RegulonDB RegulonDB 10.9: Gene Form
   

ygiS gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

parC ygiS mqsA anti-terminator terminator TSS_3325 TSS_3325 ygiSp4 ygiSp4 parCp4 parCp4 TSS_3324 TSS_3324

Gene      
Name: ygiS    Texpresso search in the literature
Synonym(s): ECK3011, G7570, b3020
Genome position(nucleotides): 3166111 <-- 3167718 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.3
External database links:  
ASAP:
ABE-0009920
ECHOBASE:
EB2839
ECOLIHUB:
ygiS
OU-MICROARRAY:
b3020
STRING:
511145.b3020
COLOMBOS: ygiS


Product      
Name: putative deoxycholate binding periplasmic protein
Synonym(s): YgiS
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane,periplasmic space
Molecular weight: 60.694
Isoelectric point: 6.81
Motif(s):
 
Type Positions Sequence
21 -> 535 ADVPANTPLAPQQVFRYNNHSDPGTLDPQKVEENTAAQIVLDLFEGLVWMDGEGQVQPAQAERWEILDGGKRYIFHLRSGLQWSDGQPLTAEDFVLGWQRAVDPKTASPFAGYLAQAHINNAAAIVAGKADVTSLGVKATDDRTLEVTLEQPVPWFTTMLAWPTLFPVPHHVIAKHGDSWSKPENMVYNGAFVLDQWVVNEKITARKNPKYRDAQHTVLQQVEYLALDNSVTGYNRYRAGEVDLTWVPAQQIPAIEKSLPGELRIIPRLNSEYYNFNLEKPPFNDVRVRRALYLTVDRQLIAQKVLGLRTPATTLTPPEVKGFSATTFDELQKPMSERVAMAKALLKQAGYDASHPLRFELFYNKYDLHEKTAIALSSEWKKWLGAQVTLRTMEWKTYLDARRAGDFMLSRQSWDATYNDASSFLNTLKSDSEENVGHWKNAQYDALLNQATQITDATKRNALYQQAEVIINQQAPLIPIYYQPLIKLLKPYVGGFPLHNPQDYVYSKELYIKAH
1 -> 20 MYTRNLLWLVSLVSAAPLYA
75 -> 453 QVQPAQAERWEILDGGKRYIFHLRSGLQWSDGQPLTAEDFVLGWQRAVDPKTASPFAGYLAQAHINNAAAIVAGKADVTSLGVKATDDRTLEVTLEQPVPWFTTMLAWPTLFPVPHHVIAKHGDSWSKPENMVYNGAFVLDQWVVNEKITARKNPKYRDAQHTVLQQVEYLALDNSVTGYNRYRAGEVDLTWVPAQQIPAIEKSLPGELRIIPRLNSEYYNFNLEKPPFNDVRVRRALYLTVDRQLIAQKVLGLRTPATTLTPPEVKGFSATTFDELQKPMSERVAMAKALLKQAGYDASHPLRFELFYNKYDLHEKTAIALSSEWKKWLGAQVTLRTMEWKTYLDARRAGDFMLSRQSWDATYNDASSFLNTLKSDSE

 

Classification:
Multifun Terms (GenProtEC)  
  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:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space
GO:0043190 - ATP-binding cassette (ABC) transporter complex
molecular_function GO:1904680 - peptide transmembrane transporter activity
biological_process GO:0015833 - peptide transport
GO:0055085 - transmembrane transport
GO:0015721 - bile acid and bile salt transport
Note(s): Note(s): ...[more].
Evidence: [AUP] Assay of unpurified protein
Reference(s): [1] Jindal S., et al., 2019
[2] Kwan BW., et al., 2015
External database links:  
ECOCYC:
YGIS-MONOMER
ECOLIWIKI:
b3020
INTERPRO:
IPR030678
INTERPRO:
IPR039424
INTERPRO:
IPR000914
MODBASE:
Q46863
PANTHER:
PTHR30290
PFAM:
PF00496
PRIDE:
Q46863
REFSEQ:
NP_417492
SMR:
Q46863
SWISSMODEL:
Q46863
UNIPROT:
Q46863


Operon      
Name: ygiS         
Operon arrangement:
Transcription unit        Promoter
ygiS


RNA cis-regulatory element    
Attenuation: Transcriptional


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_3324 3166021 reverse nd [RS-EPT-CBR] [3]
  promoter parCp4 3166030 reverse Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter ygiSp4 3167731 reverse Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter TSS_3325 3167746 reverse nd [RS-EPT-CBR] [3]


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] 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] Kwan BW., Lord DM., Peti W., Page R., Benedik MJ., Wood TK., 2015, The MqsR/MqsA toxin/antitoxin system protects Escherichia coli during bile acid stress., Environ Microbiol 17(9):3168-81

 [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.

 [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


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