RegulonDB RegulonDB 10.9: Gene Form
   

ydiJ gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ydiJ ydiK menI ydiH terminator TSS_1988 TSS_1988 TSS_1987 TSS_1987 ydiHp2 ydiHp2 ydiHp3 ydiHp3 TSS_1986 TSS_1986

Gene      
Name: ydiJ    Texpresso search in the literature
Synonym(s): ECK1684, G6913, b1687
Genome position(nucleotides): 1765629 <-- 1768685 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.81
External database links:  
ASAP:
ABE-0005632
ECHOBASE:
EB3726
ECOLIHUB:
ydiJ
OU-MICROARRAY:
b1687
STRING:
511145.b1687
COLOMBOS: ydiJ


Product      
Name: putative FAD-linked oxidoreductase YdiJ
Synonym(s): YdiJ
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 113.248
Isoelectric point: 7.117
Motif(s):
 
Type Positions Sequence
48 -> 281 YQLLPDAVVFPRSTADVALIARLAAQERYSSLIFTPRGGGTGTNGQALNQGIIVDMSRHMNRIIEINPEEGWVRVEAGVIKDQLNQYLKPFGYFFAPELSTSNRATLGGMINTDASGQGSLVYGKTSDHVLGVRAVLLGGDILDTQPLPVELAETLGKSNTTIGRIYNTVYQRCRQQRQLIIDNFPKLNRFLTGYDLRHVFNDEMTEFDLTRILTGSEGTLAFITEARLDITRL
52 -> 192 PDAVVFPRSTADVALIARLAAQERYSSLIFTPRGGGTGTNGQALNQGIIVDMSRHMNRIIEINPEEGWVRVEAGVIKDQLNQYLKPFGYFFAPELSTSNRATLGGMINTDASGQGSLVYGKTSDHVLGVRAVLLGGDILDT
281 -> 539 LPKVRRLVNVKYDSFDSALRNAPFMVEARALSVETVDSKVLNLAREDIVWHSVSELITDVPDQEMLGLNIVEFAGDDEALIDERVNALCARLDELIASHQAGVIGWQVCRELAGVERIYAMRKKAVGLLGNAKGAAKPIPFAEDTCVPPEHLADYIAEFRALLDSHGLSYGMFGHVDAGVLHVRPALDMCDPQQEILMKQISDDVVALTAKYGGLLWGEHGKGFRAEYSPAFFGEELFAELRKVKAAFDPHNRLNPGKI
576 -> 687 MECNGNGLCFNFDARSPMCPSMKITQNRIHSPKGRATLVREWLRLLADRGVDPLKLEQELPESGVSLRTLIARTRNSWHANKGEYDFSHEVKEAMSGCLACKACSTQCPIKI
662 -> 695 FSHEVKEAMSGCLACKACSTQCPIKIDVPEFRSR

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
molecular_function GO:0003824 - catalytic activity
GO:0046872 - metal ion binding
GO:0016491 - oxidoreductase activity
GO:0050660 - flavin adenine dinucleotide binding
GO:0051536 - iron-sulfur cluster binding
GO:0051539 - 4 iron, 4 sulfur cluster binding
GO:0004458 - D-lactate dehydrogenase (cytochrome) activity
GO:0008720 - D-lactate dehydrogenase activity
GO:0071949 - FAD binding
biological_process GO:0055114 - oxidation-reduction process
GO:1903457 - lactate catabolic process
Note(s): Note(s): ...[more].
Reference(s): [1] Chen SS., et al., 2013
External database links:  
DIP:
DIP-11751N
ECOCYC:
G6913-MONOMER
ECOLIWIKI:
b1687
INTERPRO:
IPR016166
INTERPRO:
IPR017896
INTERPRO:
IPR017900
INTERPRO:
IPR036318
INTERPRO:
IPR009051
INTERPRO:
IPR006094
INTERPRO:
IPR004113
INTERPRO:
IPR016164
MODBASE:
P77748
PFAM:
PF02913
PFAM:
PF01565
PFAM:
PF13183
PRIDE:
P77748
PROSITE:
PS00198
PROSITE:
PS51379
PROSITE:
PS51387
REFSEQ:
NP_416202
SMR:
P77748
UNIPROT:
P77748


Operon      
Name: ydiJ-menI-ydiH         
Operon arrangement:
Transcription unit        Promoter
ydiJ-menI-ydiH


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_1986 1765146 reverse nd [RS-EPT-CBR] [2]
  promoter ydiHp3 1765147 reverse Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter ydiHp2 1765291 reverse Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter TSS_1987 1767630 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_1988 1768977 forward nd [RS-EPT-CBR] [2]


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] Chen SS., Williamson JR., 2013, Characterization of the ribosome biogenesis landscape in E. coli using quantitative mass spectrometry., J Mol Biol 425(4):767-79

 [2] 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.

 [3] 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


RegulonDB