SEA-PHAGES | Calling an ADP riboosyltransferase in DZ phage Morgana

Link to this post \| posted 23 Jun, 2023 20:32
fogartym1	There are three DZ cluster phages in addition to Morgana. In each of the three DZ phages, there is a large gene of 2622 bp annotated as ADP-ribosyltransferase In Morgana, in the same area, there are two smaller genes encoded in two different frames - gp 141 ( ~ 80 bp) and gp 142. While BLAST gives hits for ADP-ribosyltransferase for both genes, only the second gene has a HHPRED hit and also 2 conserved domain hits from CDD for ADP-ribosyltransferses. I think that there is likely a frameshift in gp 141 (since there are no 1:1 matches for gp 42) and that is why there are two separate ORFs. I know that we cannot call a frameshift, but what should we do in terms of functional annotation? I am leaning towards calling gp141 as NKF and GP 142 as ADP-ribosyltransferase. I have attached the HHPRED hit for the ADP-ribosyltransferase hit. 93Kb

Link to this post | posted 23 Jun, 2023 20:32

There are three DZ cluster phages in addition to Morgana. In each of the three DZ phages, there is a large gene of 2622 bp annotated as ADP-ribosyltransferase

In Morgana, in the same area, there are two smaller genes encoded in two different frames - gp 141 ( ~ 80 bp) and gp 142. While BLAST gives hits for ADP-ribosyltransferase for both genes, only the second gene has a HHPRED hit and also 2 conserved domain hits from CDD for ADP-ribosyltransferses. I think that there is likely a frameshift in gp 141 (since there are no 1:1 matches for gp 42) and that is why there are two separate ORFs.
I know that we cannot call a frameshift, but what should we do in terms of functional annotation? I am leaning towards calling gp141 as NKF and GP 142 as ADP-ribosyltransferase.
I have attached the HHPRED hit for the ADP-ribosyltransferase hit.

Link to this post \| posted 23 Jun, 2023 20:37
fogartym1	fogartym1 There are three DZ cluster phages in addition to Morgana. In each of the three DZ phages, there is a large gene of 2622 bp annotated as ADP-ribosyltransferase In Morgana, in the same area, there are two smaller genes encoded in two different frames - gp 141 ( ~ 80 bp) and gp 142. While BLAST gives hits for ADP-ribosyltransferase for both genes, only the second gene has a HHPRED hit and also 2 conserved domain hits from CDD for ADP-ribosyltransferses. I think that there is likely a frameshift in gp 141 (since there are no 1:1 matches for gp 42) and that is why there are two separate ORFs. I know that we cannot call a frameshift, but what should we do in terms of functional annotation? I am leaning towards calling gp141 as NKF and GP 142 as ADP-ribosyltransferase. I have attached the HHPRED hit for the ADP-ribosyltransferase hit. 58Kb

Link to this post | posted 23 Jun, 2023 20:37

fogartym1

fogartym1
There are three DZ cluster phages in addition to Morgana. In each of the three DZ phages, there is a large gene of 2622 bp annotated as ADP-ribosyltransferase

In Morgana, in the same area, there are two smaller genes encoded in two different frames - gp 141 ( ~ 80 bp) and gp 142. While BLAST gives hits for ADP-ribosyltransferase for both genes, only the second gene has a HHPRED hit and also 2 conserved domain hits from CDD for ADP-ribosyltransferses. I think that there is likely a frameshift in gp 141 (since there are no 1:1 matches for gp 42) and that is why there are two separate ORFs.
I know that we cannot call a frameshift, but what should we do in terms of functional annotation? I am leaning towards calling gp141 as NKF and GP 142 as ADP-ribosyltransferase.
I have attached the HHPRED hit for the ADP-ribosyltransferase hit.

Link to this post \| posted 28 Jun, 2023 20:17
debbie	Hi Marie, I agree,141 is Hypothetical Protein for now and you can assign ADP-ribosyltransferase to 142. interesting, GeneMark seems to include the preceding gene in a frameshift like thing….. (not that we are calling any of that… Thanks for including the data. debbie

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Calling an ADP riboosyltransferase in DZ phage Morgana