RegulonDB RegulonDB 10.8: 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
OU-MICROARRAY:
b1687
PortEco:
ydiJ
STRING:
511145.b1687
COLOMBOS: ydiJ


Product      
Name: putative FAD-linked oxidoreductase
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].
External database links:  
DIP:
DIP-11751N
ECOCYC:
G6913-MONOMER
ECOLIWIKI:
b1687
INTERPRO:
IPR016166
INTERPRO:
IPR036318
INTERPRO:
IPR017900
INTERPRO:
IPR017896
INTERPRO:
IPR016164
INTERPRO:
IPR009051
INTERPRO:
IPR006094
INTERPRO:
IPR004113
MODBASE:
P77748
PFAM:
PF02913
PFAM:
PF01565
PFAM:
PF13183
PRIDE:
P77748
PROSITE:
PS51387
PROSITE:
PS51379
PROSITE:
PS00198
REFSEQ:
NP_416202
SMR:
P77748
UNIPROT:
P77748


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


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] [1]
  promoter ydiHp3 1765147 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter ydiHp2 1765291 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_1987 1767630 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1988 1768977 forward nd [RS-EPT-CBR] [1]


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] 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.

 [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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