Difference between revisions of "Part:BBa K1981005"
(→‎Characterization)
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===Characterization===
 
===Characterization===
 +
The colony PCR verification result for <i>lsrFG</i> is shown in <b>Figure 1</b>.
 +
<div>[[File:T--NKU China--lsrFG Colony PCR.jpeg|400px|thumb|center|<b>Figure 1:</b> Colony PCR Verification for <i>lsrFG</i>]]</div>
  
 
===Protein-Data Table===
 
===Protein-Data Table===

Revision as of 03:32, 15 October 2016


lsrFG

A Protein complex involved in the degradation of phospho-AI-2, thereby terminating induction of the lsr operon and closing the AI-2 signaling cycle. LsrF is responsible for catalyzing the transfer of an acetyl moiety from 3-hydroxy-5-phosphonooxypentane-2,4-dione to CoA to form glycerone phosphate and acetyl-CoA. LsrG is responsible for catalyzing the conversion of (4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione (P-DPD) to 3-hydroxy-5-phosphonooxypentane-2,4-dione (P-HPD). In the absence of AI-2, LsrFG is repressed by LsrR. It can be induced by AI-2, via releasing of the LsrR repressor. In the absence of glucose, LsrFG was induced by cAMP-CRP by direct binding to the upstream region of the lsr promoter.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Usage and Biology

AI-2 “Consumer” was constructed by overexpressing the lsrFG gene.

This part is originated from Escherichia coli strain K12.

Characterization

The colony PCR verification result for lsrFG is shown in Figure 1.

Figure 1: Colony PCR Verification for lsrFG

Protein-Data Table

  • lsrF

Protein data table for BioBrick BBa_K1981005 automatically created by the BioBrick-AutoAnnotator version 1.0
Nucleotide sequence in RFC 10: (underlined part encodes the protein)
 ATGGCAGAT ... GAAAAACAGTAA
 ORF from nucleotide position 1 to 873 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 
101 
201 		MADLDDIKDGKDFRTDQPQKNIPFTLKGCGALDWGMQSRLSRIFNPKTGKTVMLAFDHGYFQGPTTGLERIDINIAPLFEHADVLMCTRGILRSVVPPAT
NRPVVLRASGANSILAELSNEAVALSMDDAVRLNSCAVAAQVYIGSEYEHQSIKNIIQLVDAGMKVGMPTMAVTGVGKDMVRDQRYFSLATRIAAEMGAQ
IIKTYYVEKGFERIVAGCPVPIVIAGGKKLPEREALEMCWQAIDQGASGVDMGRNIFQSDHPVAMMKAVQAVVHHNETADRAYELYLSEKQ*
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
None of the supported features appeared in the sequence
Amino acid composition:
Ala (A)31 (10.7%)
Arg (R)16 (5.5%)
Asn (N)10 (3.4%)
Asp (D)19 (6.5%)
Cys (C)5 (1.7%)
Gln (Q)14 (4.8%)
Glu (E)15 (5.2%)
Gly (G)23 (7.9%)
His (H)6 (2.1%)
Ile (I)20 (6.9%)
Leu (L)20 (6.9%)
Lys (K)15 (5.2%)
Met (M)14 (4.8%)
Phe (F)9 (3.1%)
Pro (P)13 (4.5%)
Ser (S)14 (4.8%)
Thr (T)13 (4.5%)
Trp (W)2 (0.7%)
Tyr (Y)8 (2.7%)
Val (V)24 (8.2%)
Amino acid counting
Total number:291
Positively charged (Arg+Lys):31 (10.7%)
Negatively charged (Asp+Glu):34 (11.7%)
Aromatic (Phe+His+Try+Tyr):25 (8.6%)
Biochemical parameters
Atomic composition:C1401H2244N392O419S19
Molecular mass [Da]:31892.7
Theoretical pI:6.09
Extinction coefficient at 280 nm [M-1 cm-1]:22920 / 23233 (all Cys red/ox)
Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges 
Codon usage
Organism:E. coliB. subtilisS. cerevisiaeA. thalianaP. patensMammals
Codon quality (CAI):excellent (0.84)excellent (0.82)acceptable (0.60)good (0.66)good (0.77)good (0.65)
Alignments (obtained from PredictProtein.org)
   There were no alignments for this protein in the data base. The BLAST search was initialized and should be ready in a few hours.
Predictions (obtained from PredictProtein.org)
Subcellular Localization (reliability in brackets)
Archaea: -
Bacteria: -
Eukarya: -
Gene Ontology (reliability in brackets)
Molecular Function Ontology: -
Biological Process Ontology:0006096 0. (NaN%)
 
Predicted features:
Disulfid bridges: -
Transmembrane helices: -
The BioBrick-AutoAnnotator was created by TU-Munich 2013 iGEM team. For more information please see the documentation.
If you have any questions, comments or suggestions, please leave us a comment.

  • lsrG

Protein data table for BioBrick BBa_K1981005 automatically created by the BioBrick-AutoAnnotator version 1.0
Nucleotide sequence in RFC 10: (underlined part encodes the protein)
 ATGCACGTC ... TTGATGCCGTGA
 ORF from nucleotide position 1 to 288 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 MHVTLVEINVHEDKVDEFIEVFRQNHLGSVQEEGNLRFDVLQDPEVNSRFYIYEAYKDEDAVAFHKTTPHYKTCVAKLESLMTGPRKKRLFNGLMP*
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
None of the supported features appeared in the sequence
Amino acid composition:
Ala (A)4 (4.2%)
Arg (R)5 (5.2%)
Asn (N)5 (5.2%)
Asp (D)6 (6.3%)
Cys (C)1 (1.0%)
Gln (Q)3 (3.1%)
Glu (E)10 (10.4%)
Gly (G)4 (4.2%)
His (H)5 (5.2%)
Ile (I)3 (3.1%)
Leu (L)8 (8.3%)
Lys (K)7 (7.3%)
Met (M)3 (3.1%)
Phe (F)6 (6.3%)
Pro (P)4 (4.2%)
Ser (S)3 (3.1%)
Thr (T)5 (5.2%)
Trp (W)0 (0.0%)
Tyr (Y)4 (4.2%)
Val (V)10 (10.4%)
Amino acid counting
Total number:96
Positively charged (Arg+Lys):12 (12.5%)
Negatively charged (Asp+Glu):16 (16.7%)
Aromatic (Phe+His+Try+Tyr):15 (15.6%)
Biochemical parameters
Atomic composition:C504H778N136O149S4
Molecular mass [Da]:11254.8
Theoretical pI:5.68
Extinction coefficient at 280 nm [M-1 cm-1]:5960 / 6023 (all Cys red/ox)
Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges 
Codon usage
Organism:E. coliB. subtilisS. cerevisiaeA. thalianaP. patensMammals
Codon quality (CAI):excellent (0.81)good (0.79)good (0.63)good (0.69)good (0.76)good (0.68)
Alignments (obtained from PredictProtein.org)
   There were no alignments for this protein in the data base. The BLAST search was initialized and should be ready in a few hours.
Predictions (obtained from PredictProtein.org)
Subcellular Localization (reliability in brackets)
Archaea: -
Bacteria: -
Eukarya: -
Gene Ontology (reliability in brackets)
Molecular Function Ontology: -
Biological Process Ontology:0017000 0. (NaN%), 0019439 0. (NaN%)
 
Predicted features:
Disulfid bridges: -
Transmembrane helices: -
The BioBrick-AutoAnnotator was created by TU-Munich 2013 iGEM team. For more information please see the documentation.
If you have any questions, comments or suggestions, please leave us a comment.