Talk:20.109(S07): Bio-material engineering/Sequence analysis

Tuesday/Thursday Lab Sequence Data

team color	candidate number	sequence	relative strength	comments/notes
Green	A	XXXXXYXXXXXXXXXSGGXXSGGGXSAXQGXXXXGXXXXXXXXRXXXXXAXPXXXXXXXTXAYFXXXLXIXXXXXXTXXXXXXXXXSXXVFXDNS STIEGXXPXXXPXXALXXXXXXXXXXXXXXXXXXAXXXDXXXGXXXXXXXGXXXXXXXXXXAXXXXXTKXXXXXXXXXXXXXXXXXXXXXXXXXXX	as strong as pAu1	too many unknown codons to analyze
Green	D	XXXXXYALQASGGGGSGGGGSGGGGSASQGGGGSGTRMRDAWXLMKGYLARPVAXXRIRTKAYF*RGLVIARDLITTXXM*XXXLXXXXVFXDN XSXXXXXXXXKTXXTXXXY*VXXXXNSLXXXXXGXXXXR*XXXRRXFXXW*GDLXXXXXQFLXXXXXXNXXXXXTXXXLXLX*XXMXXNSIXYXXX	as strong as pAu1	seems as if the first stop codon may have mutated into a tyrosine, thus giving a longer gold-binding sequence
Purple	D	SGGGG SGGGG SGGGA SEIVL TQSPA LLSLS PGXRA TLSCR TSQSI SSTYL AWYQQ KPGQA PRLLI YGTSG RXTGI PYRFQ WXGSG XDFTX TISRL EPEDF AVXYC QQXAT SPRLL XGDQG GDQIR NSRTK AYF*R RLXXX XAASR SDTXC XC	weaker than pAU1	a few of the amino acids are conserved although the order is not. our sequence is longer than that of pAU1
Yellow	B	YALQA SGGGG SGGGG SGGGG SASQG GGXXX XXLXR XCXXL XXYXA RPVAX XRIRT KAYF*	weaker than pAu1	most of amino acids in variable region are uncertain
Yellow	D	YALQA SGGGG SGGGG SGGGG SASQG GGGXX LXLPT XCTXX GXXLA RXVAX XRIRT KAYF*	weaker than pAu1	sequence also fairly uncertain; no conserved amino acids observed, however, through trend of hydrophobic residues maintained
Blue	C	YALQA SGGGG SGGGG SGGGG SASQG GGGSG RMXD* TAXSN YF*LX RPV AXXRI RTKAY F*RGL VIARD LITTX XM*	weaker than pAu1	sequence was uncertain. There were no conserved amino acids. The sequence also has closely spaced stop codons compared to pAu1
Blue	D	YALQA SGGGG SGGGG SGGGX SASQG GGGSX XRGXR RXXEX GS*LX RPVAX XRIRT KAYF* RGLVI ARDLI TTXXM*	weaker than pAu1, but stronger than candidate C.	There are some conserved amino acids with pAu1. This might account for it being a better gold binder than candidate C.
sequence is very uncertain.	Pink	A	YAXQA SGGGG SGGGG SGGGG SASQG GGGSG SRXXX SXLYH FLXLA XPVAX XRIRT KAYF* RGLVI XXDLI TXXXM*	weaker binder than pAU1	presence of many uncertain amino acids
Pink	C	YALQA SGGGG SGGGG SGGGG SASQG GGGSG GRWIR CWQXX PXXLA RPVAX XRIRT KAYF*	weaker binder than pAU1	presence of many uncertain amino acids. Compared to candidate A, more amino acids match up with pAu1, better gold binder than candidate A.
Red	D	YALQA SGGGG SGGGG SGGGG SASQG GGGSG ERXLA CXKKF EWYLX RPVAX XRIRT KAYF	not really a gold binder (less colonies than pCT-CON)	Colony C sequencing failed, two glutamates in variable region
Purple	B	XXXYALQASGGGGSGGGGSGGGGSASQGGGGSGTGVLQLVKARDLARPVAXGRIRTKAYFRGLVIARDLITTVXMQNXLCSXXXXXXMGLXLLVVEGXPQLLTNVTDLYSKTPCIAFPLAKIVVVDKEYGVDSKVGEGICSHIVVSSCAKTEAITENIEKQRSNCILIENVSRIRSFITF
Purple	C	XXXYALQASGGGGSGGGGSGGGGSASQGGGGSSTRISGARRPRVRLAXPVXXGRIRTKAYFRXLXIARDLITTXXMQNXLCSXXXXXVYGXAFASCGVRTAITDKRYFVIFKNSLHCLPVGQNSSRQRVRRRFSWGDLLAYSCQFLCNSNNRKYKTAKLHLNKCMKNSIFYYIX

Wednesday/Friday Lab Sequence Data

team color	candidate number	sequence	relative strength	comments/notes
General	pCTCON	YALQA SGGGG SGGGG SGGGG SASCG GGGTS KISHF LKMES LNFIR AHTPYI NIYNC EPANP SEKNS PSTQY CYSIQ SSQVD CGGGS EQKLI SEEDL LEIQC CNKIF VQTYC VFMGL PLLVV EGEPQ LLTNV TDLYS KTPCI AFPLA KIVVV DKEYG VDSKV GEGIC SHIVV SSCAK TEAIT ENIEK QRSNC ILIES RISIF
General	pAu1	XXXXXXXXSXXXXXXXSRXXXXRXXXXCXXGTXXAXKXXTXEALXDXLTHLXHLXXXCLW QXXCL*XXXXXXIERXXXXXXXILHXXXXXXXXXSXXXXXXXXXXXXXXXXPXXXXSXTP GXXXXXXCXXXGX		failed sequencing
Green	B	YALQA SGGGG SGGGG SGGGG SASQG GGGSG LFMQL LWAHL GCLAR PVAWG RIRTK AYFRG LVIRD LITTM QNLCS CVLLV VEGEP QLLTN VTDLY SKTPC IAFPL AKIVV DKEYG VSKVG EGICS HIVVS SCAKT EAITE NIEKQ RSNCI LIENV SISFI TF	bound very well
Green	C	YALQA SGGGG SGGGG SGGGG SASQT LWELR PSTTT SSPCT LLPTL CITVQ LGTSS IATGP WLSPE FDPVA VVKLS LRPFC LCLGK PSPAG PVLAA PTTSN LRLPS PALAS GLGTS LSPST TRFCL ACLTF WVEIK SIEQN LRF	bound very well
Purple	B	XXXYALQASGGGGSGGGGSGGGGSASQGGGGSGTGVLQLVKARDLARPVAXGRIRTKAYF RGLVIARDLITTVXMQNXLCSXXXXXXMGLXLLVVEGXPQLLTNVTDLYSKTPCIAFPLA KIVVVDKEYGVDSKVGEGICSHIVVSSCAKTEAITENIEKQRSNCILIENVSRIRSFITF	Weaker than pAU1
Purple	C	XXXYALQASGGGGSGGGGSGGGGSASQGGGGSSTRISGARRPRVRLAXPVXXGRIRTKAY FRXLXIARDLITTXXMQNXLCSXXXXXVYGXAFASCGVRTAITDKRYFVIFKNSLHCLPV GQNSSRQRVRRRFSWGDLLAYSCQFLCNSNNRKYKTAKLHLNKCMKNSIFYYIX	Weaker than pAU1
Yellow	A & C	YALQA SGGGG SGGGG SGGGG SASQG GGGSG FAPVF FXR*	Very strong binder	Our protocol allowed gold binders still attached after vortexing to bud off overnight. Both sequenced candidates were the same.
Blue
Pink	7	XXXXYALQA SGGGG SGGGX SGGGX XAXXX GGGXG PRXXX XXXXX XXXXX XXXXX XXXXX XXXXX XXXXX XNXXX XXXMX XXXXX SXTXC VFMGL PLLVV EG*EP QLLTN VTDL* YSKTPC IAFPLAKIVVVDKEYGVDSKVGEGICSHIVVSSCAKTEAITENIEKQRSNCILIENV*SR IRSFITF	Approximately 3% of pAU1 binding	Sequencing failed.
Pink	8	XXXYALQA SGGGG SGGGG SGGGG SASQG GGGSG TGPVR PKGXX KDXLA RPVXW GRIRTKA YF*RXXVXXXXLITTXXM*QNXLCSXXXXXXLWXCLC*LLRGENRNY*QTLLICNIQKLL ALPSRWPK**SLTKSTASILKLVRGFARI*LSVPVLKLKQ*QKILKNSEVTAS*LKMYEV EFDLLLHLX	Approximately 5% of pAU1 Binding	Sequence may suggest gold binding
Red	sample b	YALQASGGGGSGGGGSGGGGSASQGGGXXX HAQPWGXXXXXX XLXXXXXXGXIXTKXYF*XGLVIXRDXITXXXM*XNXLCSXXXXXXXGXAFASC*GVRTAITDKRY*FVIFKNSLHCLPVGQNSSR*QRVRRRF*SW*GDLLAYSCQFLC*N*SNNRKY*KTAK*LHLN*KCMKXNSIFYYI*X	not too strong of a gold binder. only showed two more colonies over the PCT-CON. 8 compared to 6	sequencing obviously failed in the worst possible area. Our library potentially formed some sort of secondary structure obstructing the sequencing.
Red	sample c	YALQASGGGGSGGGGSGGGGSASQXGGGTX XXHGXXXXXXXL XLXXPVXXGXIXTKXYF*XGLVIXRDXXTTXXM*XXXLCSXXXXXGXGXAFASC*GVRTAITDKRY*FVIFKNSLHCLPVGQNSSR*QRVRRXF*SW*GDLLAYSCQFLC*N*SNNRKY*KTAK*LHLN*KCMKXNSIFYYI*X	moderately strong. 25 compared to the 6 on PCT-CON.	sequence failed in the library again....poor.
Blue	Sample A	YALQA SGGGG SGGGG SGGGG SASQG GGGSG WXWXK PXXXX A*XLX XXVAX XXIRT KAYF*	relatively weak gold binder, much weaker than pAu1 (200 colonies bound for Sample B vs. 1000 for pAu1)	sequencing failed to completely annotate 12 amino acid sequence
Blue	Sample B	YALQA SGGGG SGGGG SGGGG SASQG GGGXG RRRXL MXXXG TX*LX XPXXX XXIRT KAYF*	relatively weak gold binder, much weaker than pAu1 (200 vs. 1000)	sequencing failed to completely annotate 12 amino acid sequence
Blue	Sample C	YALQA SGGGG SGGGG SGGGG SASQG GGGSG KVPKL RTTSP VYXLA RPVAX XRIRT KAYF*	relatively weak gold binder, much weaker than pAu1 (200 vs. 1000)	full 12 amino acids sequenced
Blue	Sample D	YALQA SGGGG SGGGG SGGGG SASQG GGGSG XXSLK QRAAS RL*LX XPVAX XRIRT KAYF*	relatively weak gold binder, much weaker than pAu1 (200 vs. 1000)	most of 12 amino acid sequence was sequenced

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