CDS 104 - 412 /note=I chose the function DNA Binding Protein for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. To further support this, I used HHPred, which confirmed a high probability of the match and showed good alignment with known DNA Binding proteins. Finally, I used Phamerator to compare this gene’s location and function with those in related phages, which helped reinforce the functional call. /note= /note=I found my gene calling for this to also be DNA binding protein. This was because of the equal sizing of genes on phamerator and from when I put the gene on BLASt. It came back with it having a high likelyhood of it being a DNA binding protein. /note= /note=Chennai: I did quality control (QC) for this gene and agree that this gene is included in addition to it`s function being a DNA binding protein. When blasted this gene highly matches others that hold the function as a DNA binding protein as seen on Blast and HHpred. This function is on the official functions list and is supported by information in the notebooks. /note= /note=BG: weak evidence supporting a function call. Although others in AS3 call this terminase or DNA binding protein, we`re opting to not to call function given weak evidence. CDS 372 - 1994 /note=I chose the function Terminase Large Subunit for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. To further support this, I used HHPred, which confirmed a high probability of the match and showed good alignment with known Terminase Large Subunits. Finally, I used Phamerator to compare this gene’s location and function with those in related phages, which helped reinforce the functional call. /note= /note=(I did the same and can confirm this is correct) /note= /note=Chennai: I did QC by looking at the gene`s protein sequence on BLAST and HHpred. This gene is indeed included and has high probability of having the function of a terminase large subunit as seen in matches with other genes in completed phages. This function is listed in the official list provided and evidence in the notebook supports the assignments of this function to this gene. /note= /note=BG: Changing this to terminase because in order to call a large subunit, there must be a small subunit. There are some candidate genes (ie gene 1 or last gene) that could be small terminase subunits, but evidence is too weak to call them as such. CDS 1991 - 2365 /note=I chose the function RNA binding protein for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. To further support this, I used HHPred, which confirmed a high probability of the match and showed good alignment with known RNA binding protein. Finally, I used Phamerator to compare this gene’s location and function with those in related phages, which helped reinforce the functional call. /note= /note=For this gene I enountered many pieces of evidence pointing otwards this being an RNA binding protein. This is due to the fact that it was mentioned on phamerator next to the genes listed. But mostly mainly due to the fact that it was overwhelming positive when I BLASted it on BLAST. Almost all the hits came back as an RNA binding protein. So I agree with this assessment. CDS 2382 - 4301 /note=I chose the function Portal Protein for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. To further support this, I used HHPred, which confirmed a high probability of the match and showed good alignment with known Portal Proteins. Finally, I used Phamerator to compare this gene’s location and function with those in related phages, which helped reinforce the functional call. /note= /note=This gene is undoubtedly a portal protien. Hpred, BLAST, and phamerator all display gene 4`s traits as being a Portal Protein. /note= /note=QC done by Ramanpreet Kaur CDS 4321 - 5073 /note=I chose the function Capsid Maturation Protease for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. I used Phamerator to compare this gene’s location and function with those in related phages, which helped reinforce the functional call. /note= /note=There is overwhelming evidence for this gene being a sapsid maturation protease. On phamerator it is listed as the function and on BLAST, it is the first hit. /note= /note=QC done by Ramanpreet Kaur CDS 5157 - 6470 /note=I chose the function Major Capsid Protein for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. To further support this, I used HHPred, which confirmed a high probability of the match and showed good alignment with known Major Capsid Proteins. Finally, I used Phamerator to compare this gene’s location and function with those in related phages, which helped reinforce the functional call. /note= /note= I`ve looked through all the datbase and found evidence poitning towards this function being the Major Capsid protein. This is because on Phamerator it gave multiple hits based on its location that showed it was the function of the major capsid protein. And on BlAST too. Hpred didn`t give a lot, but I still was able to use the other databases to determine this. /note= /note=QC done by Ramanpreet Kaur CDS 6552 - 6740 /note=I chose no function for this gene because there was a significant match in BLAST, showing similarity to hypothetical proteins from similiar genes in other phages in the AS3 cluster. To further support this, I used HHPred, which confirmed a high probability of the match and showed good alignment with known hypothetical proteins. Finally, I used Phamerator to compare this gene’s location and function with those in related phages, which helped reinforce the functional call. /note= /note= A lot of the databases gave me incosistent results. And when I try to load an existing job for BLAST, it doesn’t load. So I can reasonably inffer the job doesn`t exist because the function doesn’t exist either. /note= /note=QC done by Ramanpreet Kaur CDS 6762 - 7349 /note=I chose the function Head to Tail Adapter for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. I used Phamerator to compare this gene’s location and function with those in related phages, which helped reinforce the functional call. /note= /note=There are many databases that show evidence that points towards the fact that this gene`s funciton is the Head to Tail Adaptor. This can be found on Phamerator when it gave a high likelihood of the function. And also on BLAST. Where most the hits were the Head to Tail adaptor function. /note= /note=QC done by Ramanpreet Kaur CDS 7360 - 7698 /note=I chose the function Head to Tail Stopper for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. To further support this, I used HHPred, which confirmed a high probability of the match and showed good alignment with known Head to Tail Stoppers. Finally, I used Phamerator to compare this gene’s location and function with those in related phages, which helped reinforce the functional call. /note= /note= The reason I thin that this function is a head to tail stopper is because of the fact that phamerator and Blast both provide evidence towards it being that function. H-Pred also provides adequate evidence of it being hgead-to-tail Stopper. /note= /note=QC done by Ramanpreet Kaur CDS 7703 - 7957 /note=I chose no function for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. I used Phamerator to compare this gene’s location and function with those in related phages, which helped reinforce the functional call. /note= /note=  This function isn`t very apparent. It doesn`t appear on the list of genes on phamerator. So I can`t determine it there. And it also isn`t consistently hitting on H Pred. And on BLAST, its gives a lot of hits for a "hypothetical protein". This all leads me to believe that the function for this gene doesn`t exist. /note= /note=QC done by Ramanpreet Kaur CDS 7950 - 8390 /note=I chose the function Tail Terminase for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. To further support this, I used HHPred, which confirmed a high probability of the match and showed good alignment with known Tail Terminases. Finally, I used Phamerator to compare this gene’s location and function with those in related phages, which helped reinforce the functional call. /note= /note=There is a lot of evidence pointing towards this gene being a tail terminator. This is because the phamerator suggests that gene 11 is a tail terminator as well as Blast. Blast gave many hits towards a tail terminator function. H-Pred alongside BLAST also gave a lot of hits towards tail terminator. /note= /note=QC done by Ramanpreet Kaur CDS 8426 - 9007 /note=I chose the function Major Tail Protein for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. To further support this, I used HHPred, which confirmed a high probability of the match and showed good alignment with known Major Tail Proteins. Finally, I used Phamerator to compare this gene’s location and function with those in related phages, which helped reinforce the functional call. /note= /note=QC done by Ramanpreet Kaur /note= /note= I think it is most likely a major tail protein because of the phamerator hits as well as the hits on H pred. Both of these databases both show high likelyhood of it having the function of the major tail protein. The BLAST results also show many hits for the major tail protein. CDS 9108 - 9461 /note=I chose the function Tail Assembly Chaperone for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. I used Phamerator to compare this gene’s location and function with those in related phages, which helped reinforce the functional call. /note= /note=QC done by Ramanpreet Kaur /note= /note=  I believe that the function of this gene is Major Tail Assembly Chaperone. This is because the BLAST results come back with this function. And the gene`s position and function on Phamerator suggests that it is major Tail Assembly Chaperone. I didn`t get much to work on in H pred though. CDS join(9108..9434,9434..9832) /note=I chose the function Tail Assembly Chaperone for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. /note= /note= I think it is the tail assembly chaperone because that function has a lot of hits on BLAST. As well as it also being shown multiple times on phamerator. /note= /note=Chennai: I completed QC and can confirm this gene can be included with the function of being a tail assembly protein. There is not much evidence provided in the notebooks but through BLAST and partially HHpred I was able to confirm this function. In addition, we annotated this gene as a class increasing the chance of this function being accurately assigned. This is an official function on the official list. CDS 9836 - 12124 /note=I chose the function Major Capsid Protein for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. To further support this, I used HHPred, which confirmed a high probability of the match and showed good alignment with known Major Capsid Proteins. Finally, I used Phamerator to compare this gene’s location and function with those in related phages, which helped reinforce the functional call. /note= /note=QC done by Ramanpreet Kaur /note= /note=Based on the size of the gene as well as it`s location to other well known tape measure proteins, I can reasonably infer that this gene`s function is also a tape measure protein. This data was taken from phamerator. CDS 12125 - 12973 /note=I chose the function Minor Tail Protein for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. I used Phamerator to compare this gene’s location and function with those in related phages, which helped reinforce the functional call. /note= /note= /note=QC done by Ramanpreet Kaur /note= /note=Phameratior provides much evidence for the function being a minor tail protein. BLAST also has many hits for Minor tail Protein. CDS 12984 - 14228 /note=I chose the function Minor Tail Protein for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. To further support this, I used HHPred, which confirmed a high probability of the match and showed good alignment with known Minor Tail Proteins. Finally, I used Phamerator to compare this gene’s location and function with those in related phages, which helped reinforce the functional call. /note= /note=QC done by Ramanpreet Kaur /note= /note=This gene shows signs of it having the minor tail protein function. This is because it shows up on phamerator and has multiple hits on BLAST. CDS 14233 - 15198 /note=I chose the function Minor Tail Protein for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. I used Phamerator to compare this gene’s location and function with those in related phages, which helped reinforce the functional call. /note= /note=QC done by Ramanpreet Kaur /note= /note=This gene has a high probability of having the minor tail protien function. This is due to the fact that it has multiple hits on BLAST. It also shows this function on Phamerator with this gene. CDS 15208 - 15831 /note=I chose the function Minor Tail Protein for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. To further support this, I used HHPred, which confirmed a high probability of the match and showed good alignment with known Minor Tail Proteins. Finally, I used Phamerator to compare this gene’s location and function with those in related phages, which helped reinforce the functional call. /note= /note=Phameratior provides much evidence for the function being a minor tail protein. BLAST also has many hits for Minor tail Protein. There isn`t much to find on H pred though. It doesn`t mention the minor tail protein at all. /note= /note=Chennai: Through QC I confirmed this gene is included. The function of being a minor tail protein is included officially on the functions list and can be supported by information provided in the notebooks. This support is mostly seen through the BLAST which shows many matches with other genes in phages that share this function. CDS 15831 - 16253 /note=I chose the function Membrane Protein for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. To further support this, I used HHPred, which confirmed a high probability of the match and showed good alignment with known DNA Binding proteins. /note= /note=There really isn`t much evidence for this gene. But I was able to use BLAST to get a lot of hits for Membrane protein being the function for this gene. /note= /note=Chennai: QC confirmed this gene is included. Function of being a membrane protein is supported by BLAST and partially through matches seen on HHpred. This function is on the functions list and was further confirmed through evidence present in the notebooks. CDS 16263 - 16553 /note=I chose the function Hypothetical Protein for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. I used Phamerator to compare this gene’s location and function with those in related phages, which helped reinforce the functional call. /note= /note=The evidence points towards this gene having a hypotheticcal function. This is mostly due to the BLAST hits. H pred and phamerator didn`t really give sufficient evidence towards this though. /note= /note=Chennai: Through QC I concluded that this gene is included and its function can only be as a hypothetical protein. Through BLAST there are only matches with other genes with this function and no other function seen on HHpred for this gene. This information is supported by some evidence seen in the lab notebooks. CDS 16615 - 17682 /note=I chose the function Endolysin for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. I used Phamerator to compare this gene’s location and function with those in related phages, which helped reinforce the functional call. /note= /note= This gene shows signs of having the Endolysin function. This is because by using phamerator we can find similar sized genes that are Endolysin functioned. It also has many hits on BLAST. /note= /note=Chennai: QC; This gene is included and has the official function of a endolysin which is on the functions list. This evidence is supported by matches seen on BLAST and similarities seen in genes from other phages on phamerator. CDS 17682 - 18029 /note=I chose the function Membrane Protein for this gene because there was a significant match in BLAST, showing similarity to genes from other phages in the AS3 cluster. I used Phamerator to compare this gene’s location and function with those in related phages, which helped reinforce the functional call. /note= /note=There is an adequate amount of evidence to support the idea that this gene`s function is the Membrane protein. This is because Membrane protein got many hits on BLAST. It wasn`t shown on Phamerator or H pred though. But there still stands a higher probability that the gene`s function is Membrane protein. /note= /note=Chennai: Mainly through BLAST, for QC I was able to determine that this gene exists and its function is to work as a membrane protein. This function is on the official list. /note= /note=BG note: We are calling it a holin. DeepTMHMM indicates two transmembrane domains (type II holin then presumably - do see some GA-rich motifs here). Only RedFox (among related phage) has made this call. Proximity to endolysin supports this product as a potential holin. No good HHPred hits. CDS complement (18352 - 18564) /note=I figured this gene is a hypothetical protein because of my NCBI blast results. All of the hits I got said that the gene is a hyothetical protein. /note= /note=My HHPRED results are not very good as their E value is very high, so I didnt use those results for evidence /note= /note=Chennai: For QC I agree that this gene is included however, I believe this gene should be listed as NKF rather than it being a hypothetical protein due to the small amount of evidence able for collection. BLAST showed no results and there wasn`t much information provided by HHpred either. CDS complement (18566 - 18964) /note=I believe this is a hypothetical protein because of my NCBI blast results and my HHPRED results. Both show that the gene is a hypothetical protein /note= /note=Chennai: QC; I agree with this gene being included and being given the function of a hypothetical protein due to the small evidence given by BLAST assigning this functions. Alternatively, the gene may also be listed as NKF due to the little evidence provided. CDS complement (19036 - 19767) /note=Gene 28 is a hypothetical protein or NKF, with no significant hits from BLAST, SIF-BLAST, or HHPred. The surrounding genes related to Babushka are also showing "function unknown". /note= /note=(I also got the same conclusion, I used HHPRED AND NCBI BLAST results to come to this conclusion) (QC) CDS complement (20432 - 20785) /note=I chose this because of the exceptionally good hits I got in NCBI blast as well as HHPRED BLAST. Synteny also shows that the gene is supposed to be HNH endonuclease due to two completed genes in the same family as Babushka have their 29th gene named HNH endonuclease /note= /note=-- quality control Kirsty Larsen CDS complement (20782 - 21123) /note=Gene 29 is predicted to be a Helix-turn-helix DNA binding protein, based on BLAST and HHPred results. The HTH domain suggests involvement in transcriptional regulation or DNA interaction, with synteny indicating a likely role in phaGene 30 is predicted to be a Helix-turn-helix DNA binding protein, based on BLAST and HHPred results. Its HTH domain suggests it functions in DNA-binding activities, likely involved in transcription regulation or phage genome integration.ge genome integration or regulatory control. /note= /note=(I USED hhpred and NCBI blast for collecting evidence and came to the same conclusion) (QC) CDS complement (21222 - 21446) /note=Gene 32 is a hypothetical protein or NKF, with no solid hits from BLAST, SIF-BLAST, or HHPred. All surrounding genes related to Babushka are also showing "function unknown", meaning they are also NKFs. /note= /note=(yes! I came to the same conclusion aswell) (QC) CDS complement (21449 - 21892) /note=Gene 33 is a hypothetical protein or NKF, with no solid evidence hits from BLAST and SIF-BLAST, or HHPred. All other surrounding genes related to Babushka are also NKF. /note= /note=(yes! i came to the same conclusion aswell) (QC) CDS complement (21952 - 22143) /note=Gene 34 is a hypothetical protein or NKF, with no solid evidence from BLAST or SIF-BLAST, or HHPred. /note= /note=(yes! i came to the same conclusion) (QC) CDS complement (22288 - 22548) /note=Gene 35 is a hypothetical protein or NKF, with no significant matches in BLAST or SIF-BLAST, as well as no strong HHPred support. There is no structural evidence to assign a function. /note= /note=(yes! I came to the same conclusion) (QC) CDS complement (22650 - 23843) /note=Gene 38 is predicted to be a tyrosine integrase based primarily on genomic context and typical features observed in a temperate phages, Although BLAST did not give significant hits and HHPred returned matches to Baeyer-Villiger monooxygenases, these hits may reflect shared structural folds rather than function. /note= /note=(yes! I came to the same conclusion) (QC) CDS complement (23836 - 24207) /note=Gene 39 is predicted to be an immunity repressor, supported by top BLAST and SIF-BLAST hits to phage repressors. HHPred results align with DNA-binding transcriptional repressors, often using helix-turn-helix motifs. This protein likely regulates the switch between lysogenic and lytic cycles and confers superinfection immunity. /note= /note=(yes! I came to the same conclusion as well) (QC) CDS 24426 - 24695 /note=Gene 40 is predicted to encode a helix-turn-helix DNA binding domain, based on top BLAST and SIF-BLAST hits. HHPred results show high confidence alignment to transcriptional regulators. This protein is likely involved in DNA sequence recognition and transcriptional control. /note= /note=(yes! i came to the same conclusion as well) (QC) /note= /note=BG: Maybe Cro, but not sure we have enough evidence to call it as such yet. CDS 24696 - 24935 /note=Gene 41 is predicted to be a helix-turn-helix DNA biding domain, based on top BLAST and SIF-BLAST hits aligning it with characterized HTH domain-containing proteins. HHPred further supports this prediction with high confidence matches to known transcription factors and regulatory proteins, such as Renna12. The presence of this domain suggests that gene 41 is likely involved in DNA binding and regulation of transcriptional processes. /note= /note=(yes! i came to the same conclusion) (QC) CDS 24932 - 25945 /note=Babushka Gene 42 is predicted to be a RecE-like exonuclease based on top BLASTS and SIF-BLAST hits to known RecE family proteins. HHPred results strongly support this function, with high confidence to RecE-like exonucleases involved in DNA end processing during recombination, such as the phage Renna12. This protein is likely involved in DNA repair and recombination processes. /note= /note=(yes! I agree with you, I came to the same conclusion) (QC) CDS 25948 - 26745 /note=Babushka 43 is predicted to be a RecT-like DNA pairing protein based on top BLAST and SIF-BLAST hits to known RecT family proteins. HHPred results strongly support this function, showing high confidence matches to RecT-like structures involved in homologous recombination like the phage KHumphrey. This protein is likely involved in DNA repair and integration process. /note= /note=(yes! I agree with you. i came to the same conclusion) (QC) CDS 26742 - 27350 /note=Predicted to be a DNA methyltransferase based on top BLAST and SIF-BLAST hits. HHPred results strongly support this call, showing alignment with known DNA methyltransferase structures such as KHumphrey. Detection of a conserved methylase domain reinforces the predicted function in DNA modification and phage defense mechanims. /note= /note=(YES! i came to the same conclusion aswell) (QC) CDS 27331 - 27798 /note=For Babushka Gene 45, I identified it as a DNA methyltransferase based on solid evidence from multiple sources. Both NCBI BLAST and SIF-BLAST returned top hits corresponding to known DNA methyltransferase such as phage Renna12. HHPred also supported this identification, with highly-probability matches to characterized methyltransferase domains. /note= /note=(YES! i agree with you i came to the same conclusion) (QC) /note= /note=BG note: SMART team, this is a confusing gene to annotate. The preceding gene has strong coding potential for about 50% of the gene, then it drops off. At the place it drops off is where the ORF for this gene starts. There is some coding potential for the start here, which overlaps the preceding gene. But coding potential is somewhat weak, then it spikes again in the second half of the ORF where it doesn`t overlap. The question is-- call the longer gene, which overlaps by about 240 bp (others have), or call the shorter version with no overlap. Could be some funny business going on here. CDS 27795 - 28172 /note=Gene 46 encodes a protein that contains a helix-turn-helix DNA binding domain, indicating its role is likely in DNA recognition and transcription regulation. This emphasizes that gene 46 functions as a regulatory protein, possibly a transcription factor, that helps control the activity of the other genes /note= /note=(yes! i came to the same conclusion as well) (QC) CDS 28169 - 28636 /note=For Babushka`s gene 47, I identified it as a RusA-like resolvase as supported consistently by both Blasts. Both NCBI BLAST and SIF-BLAST returned top hits aligning with RusA-like resolvases. HHPred results also supported this identification, matching the protein to a known RusA-like resolvases. Additionally, gene 47 shows strong similarity to phage Juno112, which is also annotated as a RusA-like resolvase, further supporting the function call. /note= /note=(YES! I came to the same conclusion as well) (QC) CDS 28633 - 29409 /note=For Babushka`s gene 48, I called it a helix-turn-helix DNA binding domain because based from the NCBI`s blast, its top hit is a helix-turn-helix DNA binding protein. This function is further supported by the results from the SIF-blast analysis CDS 29406 - 30809 /note=I choose this function because there are many matches on blast but, this gene matched phages in the AS3 cluster more in HHpred. I used HHPred to check the probability of the match and its alignment with other phage genes and a lot of results came up. I used phamerator for comparison. CDS 30806 - 31297 /note=I choose this function because there are many matches on blast but, this gene matched phages in the AS3 cluster more in HHpred. I used HHPred to check the probability of the match and its alignment with other phage genes and a lot of results came up. I used phamerator for comparison. /note= /note=Chennai: QC; This gene is included, for BLAST there are many matches with hypothetical proteins from other phages therefore I would change this gene from NKF to being a hypothetical protein functions. /note= /note=BG: Strong hit to 1NO1_A in HHPred. Agree with assessment of call done by Atlantica. CDS 31269 - 31856 /note=I choose this function because there are matches on blast where the gene matched other phages in the AS3 cluster. I used HHPred to check the probability of the match and its alignment with other phage genes and a lot of results came up but not really significant. I used phamerator for comparison. /note= /note=Chennai: QC; I`m sure this gene is included and I`m also unsure about the function therefore it could be NKF. On BLAST there are mainly matches with hypothetical proteins, however, on HHpred there are matches with other genes with various functions making it hard to predict what this gene`s function could be. CDS 31999 - 32226 /note=I choose this function because there are not a lot matches on blast where the gene matched other phages in the AS3 cluster. I used HHPred to check the probability of the match and its alignment with other phage genes and a small amount of results came up. I used phamerator for comparison and there is a match with the same/similar function. /note= /note=Chennai: QC; Similar to the other NKF genes in Babushka, BLAST shows several matches with hypothetical proteins but HHpred shows several genes with different functions. Due to this I know the gene is included but the function isn`t assigned easy with the evidence provided. CDS 32292 - 32447 /note=I choose this function because there are not a lot matches on blast where the gene matched other phages in the AS3 cluster. I used HHPred to check the probability of the match and its alignment with other phage genes and a small amount of results came up. I used phamerator for comparison. there is a match with the same/similar function using blast. Im using blast for my reasoning. /note= /note=Chennai: QC; This gene is included and has the function of being a membrane protein. This function is on the official list and its assigning can me supported by BLAST results, HHpred, and details provided in the notebook. CDS 32444 - 32716 /note=I choose this function because there are not a lot matches on blast where the gene matched other phages in the AS3 cluster. I used HHPred to check the probability of the match and its alignment with other phage genes and a small amount of results came up. I used phamerator for comparison and there is a match with the same/similar function. CDS 32713 - 32955 /note=I didn`t find a function that will match the result I blasted and also used Phamerator to confirm it. CDS 32952 - 33320 /note=There were two choices I was between. I choose this function because there are many matches on blast where the gene matched other phages in the AS3 cluster. I used HHPred to check the probability of the match and its alignment with other phage genes and a lot of results came up. I used phamerator for comparison and there is a match with the same/similar function. /note= /note=-- quality control Kirsty Larsen CDS 33317 - 33829 /note=I choose this function because there are many matches on blast where the gene matched other phages in the AS3 cluster. I used HHPred to check the probability of the match and its alignment with other phage genes and a lot of results came up. I used phamerator for comparison and there is a match with the same/similar function. /note= /note=-- quality control Kirsty Larsen CDS 33984 - 34718 /note=I choose this function because there are many matches on blast where the gene matched other phages in the AS3 cluster. I used HHPred to check the probability of the match and its alignment with other phage genes and a lot of results came up. I used phamerator for comparison and there is a match with the same/similar function. /note= -- quality control Kirsty Larsen CDS 34718 - 35062 /note=I chose this function because there are many matches on blast where the gene matched other phages in the AS3 cluster. I used HHPred to check the probability of the match and its alignment with other phage genes and a lot of results came up. I used phamerator for comparison and there is a match with the same/similar function. /note= /note=--Annotation QC Kirsty Larsen /note= /note=QC done by Ramanpreet Kaur CDS 35059 - 35397 /note=I choose this function because there are many matches on blast where the gene matched other phages in the AS3 cluster. I used HHPred to check the probability of the match and its alignment with other phage genes and a lot of results came up. /note= /note=--Annotation QC Kirsty Larsen CDS 35400 - 35561 /note=I choose this function because there are not a lot matches on blast where the gene matched other phages in the AS3 cluster. I used HHPred to check the probability of the match and its alignment with other phage genes and many results came up but, with small similarities. I used phamerator for comparison and there is a match with the same/similar function. /note= /note=--Annotation QC Kirsty Larsen CDS 35558 - 35683 /note=I choose this function because there are many matches on blast where the gene matched other phages in the AS3 cluster. I used HHPred to check the probability of the match and its alignment with other phage genes and a lot of results came up. I used phamerator for comparison and there is a match with the same/similar function. /note= /note=--Annotation QC Kirsty Larsen /note=--add DeepTMHMM ad evidence CDS 35862 - 36077 /note=I choose this function because there are not a lot matches on blast where the gene matched other phages in the AS3 cluster. I used HHPred to check the probability of the match and its alignment with other phage genes and a small amount of results came up. I used phamerator for comparison and there is a match with the same/similar function. /note= /note=--Annotation QC Kirsty Larsen CDS 36074 - 36382 /note=I choose this function because there are not a lot matches on blast where the gene matched other phages in the AS3 cluster. I used HHPred to check the probability of the match and its alignment with other phage genes and a small amount of results came up. I used phamerator for comparison and there is a match with the same/similar function. /note= /note=--Annotation QC Kirsty Larsen CDS 36379 - 36597 /note=I choose this function because there are not a lot matches on blast where the gene matched other phages in the AS3 cluster. I used HHPred to check the probability of the match and its alignment with other phage genes and a small amount of results came up. I used phamerator for comparison and there is a match with the same/similar function. /note= /note=--Annotation QC Kirsty Larsen /note=--Hypothetical Protein Maybe(double check the probability, evalue and coverage compared to NFK) CDS 36594 - 36809 /note=I choose this function because there are many matches on blast where the gene matched similarly to other phages in the AS3 cluster. I used HHPred to check the probability of the match and its alignment with other phage genes and some results came up. I used phamerator for comparison. /note= /note=--Annotation QC Kirsty Larsen /note= /note=BG note: Changed start to -4. Other AS3 phage only have the -1 bp start, which is call more frequently, but the -4 isn`t there by accident. CDS 36809 - 37000 /note=I choose this function because there are not many matches on blast where the gene matched other phages in the AS3 cluster but, theres more then on HHPred. I used HHPred to check the probability of the match and its alignment with other phage genes and not many results came up. I used phamerator for comparison. /note= /note=--Annotation QC Kirsty Larsen CDS 36997 - 37275 /note=I choose this function because there are not many matches on blast where the gene matched other phages in the AS3 cluster but, theres more then on HHPred. I used HHPred to check the probability of the match and its alignment with other phage genes and not many results came up. I used phamerator for comparison. /note= /note=--Annotation QC Kirsty Larsen CDS 37286 - 37513 /note=I choose this function because there are not a lot matches on blast where the gene matched other phages in the AS3 cluster. I used HHPred to check the probability of the match and its alignment with other phage genes and a small amount of results came up. I used phamerator for comparison and there is a match with the same/similar function. Im using blast for my reasoning since it has a 92% similarity /note= /note=--Annotation QC Kirsty Larsen /note= /note=BG: Changed start to 37286 from 37394 because it fills the space best and covers some extra coding potential. This gene has weak coding potential by genemark, which is why GM didn`t call it-- just glimmer. Other phages with this gene do call the shorter version- 37394 start site has 7 manual annotations. But if this is a real gene, then I see no reason to not call the longer version of it given the available evidence. CDS 37513 - 37767 /note=I chose this function because there are many matches on blast where the gene matched other phages in the AS3 cluster. I used HHPred to check the probability of the match and its alignment with other phage genes and a lot of results came up. I used phamerator for comparison and there is a match with the same/similar function. /note= /note=--Annotation QC Kirsty Larsen CDS 38003 - 38302 /note=I chose this function because there are multiple matches on blast where the gene matched other phages in the AS3 cluster. I used HHPred to check the probability of the match and its alignment with other phage genes, and lastly, I used phamerator for comparison and there is a match with the same function. /note= /note=--Annotation QC Kirsty Larsen