RegulonDB RegulonDB 10.8: Gene Form
   

potD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

potD potB potC ymfA ycfZ terminator TSS_1462 (cluster) TSS_1462 (cluster) TSS_1461 TSS_1461 TSS_1460 TSS_1460 TSS_1459 TSS_1459 TSS_1458 TSS_1458 potDp6 potDp6 potDp5 potDp5 TSS_1457 TSS_1457 TSS_1456 TSS_1456 ycfZp5 ycfZp5 ycfZp6 ycfZp6

Gene      
Name: potD    Texpresso search in the literature
Synonym(s): ECK1109, EG10752, b1123
Genome position(nucleotides): 1181783 <-- 1182829 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
50.81
External database links:  
ASAP:
ABE-0003789
CGSC:
31908
ECHOBASE:
EB0745
OU-MICROARRAY:
b1123
PortEco:
potD
STRING:
511145.b1123
COLOMBOS: potD


Product      
Name: spermidine preferential ABC transporter periplasmic binding protein
Synonym(s): PotD
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space
Molecular weight: 38.867
Isoelectric point: 5.003
Motif(s):
 
Type Positions Sequence
42 -> 313 LLEQFTKETGIKVIYSTYESNETMYAKLKTYKDGAYDLVVPSTYYVDKMRKEGMIQKIDKSKLTNFSNLDPDMLNKPFDPNNDYSIPYIWGATAIGVNGDAVDPKSVTSWADLWKPEYKGSLLLTDDAREVFQMALRKLGYSGNTTDPKEIEAAYNELKKLMPNVAAFNSDNPANPYMEGEVNLGMIWNGSAFVARQAGTPIDVVWPKEGGIFWMDSLAIPANAKNKEGALKLINFLLRPDVAKQVAETIGYPTPNLAARKLLSPEVANDKT
1 -> 23 MKKWSRHLLAAGALALGMSAAHA
24 -> 348 DDNNTLYFYNWTEYVPPGLLEQFTKETGIKVIYSTYESNETMYAKLKTYKDGAYDLVVPSTYYVDKMRKEGMIQKIDKSKLTNFSNLDPDMLNKPFDPNNDYSIPYIWGATAIGVNGDAVDPKSVTSWADLWKPEYKGSLLLTDDAREVFQMALRKLGYSGNTTDPKEIEAAYNELKKLMPNVAAFNSDNPANPYMEGEVNLGMIWNGSAFVARQAGTPIDVVWPKEGGIFWMDSLAIPANAKNKEGALKLINFLLRPDVAKQVAETIGYPTPNLAARKLLSPEVANDKTLYPDAETIKNGEWQNDVGAASSIYEEYYQKLKAGR
46 -> 54 FTKETGIKV
168 -> 171 DARE

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.1 - carbon utilization --> 1.1.4 - amines
  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
molecular_function GO:0019809 - spermidine binding
GO:0019810 - putrescine binding
GO:0019808 - polyamine binding
biological_process GO:0015846 - polyamine transport
GO:0015848 - spermidine transport
GO:0015847 - putrescine transport
Note(s): Note(s): ...[more].
Reference(s): [1] Kashiwagi K., et al., 1996
External database links:  
ECOCYC:
POTD-MONOMER
ECOLIWIKI:
b1123
INTERPRO:
IPR006059
INTERPRO:
IPR001188
MODBASE:
P0AFK9
PANTHER:
PTHR30222:SF4
PDB:
1POT
PDB:
1POY
PFAM:
PF13416
PRIDE:
P0AFK9
PRINTS:
PR00909
PRODB:
PRO_000023570
REFSEQ:
NP_415641
SMR:
P0AFK9
SWISSMODEL:
P0AFK9
UNIPROT:
P0AFK9


Operon      
Name: potABCD         
Operon arrangement:
Transcription unit        Promoter
potABCD


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 ycfZp6 1181346 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter ycfZp5 1181380 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_1456 1182741 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1457 1182847 reverse nd [RS-EPT-CBR] [3]
  promoter potDp5 1182848 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter potDp6 1182850 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_1458 1182851 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1459 1182909 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1460 1182913 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1461 1182965 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1462 (cluster) 1182969 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [3]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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



Reference(s)    

 [1] Kashiwagi K., Pistocchi R., Shibuya S., Sugiyama S., Morikawa K., Igarashi K., 1996, Spermidine-preferential uptake system in Escherichia coli. Identification of amino acids involved in polyamine binding in PotD protein., J Biol Chem 271(21):12205-8

 [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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