Coding

Part:BBa_K1463600

Designed by: iGEM14_Glasgow   Group: iGEM14_Glasgow   (2014-10-04)
Revision as of 18:06, 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.


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.

[edit]
Categories
Parameters
None