RegulonDB RegulonDB 10.8: Gene Form
   

syd gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

queF syd csrB UvrY IHF terminator sydp2 sydp2 queFp queFp TSS_3111 TSS_3111 TSS_3110 TSS_3110 csrBp csrBp TSS_3108 (cluster) TSS_3108 (cluster) TSS_3107 TSS_3107 TSS_3106 TSS_3106 TSS_3105 TSS_3105 TSS_3104 TSS_3104 TSS_3103 (cluster) TSS_3103 (cluster) TSS_3102 (cluster) TSS_3102 (cluster) TSS_3101 TSS_3101 TSS_3100 TSS_3100 TSS_3099 TSS_3099 TSS_3098 (cluster) TSS_3098 (cluster) TSS_3097 TSS_3097 TSS_3096 (cluster) TSS_3096 (cluster) TSS_3095 TSS_3095 TSS_3094 TSS_3094 TSS_3093 TSS_3093 TSS_3092 TSS_3092 TSS_3091 TSS_3091

Gene      
Name: syd    Texpresso search in the literature
Synonym(s): ECK2788, G7451, b2793, ydr
Genome position(nucleotides): 2924735 <-- 2925280 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
47.8
External database links:  
ASAP:
ABE-0009154
ECHOBASE:
EB2792
OU-MICROARRAY:
b2793
PortEco:
syd
STRING:
511145.b2793
COLOMBOS: syd


Product      
Name: SecY-interacting protein
Synonym(s): Syd, Ydr
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane,cytosol
Molecular weight: 20.708
Isoelectric point: 4.647
Motif(s):
 
Type Positions Sequence
7 -> 179 QALKDFTARYCDAWHEEHKSWPLSEELYGVPSPCIISTTEDAVYWQPQPFTGEQNVNAVERAFDIVIQPTIHTFYTTQFAGDMHAQFGDIKLTLLQTWSEDDFRRVQENLIGHLVTQKRLKLPPTLFIATLEEELEVISVCNLSGEVCKETLGTRKRTHLASNLAEFLNQLKP

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0009898 - cytoplasmic side of plasma membrane
GO:0031234 - extrinsic component of cytoplasmic side of plasma membrane
molecular_function GO:0005515 - protein binding
biological_process GO:0043254 - regulation of protein-containing complex assembly
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
Reference(s): [1] Dalal K., et al., 2009
External database links:  
DIP:
DIP-48106N
ECOCYC:
G7451-MONOMER
ECOLIWIKI:
b2793
INTERPRO:
IPR038228
INTERPRO:
IPR009948
PDB:
3FFV
PFAM:
PF07348
PRIDE:
P0A8U0
PRODB:
PRO_000024018
REFSEQ:
NP_417273
SMR:
P0A8U0
UNIPROT:
P0A8U0


Operon      
Name: syd         
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_3091 2924349 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3092 2924385 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3093 2924391 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3094 2924394 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3095 2924415 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3096 (cluster) 2924424 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter TSS_3097 2924436 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3098 (cluster) 2924452 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter TSS_3099 2924464 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3100 2924466 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3101 2924468 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3102 (cluster) 2924473 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter TSS_3103 (cluster) 2924477 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter TSS_3104 2924484 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3105 2924496 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3106 2924507 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3107 2924509 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3108 (cluster) 2924522 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter TSS_3110 2924528 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3111 2925313 reverse nd [RS-EPT-CBR] [2]
  promoter sydp2 2925369 reverse Similarity to the consensus
Read more >
[ICWHO] [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] Dalal K., Nguyen N., Alami M., Tan J., Moraes TF., Lee WC., Maurus R., Sligar SS., Brayer GD., Duong F., 2009, Structure, binding, and activity of Syd, a SecY-interacting protein., J Biol Chem 284(12):7897-902

 [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


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