Link to this post | posted 03 Oct, 2025 17:24

cdshaffer

This raises an interesting issue about starterator numbering and while not directly related to the question at hand above (start 1 vs start 10) it is an important point in interpretation of starterator results and why Deb talks about starts 9, 10 & 11. I will give a super simple example of why it is recommended that if there are two (or more) starts that look very close in the graphical track you can consider them "the same". Here are two made up sequences that demonstrates how small sequence changes can lead clustal to artificially create different start numbers. I will use a tiny sequence right around a start codon with the smallest possible change of the insertion of a single base. Here are the two sequences: CCCATGCCC & CCCAATGCCC When clustal aligns these two the result will align like this: CCCA-TGCCC |||| ||||| CCCAATGCCC When starterator looks at this alignment the two strands do not have identical locations (the top strand has an ATG starting at base 4 of the alignment and the bottom strand has an ATG starting at base 5 of the alignment). So these two sequences will get different start numbers. But these two sequences really do have the same start, as Deb says, this is an issue with how clustal does the alignment as sequences diverge. Bottom line: don't over interpret different start numbers to mean "absolutely must be different starts if they are different numbers", instead look at the tracks at the top of the report, if the starts are tightly clustered you can assume that there are minor base differences but the starts all very likely trace back to a single start in the common ancestor and can thus be considered "the same start". Edited 03 Oct, 2025 17:37

Link to this post | posted 26 Sep, 2025 03:01
cdshaffer	Database 615 was released with 8 new phage. The whole phage starterator reports for these phage have been added to the collection found here: https://wustl.box.com/v/Actino-phage New phage in 613: ChutneyChips HippoHollow Impisi Medindi NovoPizza PaintedDog Saskia ZamZam

Link to this post | posted 14 Sep, 2025 20:09
cdshaffer	Database 613 was released with 7 new phage. The whole phage starterator reports for these phage have been added to the collection found here: https://wustl.box.com/v/Actino-phage New phage in 613: CarefulCloud HorseRider IUFootball Jalloh PhirstandPhine Rooter TailX7 Edited 14 Sep, 2025 20:09

Link to this post | posted 11 Sep, 2025 16:19
cdshaffer	Database 612 was released with 2 new phage. The whole starterator reports for these phage have been added to the collection found here: https://wustl.box.com/v/Actino-phage New phage in 612: Lunareta Montpel

Link to this post | posted 30 Aug, 2025 02:41
cdshaffer	Database 611 was released with 4 new phage. The whole starterator reports for these phage have been added to the collection found here: https://wustl.box.com/v/Actino-phage New phage in 611: Dialga, Flashwig, Grumio, WST1

Link to this post | posted 25 Aug, 2025 18:29
cdshaffer	Database 610 was released with 2 new phage. The whole starterator reports for these phage have been added to the collection found here: https://wustl.box.com/v/Actino-phage New phage in 610: ArizonaGT, Schlegelian

Link to this post | posted 17 Aug, 2025 16:02

cdshaffer

Database 609 was released with 24 new phage. The whole starterator reports for these phage have been added to the collection found here: https://wustl.box.com/v/Actino-phage Pro Tip: Sort the file by date if you want to see the most recent files like the ones below: New phage in 609: BaconCheese Blesser Bogg DanSyl44 DeerParkTS Emmetator Fingolfin ForesterFrank FrumpyGal GaloreK Kelzog Lehmann LittleMinkey Mila11 Moby Moiqah Mwanjiwa OdetoJoy PeanutPie Prudy SlySloth Topiatin TpudiCK Triad

Link to this post | posted 11 Aug, 2025 16:01

cdshaffer

Database 608 was released with 24 new phage. The whole starterator reports for these phage have been added tot he collection found here: https://wustl.box.com/v/Actino-phage Pro Tip: Sort the file by date if you want to see the most recent files like the ones below: New phage in 608: Aloe25 Amoonguss Argena Balloona BillyBobJr Blackpen Bubble Bugg CaramelLatte ChickyNuggy Clammy CocoaPuff Davielle DeGene Dirtfootball ElJefes Gwennie Kavo Kimba Lynnae PestoPenguin RockieBear Wolpertinger Zilla

Link to this post | posted 29 Jul, 2025 17:24

cdshaffer

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. Edited 29 Jul, 2025 17:30

Link to this post | posted 23 Jul, 2025 05:33
cdshaffer	database 606 was released with 21 new phage. The whole starterator reports for these phage have been added to the collection found here: https://wustl.box.com/v/Actino-phage new phage in 606: Bellris Bubbykins Caitlin Celestialunch Cloudyecho CogOmlette Dirtdigger Elfy FiveHead Gachnar JohnThicc Nikan Origami PhuzzTulsa Rocha Spinach Sultana TraderJ WorldCup Xebius YasnayaPolyana