Team:IIT Delhi/Parts

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iGEM IIT Delhi

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Parts Submitted to the Registry

What information do I need to start putting my parts on the Registry?

An important aspect of the iGEM competition is the use and creation of standard biological parts. Each team will make new parts during iGEM and will submit them to the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created. The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox.

Note that if you want to document a part you need to document it on the Registry, not on your team wiki. Future teams and other users and are much more likely to find parts on the Registry than on your team wiki.

Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without a need to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.

When should you put parts into the Registry?

As soon as possible! We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better recall you will have of all details surrounding your parts. Remember you don't need to send us the DNA to create an entry for a part on the Registry. However, you must send us the sample/DNA before the Jamboree. Only parts for which you have sent us samples/DNA are eligible for awards and medal requirements.

The information needed to initially create a part on the Registry is:

  1. Part Name
  2. Part type
  3. Creator
  4. Sequence
  5. Short Description (60 characters on what the DNA does)
  6. Long Description (Longer description of what the DNA does)
  7. Design considerations

We encourage you to put up much more information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page. Check out part BBa_K404003 for an excellent example of a highly characterized part.

You can add parts to the Registry at our Add a Part to the Registry link.

Parts Table

Any parts your team has created will appear in this table below:

nrfA extra information using TU Munich Biobrick Annotator

Protein data table for BioBrick BBa_ automatically created by the BioBrick-AutoAnnotator version 1.0
Nucleotide sequence in RFC 10: (underlined part encodes the protein)
 ATGACAAGG ... TTAAGCCAATAA
 ORF from nucleotide position 1 to 1434 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)

101 
201 
301 
401 
MTRIKINARRIFSLLIPFFFFTSVHAEQTAAPAKPVTVEAKNETFAPQHPDQYLSWKATSEQSERVDALAEDPRLVILWAGYPFSRDYNKPRGHAFAVTD
VRETLRTGAPKNAEDGPLPMACWSCKSPDVARLIQKDGEDGYFHGKWARGGPEIVNNLGCADCHNTASPEFAKGKPELTLSRPYAARAMEAIGKPFEKAG
RFDQQSMVCGQCHVEYYFDGKNKAVKFPWDDGMKVENMEQYYDKIAFSDWTNSLSKTPMLKAQHPEYETWTAGIHGKNNVTCIDCHMPKVQNAEGKLYTD
HKIGNPFDNFAQTCANCHTQDKAALQKVVAERKQSINDLKIKVEDQLVHAHFEAKAALDAGATEAEMKPIQDDIRHAQWRWDLAIASHGIHMHAPEEGLR
MLGTAMDKAADARTKLARLLATKGITHEIQIPDISTKEKAQQAIGLNMEQIKAEKQDFIKTVIPQWEEQARKNGLLSQ*
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)57 (11.9%)
Arg (R)21 (4.4%)
Asn (N)19 (4.0%)
Asp (D)30 (6.3%)
Cys (C)10 (2.1%)
Gln (Q)26 (5.4%)
Glu (E)33 (6.9%)
Gly (G)27 (5.6%)
His (H)18 (3.8%)
Ile (I)26 (5.4%)
Leu (L)28 (5.9%)
Lys (K)40 (8.4%)
Met (M)13 (2.7%)
Phe (F)19 (4.0%)
Pro (P)26 (5.4%)
Ser (S)18 (3.8%)
Thr (T)26 (5.4%)
Trp (W)10 (2.1%)
Tyr (Y)11 (2.3%)
Val (V)20 (4.2%)
Amino acid counting
Total number:478
Positively charged (Arg+Lys):61 (12.8%)
Negatively charged (Asp+Glu):63 (13.2%)
Aromatic (Phe+His+Try+Tyr):58 (12.1%)
Biochemical parameters
Atomic composition:C2377H3694N672O705S23
Molecular mass [Da]:53702.9
Theoretical pI:6.81
Extinction coefficient at 280 nm [M-1 cm-1]:71390 / 72015 (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 (0.77)good (0.61)good (0.68)good (0.80)good (0.69)
Alignments (obtained from PredictProtein.org)
SwissProt:A1AIR1 (99% identity on 478 AAs), B7MJT8 (99% identity on 478 AAs), B7UPN8 (99% identity on 478 AAs), Q0T9X8 (99% identity on 478 AAs), Q1R3J6 (99% identity on 478 AAs), Q8CVI1 (99% identity on 478 AAs)
TrEML:M9C9C0 (100% identity on 478 AAs), B2N2V6 (100% identity on 478 AAs), W2AE68 (100% identity on 478 AAs), W1ST11 (100% identity on 478 AAs), W1BF49 (100% identity on 478 AAs), B6ZVF1 (100% identity on 478 AAs), V8LM39 (100% identity on 478 AAs), V8JEI0 (100% identity on 478 AAs), C6ED55 (100% identity on 478 AAs), C6UK68 (100% identity on 478 AAs)
PDB: -
Predictions (obtained from PredictProtein.org)
Subcellular Localization (reliability in brackets)
Archaea: -
Bacteria: -
Eukarya: -
Gene Ontology (reliability in brackets)
Molecular Function Ontology: -
Biological Process Ontology:GO:0022900 (50%), GO:0006807 (37%)
 
Predicted features:
Disulfid bridges: -
Transmembrane helices:6 to 23 going outwards
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.

for sqr

Protein data table for BioBrick BBa_ automatically created by the BioBrick-AutoAnnotator version 1.0
Nucleotide sequence in RFC 10: (underlined part encodes the protein)
 ATGGCTCAT ... CCTCCAGACTAA
 ORF from nucleotide position 1 to 1278 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)

101 
201 
301 
401 
MAHIVVIGAGIGGLPTAYELRHLLTTDHTVTLIADTPHFTFIPSLPWVALGLKRLDQVQLPLPTLARRHGLHWVQGAVQQINPQERHVLVGSDAKRIDYD
YVVIAPGAALNLDALPGLGPETGFTQSVCNPHHALLAHEAWEKFIQNPGPLVVGAAPGASCFGPAYEFALLADWQLRRLGLREQVPITLVTPEPYLGHLG
IGGMAHSQELVEQVLQQQDIATRANAEITAIKPDMIGLADGEQLPFAYSMVLPSFQGPAFLRDCPAISNSQGFIPVLPTYQHPAFDSVYAAGVIVELTPH
EATPIPTGLPKTGQMTEAMGMAAAHNIARQLNSNLGAPVTATLAAICMSDFGDRGIIFIADPVQREPGMVKRRRCVALEGRWVSWSKTLFELFFLTKMRW
GLTIPWFEKLGLKTLGLQLVRPLPPD*
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)45 (10.6%)
Arg (R)20 (4.7%)
Asn (N)9 (2.1%)
Asp (D)17 (4.0%)
Cys (C)5 (1.2%)
Gln (Q)23 (5.4%)
Glu (E)19 (4.5%)
Gly (G)37 (8.7%)
His (H)15 (3.5%)
Ile (I)25 (5.9%)
Leu (L)52 (12.2%)
Lys (K)10 (2.3%)
Met (M)10 (2.3%)
Phe (F)17 (4.0%)
Pro (P)37 (8.7%)
Ser (S)14 (3.3%)
Thr (T)26 (6.1%)
Trp (W)8 (1.9%)
Tyr (Y)8 (1.9%)
Val (V)29 (6.8%)
Amino acid counting
Total number:426
Positively charged (Arg+Lys):30 (7.0%)
Negatively charged (Asp+Glu):36 (8.5%)
Aromatic (Phe+His+Try+Tyr):48 (11.3%)
Biochemical parameters
Atomic composition:C2109H3298N566O579S15
Molecular mass [Da]:46327.7
Theoretical pI:6.19
Extinction coefficient at 280 nm [M-1 cm-1]:55920 / 56233 (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):good (0.74)good (0.73)acceptable (0.60)good (0.66)good (0.78)good (0.65)
Alignments (obtained from PredictProtein.org)
SwissProt: -
TrEML:B1XRD0 (100% identity on 426 AAs), B4W2D1 (64% identity on 422 AAs)
PDB:3hyv (37% identity on 386 AAs), 3hyx (37% identity on 386 AAs)
Predictions (obtained from PredictProtein.org)
Subcellular Localization (reliability in brackets)
Archaea:cytosol (100%)
Bacteria:cytosol (98%)
Eukarya:mitochondria (73%)
Gene Ontology (reliability in brackets)
Molecular Function Ontology:GO:0051287 (2%), GO:0050660 (20%)
Biological Process Ontology:GO:0055114 (13%), GO:0006116 (9%)
 
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.

cysI

<groupparts>iGEM013 IIT_Delhi</groupparts>