RegulonDB RegulonDB 11.1: Gene Form
   

ydcS gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ydcR ydcS ydcT Nac ydcSp1 ydcSp1 TSS_1815 TSS_1815 ydcSp7 ydcSp7 ydcSp9 ydcSp9

Gene      
Name: ydcS    Texpresso search in the literature
Synonym(s): ECK1434, G6751, b1440
Genome position(nucleotides): 1511654 --> 1512799
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.79
External database links:  
ASAP:
 ABE-0004803
ECHOBASE:
 EB3525
ECOLIHUB:
 ydcS
OU-MICROARRAY:
 b1440
STRING:
 511145.b1440
COLOMBOS: ydcS


Product      
Name: putative ABC transporter periplasmic binding protein / polyhydroxybutyrate synthase
Synonym(s): YdcS
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane,periplasmic space
Molecular weight: 42.295
Isoelectric point: 7.483
Motif(s):
 
Type Positions Sequence Comment
1 -> 22 MSKTFARSSLCALSMTIMTAHA
23 -> 381 AEPPTNLDKPEGRLDIIAWPGYIERGQTDKQYDWVTQFEKETGCAVNVKTAATSDEMVSLMTKGGYDLVTASGDASLRLIMGKRVQPINTALIPNWKTLDPRVVKGDWFNVGGKVYGTPYQWGPNLLMYNTKTFPTPPDSWQVVFVEQNLPDGKSNKGRVQAYDGPIYIADAALFVKATQPQLGISDPYQLTEEQYQAVLKVLRAQHSLIHRYWHDTTVQMSDFKNEGVVASSAWPYQANALKAEGQPVATVFPKEGVTGWADTTMLHSEAKHPVCAYKWMNWSLTPKVQGDVAAWFGSLPVVPEGCKASPLLGEKGCETNGFNYFDKIAFWKTPIAEGGKFVPYSRWTQDYIAIMGGR UniProt: Bifunctional polyhydroxybutyrate synthase / ABC transporter periplasmic binding protein.
56 -> 326 WVTQFEKETGCAVNVKTAATSDEMVSLMTKGGYDLVTASGDASLRLIMGKRVQPINTALIPNWKTLDPRVVKGDWFNVGGKVYGTPYQWGPNLLMYNTKTFPTPPDSWQVVFVEQNLPDGKSNKGRVQAYDGPIYIADAALFVKATQPQLGISDPYQLTEEQYQAVLKVLRAQHSLIHRYWHDTTVQMSDFKNEGVVASSAWPYQANALKAEGQPVATVFPKEGVTGWADTTMLHSEAKHPVCAYKWMNWSLTPKVQGDVAAWFGSLPVVP

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.6 - biosynthesis of macromolecules (cellular constituents)
  4 - transport --> 4.3 - Primary Active Transporters --> 4.3.A - Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters --> 4.3.A.1 - The ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake Permeases --> 4.3.A.1.p - ABC superfamily, periplasmic binding component
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing
molecular_function GO:0016740 - transferase activity
GO:0016746 - acyltransferase activity
GO:0019808 - polyamine binding
biological_process GO:0015846 - polyamine transport
GO:0055085 - transmembrane transport
GO:0009290 - DNA import into cell involved in transformation
GO:0042619 - poly-hydroxybutyrate biosynthetic process
Note(s): Note(s): ...[more].
Reference(s): [1] Jindal S., et al., 2019
[2] Kumar A., et al., 2016
[3] Vijayakumar SR., et al., 2004
External database links:  
ALPHAFOLD:
 P76108
ECOCYC:
 YDCS-MONOMER
ECOLIWIKI:
 b1440
INTERPRO:
 IPR001188
INTERPRO:
 IPR006059
MODBASE:
 P76108
PFAM:
 PF13416
PRIDE:
 P76108
PRINTS:
 PR00909
REFSEQ:
 NP_415957
SMR:
 P76108
UNIPROT:
 P76108


Operon      
Name: ydcSTUV-patD         
Operon arrangement:
Transcription unit        Promoter
ydcSTUV-patD
patD


Transcriptional Regulation      
Display Regulation             
Activated by: Nac


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 ydcSp9 1511453 forward nd [COMP-AINF] [4]
  promoter ydcSp7 1511515 forward nd [COMP-AINF] [4]
  promoter TSS_1815 1511596 forward nd [RS-EPT-CBR] [5]


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] Kumar A., Beloglazova N., Bundalovic-Torma C., Phanse S., Deineko V., Gagarinova A., Musso G., Vlasblom J., Lemak S., Hooshyar M., Minic Z., Wagih O., Mosca R., Aloy P., Golshani A., Parkinson J., Emili A., Yakunin AF., Babu M., 2016, Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli., Cell Rep 14(3):648-61

 [3] Vijayakumar SR., Kirchhof MG., Patten CL., Schellhorn HE., 2004, RpoS-regulated genes of Escherichia coli identified by random lacZ fusion mutagenesis., J Bacteriol 186(24):8499-507

 [4] 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

 [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.

RegulonDB