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Debbie Jacobs-Sera posted in deoxycytidylate deaminase OR nucleoside deoxyribosyltransferase.
cdshaffer posted in deoxycytidylate deaminase OR nucleoside deoxyribosyltransferase.
Debbie Jacobs-Sera posted in deoxycytidylate deaminase OR nucleoside deoxyribosyltransferase.
byrumc@cofc.edu posted in How to cite...version number for Phamerator
deoxycytidylate deaminase OR nucleoside deoxyribosyltransferase.
Link to this post | posted 18 Jun, 2025 21:18 | |
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There is a protein in this cluster which has been annotated with two different functions: deoxycytidylate deaminase and nucleoside deoxyribosyltransferase. Check the pham for this protein: PhluffyCoco_CDS_54. These two enzymes appear to be related and have an ancient common ancestor but these two enzyme activities are quite different. Be wary of BLAST alignments for this function and focus on the top HHPRED alignments or 3D predictions. For several phages in the AS cluster the HHPRED evidence is clear these are nucleoside deoxyribosyltransferase. |
Link to this post | posted 28 Jul, 2025 20:36 | |
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I checked this out and realized I needed to gain some basic (very basic) biochem) to my understanding: Nucleoside Deoxyribosyltransferase (NDT): Function: NDT transfers deoxyribose from one nucleoside to another, effectively swapping bases. Deoxycytidylate Deaminase (DCTD): Function: DCTD specifically deaminates dCMP to dUMP, removing an amine group. My question is what are the residues/domains that could help to differentiate these? Maybe, my question is how do you recognize a deaminase domain vs a transferase domain? just maybe… debbie |
Link to this post | posted yesterday, 17:24 | |
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I did not do a deep dive into the critical side chains for these two activites. I just noted that the pham (currently 246509 ) had a dichotomy of annotations and both of these terms were used. An investigation into the nomenclature revealed that the terms were not synonyms nor are they different levels of specificity, there are, as you noted, quite distinct. So I used a few members of the pham in HHPRED searches and the results were consistent across the ones I tested. For PhluffyCoco_CDS_54, the HHPRED search were quite convinging: Of all PDB hits, there were 97 hits with probability scores above 90%. Of these there was only one crystal annotated with deaminase and about 20 crystals annotated with some variant of the transferase. Also of the top 10 hits (with probabilities ranging from 99.5 to 99.7 seven were annotated deoxyribosyltransferase. So the deaminase activity is simply not supported by the HHPRED results. Thus while the two proteins do share a common fold pattern (if I had to guess it would be a nucleotide binding domain) there is really little evidence for the annotation of deaminase and quite a good bit of evidence for the deoxyribosyltransferase. |
Link to this post | posted yesterday, 17:26 | |
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Thanks Chris! |