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

NCBI: 26-AUG-2013

⊟Summary

• organism: Staphylococcus aureus N315
• locus tag: SA1887 [new locus tag: SA_RS10855 ]
• pan locus tag^?: SAUPAN005356000
• symbol: ddl
• pan gene symbol^?: ddl
• synonym:
• product: D-alanyl-alanine synthetase A

⊟Genome View

⊟Gene

⊟General

• type: CDS
• locus tag: SA1887 [new locus tag: SA_RS10855 ]
• symbol: ddl
• product: D-alanyl-alanine synthetase A
• replicon: chromosome
• strand: -
• coordinates: 2139312..2140382
• length: 1071
• essential: yes DEG other strains

⊟Accession numbers

• Gene ID: 1124787 NCBI
• RefSeq: NP_375191 NCBI
• BioCyc: see SA_RS10855
• MicrobesOnline: 104217 MicrobesOnline

⊟Phenotype

Share your knowledge and add information here. [edit]

⊟DNA sequence

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  1021
  
  ATGACAAAAGAAAATATTTGTATCGTTTTTGGAGGGAAAAGTGCAGAACACGAAGTATCG
  ATTCTGACAGCACAAAATGTATTAAATGCAATAGATAAAGACAAATATCATGTTGATATC
  ATTTATATTACCAATGATGGTGATTGGAGAAAGCAAAATAATATTACAGCTGAAATTAAA
  TCTACTGATGAGCTTCATTTAGAAAATGGAGAGGCGCTTGAGATTTCACAGCTATTGAAA
  GAAAGTAGTTCAGGACAACCATACGATGCAGTATTCCCATTATTACATGGTCCTAATGGT
  GAAGATGGCACGATTCAAGGGCTTTTTGAAGTTTTGGATGTACCATATGTAGGAAATGGT
  GTATTGTCAGCTGCAAGTTCTATGGACAAACTTGTAATGAAACAATTATTTGAACATCGA
  GGGTTACCACAGTTACCTTATATTAGTTTCTTACGTTCTGAATATGAAAAATATGAACAT
  AACATTTTAAAATTAGTAAATGATAAATTAAATTACCCAGTCTTTGTTAAACCTGCTAAC
  TTAGGGTCAAGTGTAGGTATCAGTAAATGTAATAATGAAGCGGAACTTAAAGAAGGTATT
  AAAGAAGCATTCCAATTTGACCGTAAGCTTGTTATAGAACAAGGCGTTAACGCACGTGAA
  ATTGAAGTAGCAGTTTTAGGAAATGACTATCCTGAAGCGACATGGCCAGGTGAAGTCGTA
  AAAGATGTCGCGTTTTACGATTACAAATCAAAATATAAAGATGGTAAGGTTCAATTACAA
  ATTCCAGCTGACTTAGACGAAGATGTTCAATTAACGCTTAGAAATATGGCATTAGAGGCA
  TTCAAAGCGACAGATTGTTCTGGTTTAGTCCGTGCTGATTTCTTTGTAACAGAAGACAAC
  CAAATATATATTAATGAAACAAATGCAATGCCTGGATTTACGGCTTTCAGTATGTATCCA
  AAGTTATGGGAAAATATGGGCTTATCTTATCCAGAATTGATTACAAAACTTATCGAGCTT
  GCTAAAGAACGTCACCAGGATAAACAGAAAAATAAATACAAAATTGACTAA
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⊟Protein

• 2I80
  PDB
• 2I87
  PDB
• 2I8C
  PDB
• 3N8D
  PDB

Protein Data Bank: 2I80

Protein Data Bank: 2I87

Protein Data Bank: 2I8C

Protein Data Bank: 3N8D

⊟General

• locus tag: SA1887 [new locus tag: SA_RS10855 ]
• symbol: Ddl
• description: D-alanyl-alanine synthetase A
• length: 356
• theoretical pI: 4.63245
• theoretical MW: 40230.3
• GRAVY: -0.394663

⊟Function

• reaction:
  EC 6.3.2.4?  ExPASy
  D-alanine--D-alanine ligase ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine
• TIGRFAM:
  Cell structure Cell envelope Biosynthesis and degradation of murein sacculus and peptidoglycan D-alanine--D-alanine ligase (TIGR01205; EC 6.3.2.4; HMM-score: 368.6)
  and 8 more
  Metabolism Purines, pyrimidines, nucleosides, and nucleotides Purine ribonucleotide biosynthesis phosphoribosylaminoimidazole carboxylase, ATPase subunit (TIGR01161; EC 4.1.1.21; HMM-score: 33.5)
  Metabolism Purines, pyrimidines, nucleosides, and nucleotides Pyrimidine ribonucleotide biosynthesis carbamoyl-phosphate synthase, large subunit (TIGR01369; EC 6.3.5.5; HMM-score: 21.7)
  alpha-L-glutamate ligase, RimK family (TIGR00768; EC 6.3.2.-; HMM-score: 21.2)
  Metabolism Fatty acid and phospholipid metabolism Biosynthesis acetyl-CoA carboxylase, biotin carboxylase subunit (TIGR00514; EC 6.3.4.14; HMM-score: 20.9)
  Metabolism Central intermediary metabolism Nitrogen metabolism urea carboxylase (TIGR02712; EC 6.3.4.6; HMM-score: 20.4)
  Metabolism Amino acid biosynthesis Other pyrrolysine biosynthesis protein PylC (TIGR03909; HMM-score: 17.1)
  Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Other coenzyme gamma-F420-2:alpha-L-glutamate ligase (TIGR04443; EC 6.3.2.32; HMM-score: 15.2)
  Cellular processes Cellular processes Biosynthesis of natural products cyanophycin synthetase (TIGR02068; EC 6.3.2.29,6.3.2.30; HMM-score: 13.8)
• TheSEED  :
  • D-alanine--D-alanine ligase (EC 6.3.2.4)
  Cell Wall and Capsule Cell Wall and Capsule - no subcategory Peptidoglycan Biosynthesis  D-alanine--D-alanine ligase (EC 6.3.2.4)
  and 2 more
  Cell Wall and Capsule Cell Wall and Capsule - no subcategory Peptidoglycan biosynthesis--gjo  D-alanine--D-alanine ligase (EC 6.3.2.4)
  Cell Wall and Capsule Cell Wall and Capsule - no subcategory Peptidoglycan biosynthesis--gjo  D-alanine--D-alanine ligase A (EC 6.3.2.4)
• PFAM:
  ATP-grasp (CL0179) Dala_Dala_lig_C; D-ala D-ala ligase C-terminus (PF07478; HMM-score: 258.2)
  and 5 more
  PreATP-grasp (CL0483) Dala_Dala_lig_N; D-ala D-ala ligase N-terminus (PF01820; HMM-score: 109.7)
  ATP-grasp (CL0179) ATP-grasp; ATP-grasp domain (PF02222; HMM-score: 34.4)
  CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain (PF02786; HMM-score: 29.3)
  ATP-grasp_4; ATP-grasp domain (PF13535; HMM-score: 21.2)
  ATPgrasp_ST; Sugar-transfer associated ATP-grasp (PF14397; HMM-score: 14.8)

⊟Structure, modifications & cofactors

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

⊟Localization

• PSORTb: Cytoplasmic
  • Cytoplasmic Score: 9.97
  • Cytoplasmic Membrane Score: 0
  • Cellwall Score: 0.01
  • Extracellular Score: 0.02
  • 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): 0.005758
  • TAT(Tat/SPI): 0.000285
  • LIPO(Sec/SPII): 0.001329
• predicted transmembrane helices (TMHMM): 0

⊟Accession numbers

• GI: 15927658 NCBI
• RefSeq: NP_375191 NCBI
• UniProt: P63892 UniProt

⊟Protein sequence

• MTKENICIVFGGKSAEHEVSILTAQNVLNAIDKDKYHVDIIYITNDGDWRKQNNITAEIKSTDELHLENGEALEISQLLKESSSGQPYDAVFPLLHGPNGEDGTIQGLFEVLDVPYVGNGVLSAASSMDKLVMKQLFEHRGLPQLPYISFLRSEYEKYEHNILKLVNDKLNYPVFVKPANLGSSVGISKCNNEAELKEGIKEAFQFDRKLVIEQGVNAREIEVAVLGNDYPEATWPGEVVKDVAFYDYKSKYKDGKVQLQIPADLDEDVQLTLRNMALEAFKATDCSGLVRADFFVTEDNQIYINETNAMPGFTAFSMYPKLWENMGLSYPELITKLIELAKERHQDKQKNKYKID

⊟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: murF < ddl

⊟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