JT Correy Journal Week 4
Journal Week 4
Propose
The purpose of this assignment is to analyze the phylogenetic relationships between varying types of the SARS and COVID type virus based on their protein spikes.
Tasks
Part 1: GenBank
In this section you will take a closer look at a GenBank record and the type of data that is stored there. Once you reach the sequence data associated with the Wan et al. (2020) paper you will see that there are a variety of different ways to view the data.
Choose one of the GenBank records from the Data & Resources section above and view both the full record and the FASTA formatted sequence.
- What was the accession number of the sequence you chose?
- What information is provided in the GenBank record?
- Download the nucleotide sequence in FASTA format to your local hard drive.
- Click the Send to link in the upper right of the page. Select Complete Record, File as the Destination, and FASTA as the format. Click the Create File button. Be careful to remember where you put the file and what you name it so that you can find it later.
- Open the file that you saved with a word processor to confirm that you have the sequence and that it is in the FASTA format. In the FASTA format each sequence is preceded by a label which begins with the greater than sign (>). For example, the first 10 lines of the SARS-CoV-2 sequence is:
>MN908947.3 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA CGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAAC TAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTG TTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTC CCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTAC GTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGAT GCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTC GTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCT TCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTA ...continued
- While we could create a phlylogenetic tree with the entire genome sequence of the viruses, in this analysis we are mainly interested in the spike protein. Links have been provided to the individual spike protein sequences corresponding to each of the viral genome records listed in the Data & Tools section. We are going to "crowdsource" gathering the sequence data from 12 other viral strains that are listed in Figure 2 of Wan et al. (2002).
- Each student will be assigned a nucleotide sequence accession number from Figure 2 in class.
- The accession number I was assigned was ay278554, it corresponds to the SARS coronavirus CUHK-W1 complete genome.
- Search for the GenBank record associated with that sequence. Add a hyperlink to the GenBank record to the list of sequences in the Data & Tools section.
- Locate the spike protein accession number in the GenBank record. (Note that the spike protein is sometimes called the "S" protein.)
- The spike protein accession number is: AAP13567.1
- Add a hyperlink to the spike protein record to the list of sequences in the Data & Tools section. Be sure to format the list in the same way as it is already formatted.
- Download your assigned protein sequence in FASTA format, just like you did for the whole genome sequence.
- Add the protein sequence to your individual journal page.
- Sequence can be found below.
- Note that if you begin a line with a space character, it will be interpreted as a fixed width font and the sequences will like up nicely on the page.
- Also add the protein sequence to the talk page for this assignment. We will be creating a list of sequences for everyone in the class to use.
- Each student will be assigned a nucleotide sequence accession number from Figure 2 in class.
Sequences
CLUSTAL FORMAT: MUSCLE (3.8) multiple sequence alignment
QDF43825.1 ---------MKLLVLV-----FATLVSSYTIEKCTDFD------DRTPPSNTQFLSSHRG AGZ48818.1 ---------MKLLVLV-----FATLVSSYTIEKCLDFD------DRTPPANTQFLSSHRG ALK02457.1 ----------MFIFLF-----FLTLTSGSDLESCTTFD------DVQAPNYPQHSSSRRG AAS10463.1 ----------MFIFLL-----FLTLTSGSDLDRCTTFD------DVQAPNYTQHTSSMRG AAP13441.1 ----------MFIFLL-----FLTLTSGSDLDRCTTFD------DVQAPNYTQHTSSMRG AAP13567.1 ----------MFIFLL-----FLTLTSGSDLDRCTTFD------DVQAPNYTQHTSSMRG QHD43416.1 ----------MFVFLV-----LLPLVSSQ----CVNLT------TRTQLPPAYTNSFTRG AVP78031.1 -----------MLFFL-----FLQFALVN--SQCVNLT------GRTPLNPNYTNSSQRG ABD75323.1 --------MKILIFAF-----LVTLVKAQ--EGCGVIN------LRTQPKLTQVSSSRRG QDF43835.1 --------MKVLIVLL-----CLGLVTAQ--DGCGHIS------TKPQPLLDKFSSSRRG ABD75332.1 --------MKVLIFAL-----LFSLAKAQ--EGCGIIS------RKPQPKMEKVSSSRRG QDF43820.1 --------MKILIFAF-----LVTLVEAQ--EGCGIIS------RKPQPKMAQVSSSRRG AAZ67052.1 --------MKILILAF-----LASLAKAQ--EGCGIIS------RKPQPKMAQVSSSRRG AFS88936.1 ----MIHSVFLLMFLLTPTESYVDVGPDSVKSACIEVDIQQTFFDKTWPRPIDVSKA-DG YP_0010399 MTLLMCLLMSLLIFVRGCDSQFVDMSPASNTSECLESQVDAAAFSKLMWPYPIDPSKVDG ::. . * . *
QDF43825.1 VYYPDDIFRSNVLHLVQDHFLPFDSNVTRFITFGLN-------------FDN---PIIPF AGZ48818.1 VYYPDDIFRSNVLHLVQDHFLPFDSNVTRFITFGLN-------------FDN---PIIPF ALK02457.1 VYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHR-------------FDN---PVIPF AAS10463.1 VYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHT-------------FDD---PVIPF AAP13441.1 VYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHT-------------FGN---PVIPF AAP13567.1 VYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHT-------------FDN---PVIPF QHD43416.1 VYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVS------GTNGTKRFDN---PVLPF AVP78031.1 VYYPDTIYRSDTLVLSQGYFLPFYSNVSWYYSLTTN-------NAATKRTDN---PILDF ABD75323.1 VYYNDDIFRSDVLHLTQDYFLPFHSNLTQYFSLNIE-------SDKIVYFDN---PILKF QDF43835.1 VYYNDDIFRSDVLHLTQDYFLPFDTNLTRYLSFNMD-------SATKVYFDN---PTLPF ABD75332.1 VYYNDDIFRSDVLHLTQDYFLPFDSNLTQYFSLNID-------SNKYTYFDN---PILDF QDF43820.1 VYYNDDIFRSDVLHLTQDYFLPFDSNLTQYFSLNVD-------SDRYTYFDN---PILDF AAZ67052.1 VYYNDDIFRSNVLHLTQDYFLPFDSNLTQYFSLNVD-------SDRFTYFDN---PILDF AFS88936.1 IIYPQGRTYSNITITYQGLF-PYQGDHGDMYVYSAG--HATGTTPQKLFVANYSQDVKQF YP_0010399 IIYPLGRTYSNITLAYTGLF-PLQGDLGSQYLYSVSHAVGHDGDPTKAYISNYSLLVNDF : * *. . * * : : *
QDF43825.1 RDGVYF----AATEKSNVIRG-------------WVFGSTMNNKSQ---------SVIIM AGZ48818.1 KDGIYF----AATEKSNVIRG-------------WVFGSTMNNKSQ---------SVIIM ALK02457.1 KDGVYF----AATEKSNVVRG-------------WVFGSTMNNKSQ---------SVIII AAS10463.1 KDGIYF----AATEKSNVVRG-------------WVFGSTMNNKSQ---------SVIII AAP13441.1 KDGIYF----AATEKSNVVRG-------------WVFGSTMNNKSQ---------SVIII AAP13567.1 KDGIYF----AATEKSNVVRG-------------WVFGSTMNNKSQ---------SVIII QHD43416.1 NDGVYF----ASTEKSNIIRG-------------WIFGTTLDSKTQ---------SLLIV AVP78031.1 KDGIYF----AATEHSNIIRG-------------WIFGTTLDNTSQ---------SLLIV ABD75323.1 GDGVYF----AATEKSNVIRG-------------WVFGSTFDNTTQ---------SAIIV QDF43835.1 GDGIYF----AATEKSNVVRG-------------WIFGSTMDNTTQ---------SAIIV ABD75332.1 GDGVYF----AATEKSNVIRG-------------WIFGSSFDNTTQ---------SAIIV QDF43820.1 GDGVYF----AATEKSNVIRG-------------WIFGSTFDNTTQ---------SAVIV AAZ67052.1 GDGVYF----AATEKSNVIRG-------------WIFGSTFDNTTQ---------SAVIV AFS88936.1 ANGFVVRIGAAANSTGTVIISPSTSATIRKIYPAFMLGSSVGNFSDGKMGRFFNHTLVLL YP_0010399 DNGFVVRIGAAANSTGTIVISPSVNTKIKKAYPAFILGSSLTNTSAGQ-PLYANYSLTII :*. . *:.. ..:: . :::*::. . : : ::
QDF43825.1 NNSTNLVIRACNFELCDNPFFVVLRSNNTQIPSY------IFNNAFN-CTFEYVSKDFNL AGZ48818.1 NNSTNLVIRACNFELCDNPFFVVLKSNNTQIPSY------IFNNAFN-CTFEYVSKDFNL ALK02457.1 NNSTNVVIRACNFELCDNPFFAVSKPTGTQTHTM------IFDNAFN-CTFEYISDSFSL AAS10463.1 NNSTNVVIRACNFELCDNPFFVVSKPMGTRTHTM------IFDNAFN-CTFEYISDAFSL AAP13441.1 NNSTNVVIRACNFELCDNPFFAVSKPMGTQTHTM------IFDNAFN-CTFEYISDAFSL AAP13567.1 NNSTNVVIRACNFELCDNPFFAVSKPMGTQTHTM------IFDNAFN-CTFEYISDAFSL QHD43416.1 NNATNVVIKVCEFQFCNDPFLGVYY--HKNNKSWMESEFRVYSSANN-CTFEYVSQPFLM AVP78031.1 NNATNVIIKVCNFDFCYDP-YLSGY--YHNNKTWSIREFAVYSSYAN-CTFEYVSKSFML ABD75323.1 NNSTHIIIRVCYFNLCKDPMYTVSA--GTQKSSW------VYQSAFN-CTYDRVEKSFQL QDF43835.1 NNSTHIIIRVCYFNLCKEPMYAISN--EQHYKSW------VYQNAYN-CTYDRVEQSFQL ABD75332.1 NNSTHIIIRVCNFNLCKEPMYTVSK--GTQQSSW------VYQSAFN-CTYDRVEKSFQL QDF43820.1 NNSTHIIIRVCNFNLCKEPMYTVSR--GTQQSSW------VYQSAFN-CTYDRVERSFQL AAZ67052.1 NNSTHIIIRVCNFNLCKEPMYTVSR--GAQQSSW------VYQSAFN-CTYDRVEKSFQL AFS88936.1 PDGCGTLLRAFYCIL--EPRSGNHCPAGNSYTSF-----ATYHTPATDCSDGNYNRNASL YP_0010399 PDGCGTVLHAFYCIL--KPRTVNRCPSGTGYVSY-----FIYETVHNDCQ-STINRNASL :. ::.. : .* : : . . * . :
QDF43825.1 DIGEKPGNFKDLREFVFRNKDG--------FLHVYSGYQPISAASGLPTGF--NALKPIF AGZ48818.1 DLGEKPGNFKDLREFVFRNKDG--------FLHVYSGYQPISAASGLPTGF--NALKPIF ALK02457.1 DVAEKSGNFKHLREFVFKNKDG--------FLYVYKGYQPIDVVRDLPSGF--NILKPIF AAS10463.1 DVSEKSGNFKHLREFVFKNKDG--------FLYVYKGYQPIDVVRDLPSGF--NTLKPIF AAP13441.1 DVSEKSGNFKHLREFVFKNKDG--------FLYVYKGYQPIDVVRDLPSGF--NTLKPIF AAP13567.1 DVSEKSGNFKHLREFVFKNKDG--------FLYVYKGYQPIDVVRDLPSGF--NTLKPIF QHD43416.1 DLEGKQGNFKNLREFVFKNIDG--------YFKIYSKHTPINLVRDLPQGF--SALEPLV AVP78031.1 NISGNGGLFNTLREFVFRNVDG--------HFKIYSKFTPVNLNRGLPTGL--SVLQPLV ABD75323.1 DTSPKTGNFTDLREFVFKNRDG--------FFTAYQTYTPVNLLRGLPSGL--SVLKPIL QDF43835.1 DTAPQTGNFKDLREYVFKNKDG--------FLSVYNAYSPIDIPRGLPVGF--SVLKPIL ABD75332.1 DTAPKTGNFKDLREYVFKNKGG--------FLRVYQTYTAVNLPRGFPAGF--SVLRPIL QDF43820.1 DTAPKTGNFKDLREYVFKNRDG--------FLSVYQTYTAVNLPRGLPIGF--SVLRPIL AAZ67052.1 DTAPKTGNFKDLREYVFKNRDG--------FLSVYQTYTAVNLPRGLPIGF--SVLRPIL AFS88936.1 NSFKE---YFNLRNCTFMYTYNITEDEILEWFGITQTAQGVHLFSSRYVDLYGGNMFQFA YP_0010399 NSFK---SFFDLVNCTFFNSWDITADETKEWFGITQDTQGVHLYSSRKGDLYGGNMFRFA : : * : .* . : . : . .: . : :
QDF43825.1 KLPLGINITNFRTLLTAF------PPNPGYWGTSAAAYFVGYLKPTTFMLKYDENGTITD AGZ48818.1 KLPLGINITNFRTLLTAF------PPRPDYWGTSAAAYFVGYLKPTTFMLKYDENGTITD ALK02457.1 KLPLGINITNFRAILTAF------LPAQDTWGTSAAAYFVGYLKPATFMLKYDENGTITD AAS10463.1 KLPLGINITNFRAILTAF------SPAQDTWGTSAAAYFVGYLKPTTFMLKYDENGTITD AAP13441.1 KLPLGINITNFRAILTAF------SPAQDIWGTSAAAYFVGYLKPTTFMLKYDENGTITD AAP13567.1 KLPLGINITNFRAILTAF------SPAQDTWGTSAAAYFVGYLKPTTFMLKYDENGTITD QHD43416.1 DLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITD AVP78031.1 ELPVSINITKFRTLLTIHRGD---PMPNNGWTAFSAAYFVGYLKPRTFMLKYNENGTITD ABD75323.1 KLPFGINITSFRVVMAMF------SKTTSNYVPESAAYYVGNLKQSTFMLSFNQNGTIVD QDF43835.1 KLPIGINITSFKVVMSMF------SRTTSNFLPEVAAYFVGNLKYSTFMLNFNENGTITD ABD75332.1 KLPFGINITSYRVVMTMF------SQFNSNFLPESAAYYVGNLKYTTFMLSFNENGTITD QDF43820.1 KLPFGINITSYRVVMAMF------SQTTSNFLPESAAYYVGNLKYTTFMLRFNENGTITD AAZ67052.1 KLPFGINITSYRVVMAMF------SQTTSNFLPESAAYYVGNLKYTTFMLSFNENGTITN AFS88936.1 TLPVYDTIKYYSIIPHSIRSI---QSDRKAW----AAFYVYKLQPLTFLLDFSVDGYIRR YP_0010399 TLPVYEGIKYYTVIPRSFRSK---ANKREAW----AAFYVYKLHQLTYLLDFSVDGYIRR **. *. : : : **::* *: *::* :. :* *
QDF43825.1 AVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVAPSKEVVRFPNITNLCPFGEVFNATTF AGZ48818.1 AVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVAPSKEVVRFPNITNLCPFGEVFNATTF ALK02457.1 AVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVAPSKEVVRFPNITNLCPFGEVFNATTF AAS10463.1 AVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVVPSGDVVRFPNITNLCPFGEVFNATKF AAP13441.1 AVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVVPSGDVVRFPNITNLCPFGEVFNATKF AAP13567.1 AVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVVPSGDVVRFPNITNLCPFGEVFNATKF QHD43416.1 AVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRF AVP78031.1 AVDCALDPLSETKCTLKSLTVQKGIYQTSNFRVQPTQSVVRFPNITNVCPFHKVFNATRF ABD75323.1 AVDCSQDPLAELKCTTKSFNVSKGIYQTSNFRVSPVTEVVRFPNITNLCPFDKVFNATRF QDF43835.1 AIDCAQNPLSELKCTIKNFNVSKGIYQTSNFRVSPTHEVIRFPNITNRCPFDKVFNASRF ABD75332.1 AVDCSQNPLAELKCTIKNFNVSKGIYQTSNFRVTPTQEVVRFPNITNRCPFDKVFNASRF QDF43820.1 AIDCAQNPLAELKCTIKNFNVSKGIYQTSNFRVSPTQEVVRFPNITNRCPFDKVFNASRF AAZ67052.1 AIDCAQNPLAELKCTIKNFNVSKGIYQTSNFRVSPTQEVIRFPNITNRCPFDKVFNATRF AFS88936.1 AIDCGFNDLSQLHCSYESFDVESGVYSVSSFEAKPSGSVVEQAEGVE-CDFSPLLSGTP- YP_0010399 AIDCGHDDLSQLHCSYTSFEVDTGVYSVSSYEASATGTFIEQPNATE-CDFSPMLTGVA- *:**. : *:: :*: .: :..*:*..*.: . . .: .: .: * * ::..
QDF43825.1 PSVYAWERKRISNCVADYSVLYNSTSFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDV AGZ48818.1 PSVYAWERKRISNCVADYSVLYNSTSFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDV ALK02457.1 PSVYAWERKRISNCVADYSVLYNSTSFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDV AAS10463.1 PSVYAWERKRISNCVADYSVLYNSTSFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDV AAP13441.1 PSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDV AAP13567.1 PSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDV QHD43416.1 ASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEV AVP78031.1 PSVYAWERTKISDCIADYTVFYNSTSFSTFKCYGVSPSKLIDLCFTSVYADTFLIRFSEV ABD75323.1 PSVYAWERTKISDCVADYTVFYNSTSFSTFNCYGVSPSKLIDLCFTSVYADTFLIRFSEV QDF43835.1 PNVYAWERTKISDCVADYTVLYNSTSFSTFKCYGVSPSKLIDLCFTSVYADTFLIRSSEV ABD75332.1 PNVYAWERTKISDCVADYTVLYNSTSFSTFKCYGVSPSKLIDLCFTSVYADTFLIRSSEV QDF43820.1 PNVYAWERTKISDCVADYTVLYNSTSFSTFKCYGVSPSKLIDLCFTSVYADTFLIRSSEV AAZ67052.1 PNVYAWERTKISDCVADYTVLYNSTSFSTFKCYGVSPSKLIDLCFTSVYADTFLIRSSEV AFS88936.1 PQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMK YP_0010399 PQVYNFKRLVFSNCNYNLTKLLSLFAVDEFSCNGISPDSIARGCYSTLTVDYFAYPLSMK ..** ::* :::* : : : . .. *.* :*. : *::.: * * .
QDF43825.1 RQIAPGQTGVIADYNYKLPDDFMGC-VLAWNTRNIDATSTGNYNYKYRSLRHGKLRPFER AGZ48818.1 RQIAPGQTGVIADYNYKLPDDFTGC-VLAWNTRNIDATQTGNYNYKYRSLRHGKLRPFER ALK02457.1 RQIAPGQTGVIADYNYKLPDDFTGC-VLAWNTRNIDATQTGNYNYKYRSLRHGKLRPFER AAS10463.1 RQIAPGQTGVIADYNYKLPDDFMGC-VLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFER AAP13441.1 RQIAPGQTGVIADYNYKLPDDFMGC-VLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFER AAP13567.1 RQIAPGQTGVIADYNYKLPDDFMGC-VLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFER QHD43416.1 RQIAPGQTGKIADYNYKLPDDFTGC-VIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFER AVP78031.1 RQVAPGQTGVIADYNYKLPDDFTGC-VIAWNTAKQD---VGNYF--YRSHRSTKLKPFER ABD75323.1 RQVAPGQTGVIADYNYKLPDDFTGC-VIAWNTAKQD---VGSYF--YRSHRSSKLKPFER QDF43835.1 RQVAPGETGVIADYNYKLPDDFTGC-VIAWNTAKQD---QGQYY--YRSSRKTKLKPFER ABD75332.1 RQVAPGETGVIADYNYKLPDDFTGC-VIAWNTAQQD---QGQYY--YRSYRKEKLKPFER QDF43820.1 RQVAPGETGVIADYNYKLPDDFTGC-VIAWNTAKQD---TGHYY--YRSHRKTKLKPFER AAZ67052.1 RQVAPGETGVIADYNYKLPDDFTGC-VIAWNTAKQD---QGQYY--YRSHRKTKLKPFER AFS88936.1 SDLSVSSAGPISQFNYKQSFSNPTC-LILATVPHNLTTITKPLKYSYINKCSRLLSDDRT YP_0010399 SYIRPGSAGNIPLYNYKQSFANPTCRVMASVLANVTITKPHAYG--YIS-KCSRLTGANQ : ..:* *. :*** . * :: : * *
QDF43825.1 DISNVPFSPDGKPCTPP-AF-NCYW-----------PLNDYGFFTTNGIGYQPYRVVVLS AGZ48818.1 DISNVPFSPDGKPCTPP-AF-NCYW-----------PLNDYGFYITNGIGYQPYRVVVLS ALK02457.1 DISNVPFSPDGKPCTPP-AF-NCYW-----------PLNDYGFYITNGIGYQPYRVVVLS AAS10463.1 DISNVPFSPDGKPCTPP-AP-NCYW-----------PLNGYGFYTTSGIGYQPYRVVVLS AAP13441.1 DISNVPFSPDGKPCTPP-AL-NCYW-----------PLNDYGFYTTTGIGYQPYRVVVLS AAP13567.1 DISNVPFSPDGKPCTPP-AL-NCYW-----------PLNDYGFYTTTGIGYQPYRVVVLS QHD43416.1 DISTEIYQAGSTPCNGVEGF-NCYF-----------PLQSYGFQPTNGVGYQPYRVVVLS AVP78031.1 DLSSDE---------------NGVR-----------TLSTYDFNPNVPLEYQATRVVVLS ABD75323.1 DLSSEE---------------NGVR-----------TLSTYDFNQNVPLEYQATRVVVLS QDF43835.1 DLTSDE---------------NGVR-----------TLSTYDFYPNVPIEYQATRVVVLS ABD75332.1 DLSSDE---------------NGVY-----------TLSTYDFYPSIPVEYQATRVVVLS QDF43820.1 DLSSDDG--------------NGVY-----------TLSTYDFNPNVPVAYQATRVVVLS AAZ67052.1 DLSSDE---------------NGVR-----------TLSTYDFYPSVPVAYQATRVVVLS AFS88936.1 EVPQLVNANQYSPCVSI-VP-STVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMG YP_0010399 DVETPLYINPGEYSICRDFSPGGFSEDGQVFKRTLTQFEGGGLLIGVGTRVPMTDNLQMS :: . :. . : :.
QDF43825.1 FELL----NAPATVC-----GPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQF AGZ48818.1 FELL----NAPATVC-----GPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQF ALK02457.1 FELL----NAPATVC-----GPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQF AAS10463.1 FELL----NAPATVC-----GPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQF AAP13441.1 FELL----NAPATVC-----GPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQF AAP13567.1 FELL----NAPATVC-----GPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQF QHD43416.1 FELL----HAPATVC-----GPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQF AVP78031.1 FELL----NAPATVC-----GPKLSTQLVKNQCVNFNFNGLKGTGVLTDSSKRFQSFQQF ABD75323.1 FELL----NAPATVC-----GPKLSTSLVKNQCVNFNFNGFKGTGVLTDSSKTFQSFQQF QDF43835.1 FELL----NAPATVC-----GPKLSTGLVKNQCVNFNFNGLRGTGVLTDSSKRFQSFQQF ABD75332.1 FELL----NAPATVC-----GPKLSTQLVKNQCVNFNFNGLRGTGVLTTSSKRFQSFQQF QDF43820.1 FELL----NAPATVC-----GPKLSTQLVKNQCVNFNFNGLKGTGVLTDSSKRFQSFQQF AAZ67052.1 FELL----NAPATVC-----GPKLSTQLVKNQCVNFNFNGLKGTGVLTESSKRFQSFQQF AFS88936.1 FGITVQYGTDTNSVCPKLEFANDTKIASQLGNCVEYSLYGVSGRGVFQNCTAVGVRQQRF YP_0010399 FIISVQYGTGTDSVCPMLDLGDSLTITNRLGKCVDYSLYGVTGRGVFQNCTAVGVKQQRF * : . :** . . . .:**::.: *. * **: .. *.*
QDF43825.1 GRDVSD-FTDSVRDPKTSEILDISPCSFGGVSVITPGTNTSSEVAVLYQDVNCTDVPVAI AGZ48818.1 GRDVSD-FTDSVRDPKTSEILDISPCSFGGVSVITPGTNTSSEVAVLYQDVNCTDVPVAI ALK02457.1 GRDVLD-FTDSVRDPKTSEILDISPCSFGGVSVITPGTNTSSEVAVLYQDVNCTDVPVAI AAS10463.1 GRDVSD-FTDSVRDPKTSEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVSTLI AAP13441.1 GRDVSD-FTDSVRDPKTSEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVSTAI AAP13567.1 GRDVSD-FTDSVRDPKTSEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVSTAI QHD43416.1 GRDIAD-TTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAI AVP78031.1 GKDASD-FIDSVRDPQTLEILDITPCSFGGVSVITPGTNTSLEVAVLYQDVNCTDVPTTI ABD75323.1 GRDASD-FTDSVRDPQTLRILDISPCSFGGVSVITPGTNTSSAVAVLYQDVNCTDVPRTI QDF43835.1 GRDTSD-FTDSVRDPQTLEILDITPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVPTAI ABD75332.1 GRDTSD-FTDSVRDPQTLEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVPTSI QDF43820.1 GRDTSD-FTDSVRDPQTLEILDITPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVPTAI AAZ67052.1 GRDTSD-FTDSVRDPQTLEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVPAAI AFS88936.1 VYDAYQNLVGYYSDDGNYYCLR--ACVSVPVSVIY--DKETKTHATLFGSVACEHISSTM YP_0010399 VYDSFDNLVGYYSDDGNYYCVR--PCVSVPVSVIY--DKSTNLHATLFGSVACEHVTTMM * : . * . : .* **** : : *.*: .* * :. :
QDF43825.1 --HADQLTPAWRIYSTGNNVFQTQAGCLIGAEHVDTSY---ECDIPIGAGICASYHTVSS AGZ48818.1 --HADQLTPSWRVYSTGNNVFQTQAGCLIGAEHVDTSY---ECDIPIGAGICASYHTVSS ALK02457.1 --HADQLTPSWRVYSTGNNVFQTQAGCLIGAEHVDTSY---ECDIPIGAGICASYHTVSS AAS10463.1 --HAEQLTPAWRIYSTGNNVFQTQAGCLIGAEHVDTSY---ECDIPIGAGICASYHTVSS AAP13441.1 --HADQLTPAWRIYSTGNNVFQTQAGCLIGAEHVDTSY---ECDIPIGAGICASYHTVSL AAP13567.1 --HADQLTPAWRIYSTGNNVFQTQAGCLIGAEHVDTSY---ECDIPIGAGICASYHTVSL QHD43416.1 --HADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSY---ECDIPIGAGICASYQTQTN AVP78031.1 --HADQLTPAWRIYATGTNVFQTQAGCLIGAEHVNASY---ECDIPIGAGICASYHTASI ABD75323.1 --QADQLAPSWRVYTTGPYVFQTQAGCLIGAEHVNASY---QCDIPIGAGICASYHTASH QDF43835.1 --RADQLTPAWRVYSTGINVFQTQAGCLIGAEHVNASY---ECDIPIGAGICASYHTAST ABD75332.1 --HADQLTPAWRVYSTGVNVFQTQAGCLIGAEHVNASY---ECDIPIGAGICASYHTASV QDF43820.1 --RADQLTPAWRVYSTGVNVFQTQAGCLIGAEHVNASY---ECDIPIGAGICASYHTAST AAZ67052.1 --HADQLTPAWRVYSTGTNVFQTQAGCLIGAEHVNASY---ECDIPIGAGICASYHTAST AFS88936.1 SQYSRSTRSMLKRRDSTYGPLQTPVGCVLGL--VNSSLFVEDCKLPLGQSLCALPDTPST YP_0010399 S-QFSRLTQSNLRRRDSNIPLQTAVGCVIGLS--NNSLVVSDCKLPLGQSLCAV-PPVST :** .**::* : * :*.:*:* .:** . :
QDF43825.1 ----LRSTS----QKSI--------VAYTMSLGADSSIAYSNNTIAIPTNFSISITTEVM AGZ48818.1 ----LRSTS----QKSI--------VAYTMSLGADSSIAYSNNTIAIPTNFSISITTEVM ALK02457.1 ----LRSTS----QKSI--------VAYTMSLGADSSIAYSNNTIAIPTNFSISITTEVM AAS10463.1 ----LRSTS----QKSI--------VAYTMSLGADSSIAYSNNTIAIPTNFSISITTEVM AAP13441.1 ----LRSTS----QKSI--------VAYTMSLGADSSIAYSNNTIAIPTNFSISITTEVM AAP13567.1 ----LRSTS----QKSI--------VAYTMSLGADSSIAYSNNTIAIPTNFSISITTEVM QHD43416.1 SPRRARSVA----SQSI--------IAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEIL AVP78031.1 ----LRSTS----QKAI--------VAYTMSLGAENSIAYANNSIAIPTNFSISVTTEVM ABD75323.1 ----LRSTG----QKSI--------VAYTMSLGAENSVAYANNSIAIPTNFSISVTTEVM QDF43835.1 ----LRSVG----QKSI--------VAYTMSLGAENSIAYANNSIAIPTNFSISVTTEVM ABD75332.1 ----LRSTG----QKSI--------VAYTMSLGAENSIAYANNSIAIPTNFSISVTTEVM QDF43820.1 ----LRSVG----QKSI--------VAYTMSLGAENSIAYANNSIAIPTNFSISVTTEVM AAZ67052.1 ----LRSVG----QKSI--------VAYTMSLGAENSIAYANNSIAIPTNFSISVTTEVM AFS88936.1 ----LTPRS----VRSVPGEMRLASIAFNHPIQVDQ-LNSSYFKLSIPTNFSFGVTQEYI YP_0010399 ----FRSYSASQFQLAV--------LNYTSPIVV-TPINSSGFTAAIPTNFSFSVTQEYI . . :: : :. .: . : : . :*****::.:* * :
QDF43825.1 PVSMAKTSVDCNMYICGDSTECANLLLQYGSFCTQLNRALSGIAVEQDRNTREVFAQVKQ AGZ48818.1 PVSMAKTSVDCNMYICGDSTECANLLLQYGSFCTQLNRALSGIAVEQDRNTREVFAQVKQ ALK02457.1 PVSMAKTSVDCNMYICGDSTECANLLLQYGSFCTQLNRALSGIAVEQDRNTREVFAQVKQ AAS10463.1 PVSMAKTSVDCNMYICGDSTECANLLLQYGSFCRQLNRALSGIAAEQDRNTREVFVQVKQ AAP13441.1 PVSMAKTSVDCNMYICGDSTECANLLLQYGSFCTQLNRALSGIAAEQDRNTREVFAQVKQ AAP13567.1 PVSMAKTSVDCNMYICGDSTECANLLLQYGSFCTQLNRALSGIAAEQDRNTREVFAQVKQ QHD43416.1 PVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQ AVP78031.1 PVSMAKTSVDCTMYICGDSIECSNLLLQYGSFCTQLNRALSGIAIEQDKNTQEVFAQVKQ ABD75323.1 PVSMAKTSVDCTMYICGDSLECSNLLLQYGSFCTQLNRALSGIAVEQDKNTQEVFAQVKQ QDF43835.1 PVSMSKTSVDCTMYICGDSQECSNLLLQYGSFCTQLNRALTGIAIEQDKNTQEVFAQVKQ ABD75332.1 PVSIAKTSVDCTMYICGDSLECSNLLLQYGSFCTQLNRALTGIAIEQDKNTQEVFAQVKQ QDF43820.1 PVSMAKTSVDCTMYICGDSQECSNLLLQYGSFCTQLNRALTGVALEQDKNTQEVFAQVKQ AAZ67052.1 PVSMAKTSVDCTMYICGDSLECSNLLLQYGSFCTQLNRALSGIAIEQDKNTQEVFAQVKQ AFS88936.1 QTTIQKVTVDCKQYVCNGFQKCEQLLREYGQFCSKINQALHGANLRQDDSVRNLFASVKS YP_0010399 ETSIQKVTVDCKQYVCNGFTRCEKLLVEYGQFCSKINQALHGANLRQDESVYSLYSNIKT .:: *.:***. *:*.. * :** :**.** ::*.** * ** .. .:: .:*
QDF43825.1 MYKTPTLKD-FGG-FNFSQILPDPLKPTKRSF---IEDLLFNKVTLADAGFMKQYGECL- AGZ48818.1 MYKTPTLKD-FGG-FNFSQILPDPLKPTKRSF---IEDLLFNKVTLADAGFMKQYGECL- ALK02457.1 MYKTPTLKD-FGG-FNFSQILPDPLKPTKRSF---IEDLLFNKVTLADAGFMKQYGECL- AAS10463.1 MYKTPTLKD-FGG-FNFSQILPDPLKPTKRSF---IEDLLFNKVTLADAGFMKQYGECL- AAP13441.1 MYKTPTLKY-FGG-FNFSQILPDPLKPTKRSF---IEDLLFNKVTLADAGFMKQYGECL- AAP13567.1 MYKTPTLKY-FGG-FNFSQILPDPLKPTKRSF---IEDLLFNKVTLADAGFMKQYGECL- QHD43416.1 IYKTPPIKD-FGG-FNFSQILPDPSKPSKRSF---IEDLLFNKVTLADAGFIKQYGDCL- AVP78031.1 IYKTPPIKD-FGG-FNFSQILPDPSKPSKRSF---IEDLLFNKVTLADAGFIKQYGDCL- ABD75323.1 MYKTPTIRD-FGG-FNFSQILPDPLKPTKRSF---IEDLLYNKVTLADAGFMKQYADCL- QDF43835.1 MYKTPAIKD-FGG-FNFSQILPDPSKPTKRSF---IEDLLFNKVTLADAGFMKQYGECL- ABD75332.1 MYKTPAIKD-FGG-FNFSQILPDPSKPTKRSF---IEDLLFNKVTLADAGFMKQYGECL- QDF43820.1 MYKTPAIKD-FGG-FNFSQILPDPSKPTKRSF---IEDLLFNKVTLADAGFMKQYGECL- AAZ67052.1 MYKTPAIKD-FGG-FNFSQILPDPSKPTKRSF---IEDLLFNKVTLADAGFMKQYGECL- AFS88936.1 SQSSPIIPG-FGGDFNLTLLEPVSISTGSRSARSAIEDLLFDKVTIADPGYMQGYDDCMQ YP_0010399 T-STQTLEYGLNGDFNLTLLQVPQIGGSSSSYRSAIEDLLFDKVTIADPGYMQGYDDCMK .: : :.* **:: : . * *****::***:**.*::: * :*:
QDF43825.1 -GDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVSGTATAGWTFGAGAALQIPFAM AGZ48818.1 -GDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVSGTATAGWTFGAGAALQIPFAM ALK02457.1 -GDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVSGTATAGWTFGAGAALQIPFAM AAS10463.1 -GDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVSGTATAGWTFGAGAALQIPFAM AAP13441.1 -GDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVSGTATAGWTFGAGAALQIPFAM AAP13567.1 -GDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVSGTATAGWTFGAGAALQIPFAM QHD43416.1 -GDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM AVP78031.1 -GGISARDLICAQKFNGLTVLPPLLTDEMIAAYTAALISGTATAGWTFGAGAALQIPFAM ABD75323.1 -GGINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALISGTATAGWTFGAGAALQIPFAM QDF43835.1 -GDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVSGTATAGWTFGAGAALQIPFAM ABD75332.1 -GDISARDLICAQKFNGLTVLPPLLTDEMIAAYTAALVSGTATAGWTFGAGSALQIPFAM QDF43820.1 -GDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVSGTATAGWTFGAGAALQIPFAM AAZ67052.1 -GDISARDLICAQKFNGLTVLPPLLTDEMIAAYTAALVSGTATAGWTFGAGSALQIPFAM AFS88936.1 QGPASARDLICAQYVAGYKVLPPLMDVNMEAAYTSSLLGSIAGVGWTAGLSSFAAIPFAQ YP_0010399 QGPQSARDLICAQYVSGYKVLPPLYDPNMEAAYTSSLLGSIAGAGWTAGLSSFAAIPFAQ * ******** . * .***** :* * **::*:.. *** * .: ****
QDF43825.1 QMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALN AGZ48818.1 QMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALN ALK02457.1 QMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALN AAS10463.1 QMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALN AAP13441.1 QMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALN AAP13567.1 QMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALN QHD43416.1 QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN AVP78031.1 QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQESLTSTASALGKLQDVVNQNAQALN ABD75323.1 QMAYRFNGIGVTQNVLYENQKQIANQFNKAITQIQESLTTTSTALGKLQDVVNQNAQALN QDF43835.1 QMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALN ABD75332.1 QMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALN QDF43820.1 QMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALN AAZ67052.1 QMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALN AFS88936.1 SIFYRLNGVGITQQVLSENQKLIANKFNQALGAMQTGFTTTNEAFQKVQDAVNNNAQALS YP_0010399 SMFYRLNGVGITQQVLSENQKLIANKFNQALGAMQTGFTTSNLAFSKVQDAVNANAQALS .: **:**:*:**:** **** ***:**.*: :* .:::: *: *:**.** *****.
QDF43825.1 TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA AGZ48818.1 TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA ALK02457.1 TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA AAS10463.1 TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA AAP13441.1 TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA AAP13567.1 TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA QHD43416.1 TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA AVP78031.1 TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA ABD75323.1 TLVKQLSSNFGAISSALNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA QDF43835.1 TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA ABD75332.1 TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA QDF43820.1 TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA AAZ67052.1 TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA AFS88936.1 KLASELSNTFGAISASIGDIIQRLDVLEQDAQIDRLINGRLTTLNAFVAQQLVRSESAAL YP_0010399 KLASELSNTFGAISSSISDILARLDTVEQDAQIDRLINGRLISLNAFVSQQLVRSETAAR .*..:**..*****: :.**: *** :* :.******.*** :*:::*:***:*:
QDF43825.1 SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPA AGZ48818.1 SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPA ALK02457.1 SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPA AAS10463.1 SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPA AAP13441.1 SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPA AAP13567.1 SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPA QHD43416.1 SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPA AVP78031.1 SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYIPSQEKNFTTAPA ABD75323.1 SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPSQEKNFTTAPA QDF43835.1 SANLAATKMSECVLGQSKRVDFCGRGYHLMSFPQAAPHGVVFLHVTYVPSQEKNFTTAPA ABD75332.1 SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPA QDF43820.1 SANLAATKMSECVLGQSKRVDFCGRGYHLMSFPQAAPHGVVFLHVTYVPSQEKNFTTAPA AAZ67052.1 SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPA AFS88936.1 SAQLAKDKVNECVKAQSKRSGFCGQGTHIVSFVVNAPNGLYFMHVGYYPSNHIEVVSAYG YP_0010399 SAQLASDKVNECVKSQSKRNGFCGSGTHIVSFVVNAPNGFYFFHVGYVPTNYTNVTAAYG **:** *:.*** .**** .*** * *::** **:*. *:** * *:: :..:* .
QDF43825.1 ICHEGK---AYFPREGVFVFNGTS-------WFITQRNFFSPQIITTDNT-FVSGSCDVV AGZ48818.1 ICHEGK---AYFPREGVFVFNGTS-------WFITQRNFFSPQIITTDNT-FVSGSCDVV ALK02457.1 ICHEGK---AYFPREGVFVFNGTS-------WFITQRNFFSPQIITTDNT-FVSGSCDVV AAS10463.1 ICHEGK---AYFPREGVFVFNGTS-------WFITQRNFFSPQIITTDNT-FVSGNCDVV AAP13441.1 ICHEGK---AYFPREGVFVFNGTS-------WFITQRNFFSPQIITTDNT-FVSGNCDVV AAP13567.1 ICHEGK---AYFPREGVFVFNGTS-------WFITQRNFFSPQIITTDNT-FVSGNCDVV QHD43416.1 ICHDGK---AHFPREGVFVSNGTH-------WFVTQRNFYEPQIITTDNT-FVSGNCDVV AVP78031.1 ICHEGK---AHFPREGVFVSNGTH-------WFVTQRNFYEPKIITTDNT-FVSGNCDVV ABD75323.1 ICHEGK---AYFPREGVFVSNGSS-------WFITQRNFYSPQIITTDNT-FVAGSCDVV QDF43835.1 ICHEGK---AYFPREGVFVSNGTS-------WFITQRNFYSPQIITTDNT-FVAGSCDVV ABD75332.1 ICHEGK---AYFPREGVFVSNGTS-------WFITQRNFYSPQIITTDNT-FVAGNCDVV QDF43820.1 ICHEGK---AYFPREGVFVSNGTF-------WFITQRNFYSPQIITTDNT-FVAGNCDVV AAZ67052.1 ICHEGK---AYFPREGVFVSNGTS-------WFITQRNFYSPQIITTDNT-FVAGSCDVV AFS88936.1 LCDAANPTNCIAPVNGYFIKTNNT--RIVDEWSYTGSSFYAPEPITSLNTKYVA--PQVT YP_0010399 LCNNNNPPLCIAPIDGYFITNQTTTYSVDTEWYYTGSSFYKPEPITQANSRYVS--SDVK :* : . * :* *: . . * * .*: *: ** *: :*: :*
QDF43825.1 IGIINNTVYDPL---QPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRL AGZ48818.1 IGIINNTVYDPL---QPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEINRL ALK02457.1 IGIINNTVYDPL---QPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRL AAS10463.1 IGIINNTVYDPL---QPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQEEIDRL AAP13441.1 IGIINNTVYDPL---QPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRL AAP13567.1 IGIINNTVYDPL---QPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRL QHD43416.1 IGIVNNTVYDPL---QPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRL AVP78031.1 IGIINNTVYDPL---QPELDSFKEELDKYFKNHTSPDIDLGDISGINASVVNIQKEIDRL ABD75323.1 IGIINNTVYDPL---QPELDSFKQELDKYFKNHTSPDVDLGDISGINASVVDIQKEIDRL QDF43835.1 IGIINNTVYDPL---QPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRL ABD75332.1 IGIINNTVYDPL---QPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRL QDF43820.1 IGIINNTVYDPL---QPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRL AAZ67052.1 IGIINNTVYDPL---QPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRL AFS88936.1 YQNISTNLPPPLLGNSTGID-FQDELDEFFKNVSTSIPNFGSLTQINTTLLDLTYEMLSL YP_0010399 FDKLENNLPPPLLENSTDVD-FKDELEEFFKNVTSHGPNFAEISKINTTLLDLSDEMAML :...: ** .. :* *::**:::*** :: ::..:: **:::::: *: *
QDF43825.1 NEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTSCCSCLKG AGZ48818.1 NEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTSCCSCLKG ALK02457.1 NEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTSCCSCLKG AAS10463.1 NEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTSCCSCLKG AAP13441.1 NEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTSCCSCLKG AAP13567.1 NEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTSCCSCLKG QHD43416.1 NEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKG AVP78031.1 NEVARNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTSCCSCLKG ABD75323.1 NEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLVGLFMAIILLCYFTSCCSCCKG QDF43835.1 NEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMATILLCCMTSCCSCLKG ABD75332.1 NEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTSCCSCLKG QDF43820.1 NEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMATILLCCMTSCCSCLKG AAZ67052.1 NEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTSCCSCLKG AFS88936.1 QQVVKALNESYIDLKELGNYTYYNKWPWYIWLGFIAGLVALALCVFFILCCTGCGTNCMG YP_0010399 QEVVKQLNDSYIDLKELGNYTYYNKWPWYVWLGFIAGLVALLLCVFFLLCCTGCGTSCLG ::*.. **:* ***:***:* * *****:********:.: : ::: *.* : *
QDF43825.1 ACSCGSCC-KFDEDDSEPVLKGVKLHYT AGZ48818.1 ACSCGSCC-KFDEDDSEPVLKGVKLHYT ALK02457.1 ACSCGSCC-KFDEDDSEPVLKGVKLHYT AAS10463.1 ACSCGSCC-KFDEDDSEPVLKGVKLHYT AAP13441.1 ACSCGSCC-KFDEDDSEPVLKGVKLHYT AAP13567.1 ACSCGSCC-KFDEDDSEPVLKGVKLHYT QHD43416.1 CCSCGSCC-KFDEDDSEPVLKGVKLHYT AVP78031.1 CCSCGSCC-KFDEDDSEPVLKGVKLHYT ABD75323.1 MCSCGSCC-RFDEDDSEPVLKGVKLHYT QDF43835.1 ACSCGSCC-KFDEDDSEPVLKGVKLHYT ABD75332.1 ACSCGSCC-KFDEDDSEPVLKGVKLHYT QDF43820.1 ACSCGSCC-KFDEDDSEPVLKGVKLHYT AAZ67052.1 ACSCGSCC-KFDEDDSEPVLKGVKLHYT AFS88936.1 KLKCNRCCDRYEEYDLEP----HKVHVH YP_0010399 KMKCKNCCDSYEEYDVE------KIHVH .* ** ::* * * *:*
Part 2: Creating a phylogenetic tree with Phylogeny.fr
In order to analyze sequence data we will use the Phylogeny.fr, a free, simple to use web service dedicated to reconstructing and analyzing phylogenetic relationships between molecular sequences.
- In your browser, go to the website www.phylogeny.fr. Scroll down on the page to the section labeled ‘Phylogeny analysis’, and click on the text ‘One Click’.
- Click in the large text field labeled ‘Upload your set of sequences in FASTA, EMBL, or NEXUS format’. Copy the list of sequences from the talk page and use Ctrl-V (or command-V) to paste your sequences here, then click the “Submit” button.
- You will see a page named Alignment results. After your alignment is complete, you will see a new page named Phylogeny results. Finally, you will see a page named Tree rendering results. You will come back to these pages later. For now, find the numbered tabs located just beneath the text One Click Mode, and click on the tab labeled 3. Alignment.
- Within the alignment, individual positions are color-coded to indicate their conservation, or how similar the sequences are to each other at that position. Blue highlighting indicates high conservation (i.e., the sequences are identical or at least very similar), while gray highlighting indicates lower conservation and white highlighting indicates little if any conservation.
- Near the bottom of the page, under Outputs, click on Alignment in Clustal format. This will display your alignment in a text-only format in which each position's conservation is indicated by a symbol underneath the alignment block (“*” for invariant, “:” for highly conserved, “.” for weakly conserved, and a space for not conserved). Copy and paste this entire alignment into your individual journal entry. Use the space character at the beginning of each line so that the sequence lines up properly on your page.
- Now go back and click on the tab 6. Tree Rendering, and you will see a phylogenetic tree of the five sequences.
- On this tree, horizontal lines (branches) represent individual evolutionary lineages. By contrast, vertical lines (splits) represent mutation events, and the vertical length of each split is drawn purely for visual clarity with no biological meaning. The left-most split is called the root of the tree, and represents a hypothesis about the most recent common ancestor (MRCA) of the sequences within your tree.
- In Figure 2 of Wan et al. (2020), an outgroup called BtSCoV PDF2386 is used. However, I was unable to find this sequence in GenBank for us to use. Instead, the sequences from Figure 3C, MERS-CoV and HKU4 are provided, which essentially create two outgroups.
- The length of each branch represents the percentage change in amino acid sequence occurring along that branch, relative to the scale bar shown at the bottom of the tree. The scale bar will be a number between 0 and 1 and can be reinterpreted as a percent. For example, 0.05 would be 5%. The tree may also contain support values for each clade; shown in red on the branches, also expressed as a number between 0 and 1. 0.05 would be 5%. In general, a higher support value indicates a higher statistical confidence in a particular clade.
- Save the image to a file, upload it to the wiki, and display it on your individual journal page.
- This is the phylogenetic tree that I developed
- On this tree, horizontal lines (branches) represent individual evolutionary lineages. By contrast, vertical lines (splits) represent mutation events, and the vertical length of each split is drawn purely for visual clarity with no biological meaning. The left-most split is called the root of the tree, and represents a hypothesis about the most recent common ancestor (MRCA) of the sequences within your tree.
- Compare the tree to the multiple sequence alignment. See if you can relate the differences in the sequences to the topology of the tree diagram. Describe the relationship in your individual journal page.
- Relate your alignment to Figure 3 of the Wan et al. (2020) paper.
- for reference the article can be found here: Wan, et al. (2020). Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus.
- What are the similarities and differences between your alignment and the one shown in Figure 3?
- The code from the spike that I analyzed has a corresponding code of NTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPP-AL-NCYW-----------PLNDYGFYTTTGIGYQPY that mirros the highlighted region of the figure. This protein sequences is very similar to both the human-SARS-2002 and civet-SARS-2002, and much less similar to the 1029n-COV. There are section of the code that are maintained throughout all the protein spikes, but the putative E2 glycoprotein precursor [SARS coronavirus CUHK-W1] that I analyzed had signfificatn differences from the 2019-nCOV that is causing the pandemic we see today.
- Compare your tree to Figure 2 of the Wan et al. (2020) paper.
- What are the similarities and differences between your alignment and the one shown in Figure 2?
- The journal article had more proteins that they analyzed, so their figure had more branches. One major similarity is that both trees clearly show that the viruses that infected a single species were all very similar. Both trees have a branch with viruses from bats and a large group with viruses that infected humans. One major difference is the lengths of the branches. In both the article and the tree I constructed the branches represent mutations/changes in the protein sequence. There is much more variety in the lengths of the branches in the journal article then the tree I constructed. This could be due to the fact that there are just more samples in the article, or it could be attributed the the program differences. They used an aligned program called Clustal Omega instead of the free online software that I used. Overall, the trees look fairly similar and both display the major findings of the protein sequencing well, but the article had more data and thus a more detailed phylogenetic tree.
- What are the similarities and differences between your alignment and the one shown in Figure 2?
- Is enough information provided by Wan et al (2020) in their paper for us to reproduce their analysis? Explain your answer.
- There was not enough information in the article to produce an accurate replicate. The methods section was almost non-existent, all it did was list the programs they used. They left out a significant amount of crucial information such as where they got the protein sequences. The article, on multiple occasions, alluded to the decade of research that this group put into studying SARS type viruses, but gave no indication of how they conducted this research. The article draws firm conclusions about the origins of the Novel Corona Virus, but with a lack of methods describing their research it brings all their finding into a questionable area.
Conclusion
This week's assignment was very useful. Through the journal club we were able to fully understand the Wan et al. article and this week I was able to use that knowledge to contrast the article with my own findings. Through the formation of my own phylogenetic tree I was able to draw conclusions about the accuracy of the article. The tree that I formed supported the main finding of the article that the spike protein in the 2019-nCOV virus originated in some type of SARS virus that was around in the early 2000's.
Acknowledgements
- Yaniv Maddahi
- Yaniv and I worked as homework partners for this week. We communicated and worked together both at the end of the week 4 lab and throughout the week to create our phylogenic trees and assignment pages.
- Dr. Dahlquist
- Dr. Dahlquist served as a coach for how to begin our pages. She also instructed the class and provided us with the guiding homework document.
- Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
Jcorrey (talk) 21:49, 30 September 2020 (PDT)
References
- OpenWetWare. (2020). BIOL368/F20:Week 4. Retrieved September 30, 2020, from https://openwetware.org/wiki/BIOL368/F20:Week_4
- OpenWetWare. (2020). User:Yaniv Maddahi (Yaniv Maddahi). Retrieved September 30, 2020, from https://openwetware.org/wiki/User:YanivMaddahi
- Wan, Y., Shang, J., Graham, R., Baric, R. S., & Li, F. (2020). Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus. Journal of virology, 94(7). DOI: 10.1128/JVI.00127-20
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