUB:
 ydcZ
OU-MICROARRAY:
 b1447
STRING:
 511145.b1447
COLOMBOS: ydcZ


Product      
Name: putative inner membrane protein YdcZ
Synonym(s): YdcZ
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 15.855
Isoelectric point: 11.857
Motif(s):
 
Type Positions Sequence Comment
5 -> 25 LTLAFLIAAGIGLVVQNTLMV UniProt: Helical.
6 -> 143 TLAFLIAAGIGLVVQNTLMVRITQTSSTILIAMLLNSLVGIVLFVSILWFKQGMAGFGELVSSVRWWTLIPGLLGSFFVFASISGYQNVGAATTIAVLVASQLIGGLMLDIFRSHGVPLRALFGPICGAILLVVGAWL
34 -> 54 ILIAMLLNSLVGIVLFVSILW UniProt: Helical.
71 -> 91 WWTLIPGLLGSFFVFASISGY UniProt: Helical.
94 -> 114 VGAATTIAVLVASQLIGGLML UniProt: Helical.

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0016021 - integral component of membrane
molecular_function GO:0005515 - protein binding
biological_process GO:0071978 - bacterial-type flagellum-dependent swarming motility
Note(s): Note(s): ...[more].
Reference(s): [1] Jindal S., et al., 2019
External database links:  
ALPHAFOLD:
 P76111
DIP:
 DIP-11659N
ECOCYC:
 G6758-MONOMER
ECOLIWIKI:
 b1447
INTERPRO:
 IPR006750
PANTHER:
 PTHR34821
PFAM:
 PF04657
PRIDE:
 P76111
REFSEQ:
 NP_415964
UNIPROT:
 P76111


Operon      
Name: mnaT-ydcZ         
Operon arrangement:
Transcription unit        Promoter
mnaT-ydcZ


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 ydcZp1 1518375 reverse nd [COMP-AINF] [2]
  promoter TSS_1819 1518403 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1820 1518461 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1821 1518476 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1822 1518862 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1823 1518873 reverse nd [RS-EPT-CBR] [3]
  promoter yncBp4 1518892 forward nd [COMP-AINF] [2]
  promoter TSS_1824 1518999 forward nd [RS-EPT-CBR] [3]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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


Reference(s)    

 [1] Jindal S., Yang L., Day PJ., Kell DB., 2019, Involvement of multiple influx and efflux transporters in the accumulation of cationic fluorescent dyes by Escherichia coli., BMC Microbiol 19(1):195

 [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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