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

NCBI: 26-AUG-2013

⊟Summary

• organism: Staphylococcus aureus N315
• locus tag: SA0896 [new locus tag: SA_RS05085 ]
• pan locus tag^?: SAUPAN003246000
• symbol: menD
• pan gene symbol^?: menD
• synonym:
• product: menaquinone biosynthesis protein

⊟Genome View

⊟Gene

⊟General

• type: CDS
• locus tag: SA0896 [new locus tag: SA_RS05085 ]
• symbol: menD
• product: menaquinone biosynthesis protein
• replicon: chromosome
• strand: +
• coordinates: 1016502..1018175
• length: 1674
• essential: no DEG other strains

⊟Accession numbers

• Gene ID: 1123719 NCBI
• RefSeq: NP_374163 NCBI
• BioCyc: see SA_RS05085
• MicrobesOnline: 103189 MicrobesOnline

⊟Phenotype

Share your knowledge and add information here. [edit]

⊟DNA sequence

• 1
  61
  121
  181
  241
  301
  361
  421
  481
  541
  601
  661
  721
  781
  841
  901
  961
  1021
  1081
  1141
  1201
  1261
  1321
  1381
  1441
  1501
  1561
  1621
  
  ATGGGAAATCATAAAGCAGCTTTAACGAAGCAAGTTTTTACATTTGCATCTGAGTTATAT
  GCATACGGCGTAAGGGAAGTAGTTATCAGTCCGGGATCACGCTCAACGCCACTTGCACTT
  GCATTTGAAGCACATCCAAATATTAAAACATGGATACACCCCGATGAGCGAAGTGCAGCA
  TTTTTTGCAGTTGGGTTAATTAAAGGCAGTGAAAGACCTGTCGCTATATTATGTACGTCA
  GGTACAGCAGCAGCGAATTATACGCCTGCAATTGCTGAAAGCCAAATTAGTAGAATTCCA
  TTAATCGTTTTAACAAGTGACCGTCCGCATGAATTAAGAAGTGTAGGCGCACCACAAGCG
  ATTAATCAAGTAAATATGTTTAATAATTATGTAAGTTATGAGTTCGATATGCCTATTGCG
  GATGATAGTAAAGAGACCATTAATGCAATTTATTATCAAATGCAAATTGCTAGTCAATAT
  TTATATGGACCACATAAAGGGCCAATTCATTTTAACTTGCCATTTAGAGATCCGTTAACA
  CCTGATTTGAATGCAACAGAATTGTTAACTTCTGAGATGAAGATTTTACCGCACTATCAA
  AAAAGTATAGATGCATCGGCATTAAGACACATTTTAAATAAGAAAAAAGGTTTAATTATT
  GTAGGGGATATGCAGCACCAAGAAGTTGATCAAATACTAACGTATTCAACGATATATGAT
  TTGCCTATTTTAGCTGATCCTTTAAGTCATTTAAGAAAATTTGATCATCCGAATGTTATC
  TGTACATATGATTTGCTGTTTAGAAGCGGCTTAGACTTAAATGTGGATTTCGTAATTCGT
  GTTGGGAAACCAGTGATTTCTAAAAAGTTGAATCAATGGTTAAAGAAAACTGATGCATTT
  CAAATATTAGTGCAAAACAATGATAAGATTGATGTCTTTCCTATAGCGCCAGATATTTCA
  TATGAGATTTCTGCAAATGATTTCTTTAGATCATTAATGGAAGACACGACCATCAATCGC
  GTAAGTTGGTTAGAAAAATGGCAATGCTTAGAGAAAAAAGGGCGTAAAGAAATTAAATGT
  TATTTGGAACAAGCTACAGATGAGAGTGCATTCGTTGGTGAATTGATTAAGAAAACATCT
  GAAAAAGATGCATTATTTATTAGTAATAGTATGCCTATCAGAGATGTAGATAACTTGTTA
  TTGAATAAAAATATAGATGTCTATGCGAATCGTGGTGCGAATGGTATTGATGGTATCGTT
  TCAACTGCACTGGGTATGGCTGTGCATAAACGAATAACATTATTGATAGGTGATTTGTCA
  TTTTATCATGATATGAATGGACTATTAATGTCAAAATTAAATAATATTCAGATGAATATT
  GTATTATTGAACAACGATGGTGGCGGTATTTTTTCATATTTACCACAAAAAGAAAGTGCA
  ACTGACTATTTTGAACGGTTGTTTGGCACACCGACGGGATTGGATTTCGAGTATACAGCT
  AAGTTATATCAATTCGATTTTAAACGTTTTAACAGTGTTTCAGAATTTAAAAATGCCACA
  TTGTTATCTGAAACTTCGACGATTTATGAATTGATAACGAATCGCGAAGATAACTTTAAA
  CAGCATCAAATTTTATATCAGAAATTGAGTGAAATGATTCATGACACATTATAA
  60
  120
  180
  240
  300
  360
  420
  480
  540
  600
  660
  720
  780
  840
  900
  960
  1020
  1080
  1140
  1200
  1260
  1320
  1380
  1440
  1500
  1560
  1620
  1674
  

⊟Protein

⊟General

• locus tag: SA0896 [new locus tag: SA_RS05085 ]
• symbol: MenD
• description: menaquinone biosynthesis protein
• length: 557
• theoretical pI: 6.35375
• theoretical MW: 63090.8
• GRAVY: -0.187074

⊟Function

• reaction:
  EC 2.2.1.9?  ExPASy
  2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase Isochorismate + 2-oxoglutarate = 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO₂
• TIGRFAM:
  Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Menaquinone and ubiquinone 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase (TIGR00173; EC 2.2.1.9; HMM-score: 427.5)
  and 5 more
  Metabolism Amino acid biosynthesis Pyruvate family acetolactate synthase, large subunit, biosynthetic type (TIGR00118; EC 2.2.1.6; HMM-score: 37.1)
  Metabolism Energy metabolism Sugars 3,5/4-trihydroxycyclohexa-1,2-dione hydrolase (TIGR04377; EC 3.7.1.-; HMM-score: 31.4)
  Metabolism Energy metabolism Fermentation acetolactate synthase, catabolic (TIGR02418; EC 2.2.1.6; HMM-score: 19.6)
  Metabolism Central intermediary metabolism Other sulfoacetaldehyde acetyltransferase (TIGR03457; EC 2.3.3.15; HMM-score: 16.6)
  2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase (TIGR04316; EC 1.3.1.28; HMM-score: 14.5)
• TheSEED  :
  • 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase (EC 2.2.1.9)
  Cofactors, Vitamins, Prosthetic Groups, Pigments Quinone cofactors Menaquinone and Phylloquinone Biosynthesis  2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase (EC 2.2.1.9)
  and 1 more
  Cofactors, Vitamins, Prosthetic Groups, Pigments Quinone cofactors Menaquinone biosynthesis from chorismate via 1,4-dihydroxy-2-naphthoate  2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase (EC 2.2.1.9)
• PFAM:
  THDP-binding (CL0254) TPP_enzyme_N; Thiamine pyrophosphate enzyme, N-terminal TPP binding domain (PF02776; HMM-score: 110.4)
  and 4 more
  FAD_DHS (CL0085) TPP_enzyme_M_2; Middle domain of thiamine pyrophosphate (PF16582; HMM-score: 46.1)
  THDP-binding (CL0254) TPP_enzyme_C; Thiamine pyrophosphate enzyme, C-terminal TPP binding domain (PF02775; HMM-score: 23.6)
  no clan defined ANT; Phage antirepressor protein KilAC domain (PF03374; HMM-score: 13)
  NADP_Rossmann (CL0063) adh_short_C2; Enoyl-(Acyl carrier protein) reductase (PF13561; HMM-score: 11.7)

⊟Structure, modifications & cofactors

• domains:
• modifications:
• cofactors: Mg²⁺, Mn²⁺, thiamine diphosphate
• effectors:

⊟Localization

• PSORTb: unknown (no significant prediction)
  • Cytoplasmic Score: 2.5
  • Cytoplasmic Membrane Score: 2.5
  • Cellwall Score: 2.5
  • Extracellular Score: 2.5
  • 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): 0.034937
  • TAT(Tat/SPI): 0.007695
  • LIPO(Sec/SPII): 0.004206
• predicted transmembrane helices (TMHMM): 0

⊟Accession numbers

• GI: 15926630 NCBI
• RefSeq: NP_374163 NCBI
• UniProt: Q7A6B1 UniProt

⊟Protein sequence

• MGNHKAALTKQVFTFASELYAYGVREVVISPGSRSTPLALAFEAHPNIKTWIHPDERSAAFFAVGLIKGSERPVAILCTSGTAAANYTPAIAESQISRIPLIVLTSDRPHELRSVGAPQAINQVNMFNNYVSYEFDMPIADDSKETINAIYYQMQIASQYLYGPHKGPIHFNLPFRDPLTPDLNATELLTSEMKILPHYQKSIDASALRHILNKKKGLIIVGDMQHQEVDQILTYSTIYDLPILADPLSHLRKFDHPNVICTYDLLFRSGLDLNVDFVIRVGKPVISKKLNQWLKKTDAFQILVQNNDKIDVFPIAPDISYEISANDFFRSLMEDTTINRVSWLEKWQCLEKKGRKEIKCYLEQATDESAFVGELIKKTSEKDALFISNSMPIRDVDNLLLNKNIDVYANRGANGIDGIVSTALGMAVHKRITLLIGDLSFYHDMNGLLMSKLNNIQMNIVLLNNDGGGIFSYLPQKESATDYFERLFGTPTGLDFEYTAKLYQFDFKRFNSVSEFKNATLLSETSTIYELITNREDNFKQHQILYQKLSEMIHDTL

⊟Experimental data

• experimentally validated: data available for COL, NCTC8325
• protein localization: data available for COL
• quantitative data / protein copy number per cell: data available for COL
• interaction partners:

⊟Expression & Regulation

⊟Operon

• MicrobesOnline: SA0895 > menD > SA0897 > menB

⊟Regulation

• regulator:

⊟Transcription pattern

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

⊟Protein synthesis (provided by Aureolib)

• Aureolib: data available for COL

⊟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

You are kindly invited to share additional interesting facts.

⊟Literature

⊟References

⊟Relevant publications