RegulonDB RegulonDB 10.10: Gene Form
   

rpmD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rpsE rplO rpmD TSS_3731 TSS_3731 TSS_3730 TSS_3730 TSS_3729 TSS_3729 TSS_3728 (cluster) TSS_3728 (cluster) TSS_3727 TSS_3727 TSS_3726 TSS_3726 TSS_3725 TSS_3725 TSS_3724 TSS_3724 TSS_3723 TSS_3723 TSS_3722 TSS_3722 TSS_3721 TSS_3721 TSS_3720 (cluster) TSS_3720 (cluster) TSS_3719 TSS_3719 TSS_3718 (cluster) TSS_3718 (cluster) TSS_3717 TSS_3717 TSS_3716 TSS_3716 TSS_3715 (cluster) TSS_3715 (cluster) TSS_3714 TSS_3714 TSS_3713 TSS_3713 TSS_3712 TSS_3712 TSS_3711 TSS_3711

Gene      
Name: rpmD    Texpresso search in the literature
Synonym(s): ECK3289, EG10888, b3302
Genome position(nucleotides): 3444543 <-- 3444722 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 50.0
External database links:  
ASAP:
 ABE-0010821
CGSC:
 238
ECHOBASE:
 EB0881
ECOLIHUB:
 rpmD
OU-MICROARRAY:
 b3302
STRING:
 511145.b3302
COLOMBOS: rpmD


Product      
Name: 50S ribosomal subunit protein L30
Synonym(s): RpmD
Sequence: Get amino acid sequence Fasta Format
Cellular location: ribosome,cytosol
Molecular weight: 6.542
Isoelectric point: 11.608
Motif(s):
 
Type Positions Sequence
5 -> 55 IKITQTRSAIGRLPKHKATLLGLGLRRIGHTVEREDTPAIRGMINAVSFMV
2 -> 59 AKTIKITQTRSAIGRLPKHKATLLGLGLRRIGHTVEREDTPAIRGMINAVSFMVKVEE

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation
  2 - information transfer --> 2.3 - protein related --> 2.3.8 - ribosomal proteins
  6 - cell structure --> 6.6 - ribosomes
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0005840 - ribosome
GO:0015934 - large ribosomal subunit
GO:0022625 - cytosolic large ribosomal subunit
molecular_function GO:0003735 - structural constituent of ribosome
biological_process GO:0006412 - translation
GO:0000027 - ribosomal large subunit assembly
Note(s): Note(s): ...[more].
External database links:  
DIP:
 DIP-35970N
ECOCYC:
 EG10888-MONOMER
ECOLIWIKI:
 b3302
INTERPRO:
 IPR036919
INTERPRO:
 IPR018038
INTERPRO:
 IPR005996
INTERPRO:
 IPR016082
PANTHER:
 PTHR15892
PDB:
 1ML5
PDB:
 2J28
PDB:
 2RDO
PDB:
 3BBX
PDB:
 3J5L
PDB:
 3J7Z
PDB:
 3J8G
PDB:
 3J9Y
PDB:
 3J9Z
PDB:
 3JA1
PDB:
 3JBU
PDB:
 3JBV
PDB:
 3JCD
PDB:
 3JCE
PDB:
 3JCJ
PDB:
 3JCN
PDB:
 4CSU
PDB:
 4U1U
PDB:
 4U1V
PDB:
 4U20
PDB:
 4U24
PDB:
 4U25
PDB:
 4U26
PDB:
 4U27
PDB:
 4UY8
PDB:
 4V47
PDB:
 4V48
PDB:
 4V4H
PDB:
 4V4Q
PDB:
 4V4V
PDB:
 4V4W
PDB:
 4V50
PDB:
 4V52
PDB:
 4V53
PDB:
 4V54
PDB:
 4V55
PDB:
 4V56
PDB:
 4V57
PDB:
 4V5B
PDB:
 4V5H
PDB:
 4V5Y
PDB:
 4V64
PDB:
 4V65
PDB:
 4V66
PDB:
 4V69
PDB:
 4V6C
PDB:
 4V6D
PDB:
 4V6E
PDB:
 4V6K
PDB:
 4V6L
PDB:
 4V6M
PDB:
 4V6N
PDB:
 4V6O
PDB:
 4V6P
PDB:
 4V6Q
PDB:
 4V6R
PDB:
 4V6S
PDB:
 4V6T
PDB:
 4V6V
PDB:
 4V6Y
PDB:
 4V6Z
PDB:
 4V70
PDB:
 4V71
PDB:
 4V72
PDB:
 4V73
PDB:
 4V74
PDB:
 4V75
PDB:
 4V76
PDB:
 4V77
PDB:
 4V78
PDB:
 4V79
PDB:
 4V7A
PDB:
 4V7B
PDB:
 4V7C
PDB:
 4V7D
PDB:
 4V7I
PDB:
 4V7S
PDB:
 4V7T
PDB:
 4V7U
PDB:
 4V7V
PDB:
 4V85
PDB:
 4V89
PDB:
 4V9C
PDB:
 4V9D
PDB:
 4V9O
PDB:
 4V9P
PDB:
 4WF1
PDB:
 4WOI
PDB:
 4WWW
PDB:
 4YBB
PDB:
 5ADY
PDB:
 5AFI
PDB:
 5AKA
PDB:
 5GAD
PDB:
 5GAE
PDB:
 5GAF
PDB:
 5GAG
PDB:
 5GAH
PDB:
 5H5U
PDB:
 5IQR
PDB:
 5IT8
PDB:
 5J5B
PDB:
 5J7L
PDB:
 5J88
PDB:
 5J8A
PDB:
 5J91
PDB:
 5JC9
PDB:
 5JTE
PDB:
 5JU8
PDB:
 5KCR
PDB:
 5KCS
PDB:
 5KPS
PDB:
 5KPV
PDB:
 5KPW
PDB:
 5KPX
PDB:
 5L3P
PDB:
 5LZA
PDB:
 5LZB
PDB:
 5LZC
PDB:
 5LZD
PDB:
 5LZE
PDB:
 5LZF
PDB:
 5MDV
PDB:
 5MDW
PDB:
 5MDY
PDB:
 5MDZ
PDB:
 5MGP
PDB:
 5NCO
PDB:
 5NP6
PDB:
 5NWY
PDB:
 5O2R
PDB:
 5U4I
PDB:
 5U9F
PDB:
 5U9G
PDB:
 5UYK
PDB:
 5UYL
PDB:
 5UYM
PDB:
 5UYN
PDB:
 5UYP
PDB:
 5UYQ
PDB:
 5WDT
PDB:
 5WE4
PDB:
 5WE6
PDB:
 5WFK
PDB:
 6BU8
PDB:
 6BY1
PDB:
 6C4I
PDB:
 6ENF
PDB:
 6ENJ
PDB:
 6ENU
PDB:
 6GBZ
PDB:
 6GC0
PDB:
 6GC4
PDB:
 6GC6
PDB:
 6GC7
PDB:
 6GC8
PDB:
 6GWT
PDB:
 6GXM
PDB:
 6GXN
PDB:
 6GXO
PDB:
 6GXP
PDB:
 6H4N
PDB:
 6H58
PDB:
 6HRM
PDB:
 6I0Y
PDB:
 6I7V
PDB:
 6O9J
PDB:
 6O9K
PDB:
 6OFX
PDB:
 6OG7
PDB:
 6ORE
PDB:
 6ORL
PDB:
 6OST
PDB:
 6OT3
PDB:
 6OUO
PDB:
 6Q98
PDB:
 6Q9A
PDB:
 6QUL
PDB:
 6S0K
PDB:
 6SZS
PDB:
 6TBV
PDB:
 6TC3
PFAM:
 PF00327
PRIDE:
 P0AG51
PRODB:
 PRO_000023835
PROSITE:
 PS00634
REFSEQ:
 NP_417761
SMR:
 P0AG51
SWISSMODEL:
 P0AG51
UNIPROT:
 P0AG51


Operon      
Name: rplNXE-rpsNH-rplFR-rpsE-rpmD-rplO-secY-rpmJ         
Operon arrangement:
Transcription unit        Promoter
rplNXE-rpsNH-rplFR-rpsE-rpmD-rplO-secY-rpmJ


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_3711 3444116 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3712 3444233 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3713 3444262 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3714 3444279 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3715 (cluster) 3444289 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3716 3444332 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3717 3444337 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3718 (cluster) 3444340 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3719 3444345 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3720 (cluster) 3444352 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3721 3444474 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3722 3444481 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3723 3444485 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3724 3444497 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3725 3444499 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3726 3444507 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3727 3444510 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3728 (cluster) 3444704 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3729 3444805 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3730 3444813 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3731 3445015 reverse nd [RS-EPT-CBR] [1]


Evidence    

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


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.

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