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1844: Coronavirus ORF3a Prediction
Status: Closed

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bkoep's picture
User offline. Last seen 1 hour 42 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
PSIPRED Predictions

Conf: 962248952023898999555885446656789996999839985466210130014604
Pred: CCCCCCCCCCCCCCEEEEEECCCCCEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCEE
  AA: WKCRSKNPLLYDANYFLCWHTNCYDYCIPYNSVTSSIVITSGDGTTSPISEHDYQIGGYT
              10        20        30        40        50        60


Conf: 113344213899998535773786403210278740588898554368925430788941
Pred: EECCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCEEEEEEEEECCCCCHHCEEEEEEE
  AA: EKWESGVKDCVVLHSYFTSDYYQLYSTQLSTDTGVEHVTFFIYNKIVDEPEEHVQIHTID
              70        80        90       100       110       120


Conf: 7988336877533478984002479
Pred: CCCCCCCCCCCCCCCCCCCCCCCCC
  AA: GSSGVVNPVMEPIYDEPTTTTSVPL
             130       140
Joined: 01/19/2019
Groups: Go Science
Routine information

This is presumably the cytoplasmic part of ORF3a (UniProt P59632 for the very similar SARS-Cov-1 version). In line with this environment, no disulfides are expected by DiaNNA.

This thing is somewhat conserved in other betacov genomes; bat versions include A0A088DI21 and A0A1B3Q5V5. Below is an alignment of these guys; you can see the human-infecting SARSr-COVs have some extensions not found in the two bat versions.

>Pz1844
WKCRSKNPLLYDANYFLCWHTN
CYDYCIPYNSVTSSI-VITSGDGTTSPISEHDYQIGGYTEKWESGVKDCVVLHSYFTSDY
YQLYSTQLSTDTGVEHVTFFIYNKIVDEPEEHVQIHTIDGSSGVVNPVMEPIYDEPTTTCT
SVP-
>New|UniRef100_A0A088DI21 Uncharacterized protein n=1 Tax=Bat Hp-betacoronavirus/Zhejiang2013 TaxID=1541205 RepID=A0A088DI21_9BETC
IRCKSLVPLCADDDCFVNYNAG
GKTYCMPFDPNEPYLTLVVHQNGIT---------CGSYKLYGDVSIADRIYLVTLTKSVP
YSLQNI---FDAELCTIAFYIADCAV------IEDHTTAGKTPRLELKSDPIYEVPCATI
DVPL
>New|UniRef100_A0A1B3Q5V5 NS3 protein n=1 Tax=Rousettus bat coronavirus TaxID=1892416 RepID=A0A1B3Q5V5_9BETC
IRVHSMAPFVSTADNFAVLRTT
CSRFVFPVESSKDNVVVLTTSRGVF---------CNGIHVEGPTALSDNASIVSLFSTTV
LLLDRVEQGYDY---TVFVYISQQILRNSE--------SNPQGVVNPEFD----------
DVEL

This probably won't work, but just for the sake of fun I told Rosetta's GREMLIN to try and figure out what residues are changing together. This sort of correlation is usually indicative of close contact in the actual protein. http://openseq.org/sub.php?id=1591034373 The last time GREMLIN tried it was in 2013 without enough sequences to work with, and I don't really see that changing much: http://gremlin.bakerlab.org/pfam.php?id=PF11289&year=2013.

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