RegulonDB RegulonDB 11.0: Gene Form
   

yddB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

pqqL yddB yddA yddBp6 yddBp6

Gene      
Name: yddB    Texpresso search in the literature
Synonym(s): ECK1489, EG11743, b1495
Genome position(nucleotides): 1575247 <-- 1577619
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
45.98
External database links:  
ASAP:
ABE-0004982
ECHOBASE:
EB1694
ECOLIHUB:
yddB
OU-MICROARRAY:
b1495
STRING:
511145.b1495
COLOMBOS: yddB


Product      
Name: putative TonB-dependent receptor YddB
Synonym(s): YddB
Sequence: Get amino acid sequence Fasta Format
Cellular location: outer membrane
Molecular weight: 89.283
Isoelectric point: 6.427
Motif(s):
 
Type Positions Sequence Comment
1 -> 22 MKRVLIPGVILCGADVAQAVDD UniProt: In Ref. 1..
49 -> 165 YTSESIERLPTGNGNISDLLRTNPAVRMDSTQSTSLNQGDIRPEKISIHGASPYQNAYLIDGISATNNLNPANESDASSATNISGMSQGYYLDVSLLDNVTLYDSFVPVEFGRFNGG
279 -> 289 TWFASDRFTHD UniProt: In Ref. 1; CAA50733..
503 -> 503 A UniProt: In Ref. 1; CAA50733..
534 -> 545 TLTRYQDLKTPY UniProt: In Ref. 1; CAA50733..

 

Classification:
Multifun Terms (GenProtEC)  
  4 - transport --> 4.9.B - Putative uncharacterized transport protein
  6 - cell structure --> 6.1 - membrane
Gene Ontology Terms (GO)  
cellular_component GO:0009279 - cell outer membrane
GO:0045203 - integral component of cell outer membrane
biological_process GO:1901678 - iron coordination entity transport
Note(s): Note(s): ...[more].
Evidence: [IDA] Inferred from direct assay
Reference(s): [1] Grinter R., et al., 2019
External database links:  
ALPHAFOLD:
P31827
DIP:
DIP-11661N
ECOCYC:
EG11743-MONOMER
ECOLIWIKI:
b1495
INTERPRO:
IPR036942
INTERPRO:
IPR012910
INTERPRO:
IPR037066
MODBASE:
P31827
PDB:
6OFR
PFAM:
PF07715
PRIDE:
P31827
REFSEQ:
NP_416012
SMR:
P31827
UNIPROT:
P31827


Operon      
Name: yddAB         
Operon arrangement:
Transcription unit        Promoter
yddAB


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 yddBp6 1577666 reverse nd [ICWHO] [2]


Evidence    

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Grinter R., Leung PM., Wijeyewickrema LC., Littler D., Beckham S., Pike RN., Walker D., Greening C., Lithgow T., 2019, Protease-associated import systems are widespread in Gram-negative bacteria., PLoS Genet 15(10):e1008435

 [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


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