Coding

Part:BBa_K1463600

Designed by: iGEM14_Glasgow   Group: iGEM14_Glasgow   (2014-10-04)
Revision as of 20:14, 17 October 2014 by GemmaMcl (Talk | contribs)

FliC

FliC encodes the major flagellar protein of E. coli and is thus fundamental to motility.


Figure 1 shows this biobrick used in conjunction with various promoters and ribosome binding sites to restore swimming in fliC knockout strains. This data is also shown as a histogram in Figure 2. These show that, with an appropriate promoter and RBS, this biobrick can restore swimming to almost wild-type levels.


We sequenced our fliC biobrick and found that it had the expected sequence, identical to fliC of the sequenced E. coli strain MG1655 at all positions except for the changes we had made to remove three PstI sites and one SpeI site. However, there were two coding differences between our biobrick and a previous fliC biobrick in the parts registry K777109. These differences are due to different source strains (We used MG1655 genomic DNA, they used E. coli strain K-12 substr. DH10B). It is unclear if these nonsynonymous changes alter flagella formation.

Flic Motility Swarm Assay

310px-GU_Figure_1_swarm_M.png

Figure 1: FliC Swarm Motility Assays.
(A) DS941, (B) DS941 ΔfliC,
(C) DS941 ΔfliC + pSB1C3 fliC (no promoter), (D) DS941 ΔfliC + J23100 (mutant promoter) fliC,
(E) DS941 ΔfliC + J23116-fliC(1), (F) DS941 ΔfliC + J23116-fliC(2),
(G) DS941 ΔfliC + J23106-fliC(1), (H) DS941 ΔfliC + J23106-fliC(2)


Flic Motility Histogram

GU_Figure_2_Motility_histogram.png
Figure 2 - FliC Motility Histogram



For more information on the biobrick and methods used go to http://2014.igem.org/wiki/index.php?title=Team:Glasgow/Project/Mobility_Proteins#motA



Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 1224
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 301
    Illegal AgeI site found at 709
  • 1000
    COMPATIBLE WITH RFC[1000]


Protein data table for BioBrick BBa_K1463600 automatically created by the BioBrick-AutoAnnotator version 1.0
Nucleotide sequence in RFC 10: (underlined part encodes the protein)
 ATGGCACAA ... CTCCAGGGTTAA
 ORF from nucleotide position 1 to 1494 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 
101 
201 
301 
401 		MAQVINTNSLSLITQNNINKNQSALSSSIERLSSGLRINSAKDDAAGQAIANRFTSNIKGLTQAARNANDGISVAQTTEGALSEINNNLQRVRELTVQAT
TGTNSESDLSSIQDEIKSRLDEIDRVSGQTQFNGVNVLAKNGSMKIQVGANDNQTITIDLKQIDAKTLGLDGFSVKNNDTVTTSAPVTAFGATTTNNIKL
TGITLSTEAATDTGGTNPASIEGVYTDNGNDYYAKITGGDNDGKYYAVTVANDGTVTMATGATANATVTDANTTKATTITSGGTPVQIDNTAGSATANLG
AVSLVKLQDSKGNDTDTYALKDTNGNLYAADVNETTGAVSVKTITYTDSSGAASSPTAVKLGGDDGKTEVVDIDGKTYDSADLNGGNLQTGLTAGGEALT
AVANGKTTDPLKALDDAIASVDKFRSSLGAVQNRLDSAVTNLNNTTTNLSEAQSRIQDADYATEVSNMSKAQIIQQAGNSVLAKANQVPQQVLSLLQG*
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)59 (11.8%)
Arg (R)11 (2.2%)
Asn (N)48 (9.6%)
Asp (D)39 (7.8%)
Cys (C)0 (0.0%)
Gln (Q)27 (5.4%)
Glu (E)14 (2.8%)
Gly (G)44 (8.8%)
His (H)0 (0.0%)
Ile (I)28 (5.6%)
Leu (L)37 (7.4%)
Lys (K)25 (5.0%)
Met (M)4 (0.8%)
Phe (F)5 (1.0%)
Pro (P)6 (1.2%)
Ser (S)43 (8.6%)
Thr (T)65 (13.1%)
Trp (W)0 (0.0%)
Tyr (Y)10 (2.0%)
Val (V)33 (6.6%)
Amino acid counting
Total number:498
Positively charged (Arg+Lys):36 (7.2%)
Negatively charged (Asp+Glu):53 (10.6%)
Aromatic (Phe+His+Try+Tyr):15 (3.0%)
Biochemical parameters
Atomic composition:C2163H3553N631O798S4
Molecular mass [Da]:51295.0
Theoretical pI:4.50
Extinction coefficient at 280 nm [M-1 cm-1]:14900 / 14900 (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 (0.83)good (0.78)good (0.68)good (0.74)excellent (0.83)good (0.70)
Alignments (obtained from PredictProtein.org)
SwissProt:P04949 (100% identity on 498 AAs), P06179 (47% identity on 495 AAs)
TrEML:L2Z8U7 (100% identity on 498 AAs), M2PKZ4 (100% identity on 498 AAs), C6EBD8 (100% identity on 498 AAs), C9QSQ0 (100% identity on 498 AAs), F9QUT2 (100% identity on 498 AAs), G2EY21 (100% identity on 498 AAs), I0ZSG6 (100% identity on 498 AAs), C4ZQK1 (100% identity on 498 AAs), Q53ZW4 (100% identity on 498 AAs), U6N709 (100% identity on 498 AAs)
PDB: -
Predictions (obtained from PredictProtein.org)
Subcellular Localization (reliability in brackets)
Archaea:cytosol (100%)
Bacteria:secreted (65%)
Eukarya:nucleus (55%)
Gene Ontology (reliability in brackets)
Molecular Function Ontology:GO:0005515 (100%)
Biological Process Ontology:GO:0009405 (9%), GO:0001539 (63%)
 
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.

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Categories
Parameters
None