PangenomeCOLN315NCTC8325NewmanUSA300_FPR375704-0298108BA0217611819-97685071193ECT-R 2ED133ED98HO 5096 0412JH1JH9JKD6008JKD6159LGA251M013MRSA252MSHR1132MSSA476MW2Mu3Mu50RF122ST398T0131TCH60TW20USA300_TCH1516VC40

NCBI: 10-JUN-2013

⊟Summary

• organism: Staphylococcus aureus USA300_FPR3757
• locus tag: SAUSA300_0894 [new locus tag: SAUSA300_RS04820 ]
• pan locus tag^?: SAUPAN003151000
• symbol: oppD
• pan gene symbol^?: opp4F
• synonym:
• product: oligopeptide ABC transporter ATP-binding protein

⊟Genome View

⊟Gene

⊟General

• type: CDS
• locus tag: SAUSA300_0894 [new locus tag: SAUSA300_RS04820 ]
• symbol: oppD
• product: oligopeptide ABC transporter ATP-binding protein
• replicon: chromosome
• strand: +
• coordinates: 982816..983796
• length: 981
• essential: unknown other strains

⊟Accession numbers

• Gene ID: 3913946 NCBI
• RefSeq: YP_493594 NCBI
• BioCyc: see SAUSA300_RS04820
• MicrobesOnline: 1292409 MicrobesOnline

⊟Phenotype

Share your knowledge and add information here. [edit]

⊟DNA sequence

• 1
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  961
  
  ATGGAAAATATTTTAGAAGTCAACCAAATAAAAAAATACTACAAAATTAAAACTGGATTA
  TTACAAAAAACTCAGTACGTTAAAGCTGTTGATGACGTATCGTTTTCAATAAAAAAAGGA
  CAAACTTTTGGATTAGTAGGAGAATCGGGTTGTGGTAAGTCAACGTTAGGTAAAGTGATT
  ATCAGGCTTGAAGATGCAACTTCAGGCTCAATAATTGTTAATGGTGAAGATATAACAAGA
  TTACAAGGTAAAAAACTCAGAAAATCACGACAACAATATCAGATGATATTTCAAGATCCG
  TATGCATCATTGAATCCGATGCAAATGGTTGGAGATATCATTTCAGAACCTATTTTAAAT
  TATAAAAAATTGCCAAAAGAAGAAATAAAAAAAGAAGTACTATATTTATTAAAATGTGTT
  GGCCTAAGTGAAGATGCATATTATAAATATGCACATGAATTTTCAGGTGGACAGAGACAA
  AGAGTGGGAATTGCAAGAGCATTGGCTTTGCGTCCGAGTTTAATTGTTGCTGATGAGCCT
  GTAAGTGCATTAGATGTATCTGTTCAATCTCAAGTACTGAATTTATTAAAAGATTTACAA
  GAACAATTTAACTTAAGCTATTTATTTATCGCACATGATTTAAGTGTAGTAAAACATATA
  AGTGATGTCATTGGAGTTATGTATTTAGGTCATATAGTTGAAATCGCATCTGATAAAGAA
  ATTTATGAAAATCCCAAACATCCATATACAAAAGCGTTGATTTCATCAATACCACAAATT
  GATAAACATAATAACAATAGAATTATATTAAAAGGAGAATTACCTTCGCCAAGTAATCCG
  CCGCAAGGTTGTCCTTTTCATACAAGATGTCCAATTGCTCAAGATATGTGCAAAAAAAGT
  ATGCCAGAATTAAAGGACATTGGTAATGAACATCAAGTTGCTTGTTTCTACGTAGATAAA
  GTAGGTGATTTAAATGATTAA
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  981
  

⊟Protein

⊟General

• locus tag: SAUSA300_0894 [new locus tag: SAUSA300_RS04820 ]
• symbol: OppD
• description: oligopeptide ABC transporter ATP-binding protein
• length: 326
• theoretical pI: 8.32857
• theoretical MW: 36611.1
• GRAVY: -0.279755

⊟Function

• TIGRFAM:
  Metabolism Transport and binding proteins Cations and iron carrying compounds nickel import ATP-binding protein NikE (TIGR02769; EC 3.6.3.24; HMM-score: 252.5)
  and 77 more
  Metabolism Transport and binding proteins Cations and iron carrying compounds nickel import ATP-binding protein NikD (TIGR02770; HMM-score: 187.7)
  D-methionine ABC transporter, ATP-binding protein (TIGR02314; EC 3.6.3.-; HMM-score: 184.9)
  Metabolism Transport and binding proteins Amino acids, peptides and amines putative 2-aminoethylphosphonate ABC transporter, ATP-binding protein (TIGR03265; HMM-score: 176.9)
  Metabolism Transport and binding proteins Amino acids, peptides and amines glycine betaine/L-proline transport ATP binding subunit (TIGR01186; HMM-score: 174.3)
  Metabolism Transport and binding proteins Anions phosphonate ABC transporter, ATP-binding protein (TIGR02315; EC 3.6.3.28; HMM-score: 163.7)
  Metabolism Transport and binding proteins Unknown substrate energy-coupling factor transporter ATPase (TIGR04521; EC 3.6.3.-; HMM-score: 157.9)
  Metabolism Transport and binding proteins Anions sulfate ABC transporter, ATP-binding protein (TIGR00968; EC 3.6.3.25; HMM-score: 155)
  Metabolism Transport and binding proteins Amino acids, peptides and amines polyamine ABC transporter, ATP-binding protein (TIGR01187; EC 3.6.3.31; HMM-score: 147.3)
  Metabolism Transport and binding proteins Anions phosphate ABC transporter, ATP-binding protein (TIGR00972; EC 3.6.3.27; HMM-score: 145.8)
  Metabolism Transport and binding proteins Unknown substrate energy-coupling factor transporter ATPase (TIGR04520; EC 3.6.3.-; HMM-score: 145.3)
  ectoine/hydroxyectoine ABC transporter, ATP-binding protein EhuA (TIGR03005; HMM-score: 143.7)
  Metabolism Transport and binding proteins Amino acids, peptides and amines choline ABC transporter, ATP-binding protein (TIGR03415; HMM-score: 139.9)
  Cellular processes Cellular processes Cell division cell division ATP-binding protein FtsE (TIGR02673; HMM-score: 136.7)
  Genetic information processing Protein fate Protein and peptide secretion and trafficking lipoprotein releasing system, ATP-binding protein (TIGR02211; EC 3.6.3.-; HMM-score: 136.6)
  Cellular processes Cellular processes Toxin production and resistance putative bacteriocin export ABC transporter, lactococcin 972 group (TIGR03608; HMM-score: 127.9)
  Metabolism Transport and binding proteins Unknown substrate putative bacteriocin export ABC transporter, lactococcin 972 group (TIGR03608; HMM-score: 127.9)
  2-aminoethylphosphonate ABC transport system, ATP-binding component PhnT (TIGR03258; HMM-score: 125.8)
  Metabolism Energy metabolism Methanogenesis methyl coenzyme M reductase system, component A2 (TIGR03269; HMM-score: 123.8)
  ABC exporter ATP-binding subunit, DevA family (TIGR02982; HMM-score: 120.7)
  Metabolism Transport and binding proteins Other daunorubicin resistance ABC transporter, ATP-binding protein (TIGR01188; HMM-score: 113.9)
  Metabolism Transport and binding proteins Anions molybdate ABC transporter, ATP-binding protein (TIGR02142; EC 3.6.3.29; HMM-score: 109.4)
  Cellular processes Cellular processes Biosynthesis of natural products NHLM bacteriocin system ABC transporter, ATP-binding protein (TIGR03797; HMM-score: 108.5)
  Metabolism Transport and binding proteins Amino acids, peptides and amines NHLM bacteriocin system ABC transporter, ATP-binding protein (TIGR03797; HMM-score: 108.5)
  Metabolism Transport and binding proteins Amino acids, peptides and amines oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain (TIGR01727; HMM-score: 108.4)
  Metabolism Transport and binding proteins Cations and iron carrying compounds cobalt ABC transporter, ATP-binding protein (TIGR01166; HMM-score: 106.9)
  Metabolism Transport and binding proteins Anions nitrate ABC transporter, ATP-binding proteins C and D (TIGR01184; HMM-score: 105.8)
  Metabolism Transport and binding proteins Other nitrate ABC transporter, ATP-binding proteins C and D (TIGR01184; HMM-score: 105.8)
  Metabolism Central intermediary metabolism Phosphorus compounds phosphonate C-P lyase system protein PhnK (TIGR02323; HMM-score: 105.5)
  Cellular processes Cellular processes Biosynthesis of natural products NHLM bacteriocin system ABC transporter, peptidase/ATP-binding protein (TIGR03796; HMM-score: 102.2)
  Metabolism Transport and binding proteins Amino acids, peptides and amines NHLM bacteriocin system ABC transporter, peptidase/ATP-binding protein (TIGR03796; HMM-score: 102.2)
  Cell structure Cell envelope Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides lipid A export permease/ATP-binding protein MsbA (TIGR02203; HMM-score: 101.4)
  Metabolism Transport and binding proteins Other lipid A export permease/ATP-binding protein MsbA (TIGR02203; HMM-score: 101.4)
  thiol reductant ABC exporter, CydD subunit (TIGR02857; HMM-score: 99.3)
  Cellular processes Cellular processes Pathogenesis type I secretion system ATPase (TIGR03375; HMM-score: 99)
  Genetic information processing Protein fate Protein and peptide secretion and trafficking type I secretion system ATPase (TIGR03375; HMM-score: 99)
  Genetic information processing Protein fate Protein and peptide secretion and trafficking type I secretion system ATPase (TIGR01846; HMM-score: 96.7)
  ABC transporter, permease/ATP-binding protein (TIGR02204; HMM-score: 94.3)
  Metabolism Transport and binding proteins Carbohydrates, organic alcohols, and acids ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system (TIGR03864; HMM-score: 93.7)
  Cell structure Cell envelope Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides LPS export ABC transporter ATP-binding protein (TIGR04406; HMM-score: 93.2)
  Metabolism Transport and binding proteins Other LPS export ABC transporter ATP-binding protein (TIGR04406; HMM-score: 93.2)
  Genetic information processing Protein fate Protein and peptide secretion and trafficking ABC-type bacteriocin transporter (TIGR01193; HMM-score: 93)
  Genetic information processing Protein fate Protein modification and repair ABC-type bacteriocin transporter (TIGR01193; HMM-score: 93)
  Metabolism Transport and binding proteins Other ABC-type bacteriocin transporter (TIGR01193; HMM-score: 93)
  lantibiotic protection ABC transporter, ATP-binding subunit (TIGR03740; HMM-score: 91.6)
  Metabolism Transport and binding proteins Amino acids, peptides and amines urea ABC transporter, ATP-binding protein UrtE (TIGR03410; HMM-score: 90.3)
  proposed F420-0 ABC transporter, ATP-binding protein (TIGR03873; HMM-score: 89.6)
  Metabolism Transport and binding proteins Other thiamine ABC transporter, ATP-binding protein (TIGR01277; EC 3.6.3.-; HMM-score: 88.4)
  Metabolism Transport and binding proteins Other antigen peptide transporter 2 (TIGR00958; HMM-score: 88)
  Genetic information processing Protein fate Protein and peptide secretion and trafficking type I secretion system ATPase (TIGR01842; HMM-score: 86.8)
  Metabolism Transport and binding proteins Carbohydrates, organic alcohols, and acids D-xylose ABC transporter, ATP-binding protein (TIGR02633; EC 3.6.3.17; HMM-score: 86.6)
  thiol reductant ABC exporter, CydC subunit (TIGR02868; HMM-score: 86.1)
  Metabolism Transport and binding proteins Amino acids, peptides and amines urea ABC transporter, ATP-binding protein UrtD (TIGR03411; HMM-score: 84.9)
  Metabolism Transport and binding proteins Carbohydrates, organic alcohols, and acids glucan exporter ATP-binding protein (TIGR01192; EC 3.6.3.42; HMM-score: 84.4)
  gliding motility-associated ABC transporter ATP-binding subunit GldA (TIGR03522; HMM-score: 84.3)
  phosphonate C-P lyase system protein PhnL (TIGR02324; HMM-score: 81.4)
  Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Other FeS assembly ATPase SufC (TIGR01978; HMM-score: 75.5)
  Metabolism Transport and binding proteins Unknown substrate anchored repeat-type ABC transporter, ATP-binding subunit (TIGR03771; HMM-score: 73.9)
  Cellular processes Cellular processes Other nodulation ABC transporter NodI (TIGR01288; HMM-score: 61.6)
  Metabolism Transport and binding proteins Other nodulation ABC transporter NodI (TIGR01288; HMM-score: 61.6)
  Metabolism Transport and binding proteins Other pigment precursor permease (TIGR00955; HMM-score: 59.3)
  Genetic information processing Protein fate Protein and peptide secretion and trafficking heme ABC exporter, ATP-binding protein CcmA (TIGR01189; EC 3.6.3.41; HMM-score: 58.1)
  Metabolism Transport and binding proteins Other heme ABC exporter, ATP-binding protein CcmA (TIGR01189; EC 3.6.3.41; HMM-score: 58.1)
  Metabolism Transport and binding proteins Other multi drug resistance-associated protein (MRP) (TIGR00957; HMM-score: 52.2)
  ATP-binding cassette protein, ChvD family (TIGR03719; HMM-score: 50.5)
  Metabolism Transport and binding proteins Carbohydrates, organic alcohols, and acids peroxysomal long chain fatty acyl transporter (TIGR00954; HMM-score: 44.9)
  Metabolism Transport and binding proteins Anions cystic fibrosis transmembrane conductor regulator (CFTR) (TIGR01271; EC 3.6.3.49; HMM-score: 40.1)
  Metabolism Transport and binding proteins Amino acids, peptides and amines cyclic peptide transporter (TIGR01194; HMM-score: 38.1)
  Metabolism Transport and binding proteins Other cyclic peptide transporter (TIGR01194; HMM-score: 38.1)
  Metabolism Transport and binding proteins Other rim ABC transporter (TIGR01257; HMM-score: 37.1)
  Genetic information processing DNA metabolism DNA replication, recombination, and repair excinuclease ABC subunit A (TIGR00630; EC 3.1.25.-; HMM-score: 28.5)
  Metabolism Transport and binding proteins Other pleiotropic drug resistance family protein (TIGR00956; HMM-score: 27.4)
  Cellular processes Cellular processes Pathogenesis type III secretion apparatus H+-transporting two-sector ATPase (TIGR02546; EC 3.6.3.14; HMM-score: 18.1)
  Genetic information processing Protein fate Protein and peptide secretion and trafficking type III secretion apparatus H+-transporting two-sector ATPase (TIGR02546; EC 3.6.3.14; HMM-score: 18.1)
  Cellular processes Cellular processes Chemotaxis and motility flagellar protein export ATPase FliI (TIGR03497; EC 3.6.3.14; HMM-score: 16.2)
  Cellular processes Cellular processes Chemotaxis and motility flagellar protein export ATPase FliI (TIGR03496; EC 3.6.3.14; HMM-score: 15.5)
  Metabolism Energy metabolism ATP-proton motive force interconversion ATPase, FliI/YscN family (TIGR01026; EC 3.6.3.14; HMM-score: 14.4)
  flagellar protein export ATPase FliI (TIGR03498; EC 3.6.3.14; HMM-score: 12.4)
• TheSEED  :
  • Oligopeptide transport ATP-binding protein OppF (TC 3.A.1.5.1)
  Membrane Transport ABC transporters ABC transporter oligopeptide (TC 3.A.1.5.1)  Oligopeptide transport ATP-binding protein OppF (TC 3.A.1.5.1)
• PFAM:
  P-loop_NTPase (CL0023) ABC_tran; ABC transporter (PF00005; HMM-score: 112)
  and 11 more
  no clan defined oligo_HPY; Oligopeptide/dipeptide transporter, C-terminal region (PF08352; HMM-score: 73.3)
  P-loop_NTPase (CL0023) SMC_N; RecF/RecN/SMC N terminal domain (PF02463; HMM-score: 21.7)
  AAA_21; AAA domain, putative AbiEii toxin, Type IV TA system (PF13304; HMM-score: 20.3)
  AAA_22; AAA domain (PF13401; HMM-score: 19.1)
  ATP-synt_ab; ATP synthase alpha/beta family, nucleotide-binding domain (PF00006; HMM-score: 19)
  RsgA_GTPase; RsgA GTPase (PF03193; HMM-score: 18.4)
  AAA; ATPase family associated with various cellular activities (AAA) (PF00004; HMM-score: 15.4)
  AAA_29; P-loop containing region of AAA domain (PF13555; HMM-score: 13.8)
  Sigma54_activat; Sigma-54 interaction domain (PF00158; HMM-score: 11.9)
  Mg_chelatase; Magnesium chelatase, subunit ChlI (PF01078; HMM-score: 11.9)
  AAA_13; AAA domain (PF13166; HMM-score: 10)

⊟Structure, modifications & cofactors

• domains:
• modifications:
• cofactors:
• effectors:

⊟Localization

• PSORTb: Cytoplasmic Membrane
  • Cytoplasmic Score: 1.05
  • Cytoplasmic Membrane Score: 8.78
  • Cellwall Score: 0.08
  • Extracellular Score: 0.09
  • Internal Helices: 0
• LocateP: Intracellular
  • Prediction by SwissProt Classification: Cytoplasmic
  • Pathway Prediction: No pathway
  • Intracellular possibility: 1
  • Signal peptide possibility: -1
  • N-terminally Anchored Score: 1
  • Predicted Cleavage Site: No CleavageSite
• SignalP: no predicted signal peptide
  • SP(Sec/SPI): 0.100481
  • TAT(Tat/SPI): 0.000478
  • LIPO(Sec/SPII): 0.001323
• predicted transmembrane helices (TMHMM): 0

⊟Accession numbers

• GI: 87161030 NCBI
• RefSeq: YP_493594 NCBI
• UniProt: A0A0H2XHX3 UniProt

⊟Protein sequence

• MENILEVNQIKKYYKIKTGLLQKTQYVKAVDDVSFSIKKGQTFGLVGESGCGKSTLGKVIIRLEDATSGSIIVNGEDITRLQGKKLRKSRQQYQMIFQDPYASLNPMQMVGDIISEPILNYKKLPKEEIKKEVLYLLKCVGLSEDAYYKYAHEFSGGQRQRVGIARALALRPSLIVADEPVSALDVSVQSQVLNLLKDLQEQFNLSYLFIAHDLSVVKHISDVIGVMYLGHIVEIASDKEIYENPKHPYTKALISSIPQIDKHNNNRIILKGELPSPSNPPQGCPFHTRCPIAQDMCKKSMPELKDIGNEHQVACFYVDKVGDLND

⊟Experimental data

• experimentally validated:
• protein localization:
• quantitative data / protein copy number per cell:
• interaction partners:

⊟Expression & Regulation

⊟Operon

• MicrobesOnline: oppA > oppF > oppD > oppB > oppC

⊟Regulation

• regulator: CodY (repression) regulon

  CodY

  (TF)

  important in Amino acid metabolism; RegPrecise    transcription unit transferred from N315 data RegPrecise

⊟Transcription pattern

• S.aureus Expression Data Browser: data available for NCTC8325

⊟Protein synthesis (provided by Aureolib)

• Aureolib: no data available

⊟Protein stability

• half-life: no data available

⊟Biological Material

⊟Mutants

⊟Expression vector

⊟lacZ fusion

⊟GFP fusion

⊟two-hybrid system

⊟FLAG-tag construct

⊟Antibody

⊟Other Information

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⊟Literature

⊟References

⊟Relevant publications