CDS 102 - 410 /note=We`ve concluded that this gene exists and it`s function is most likely being a DNA binding protein. This function means the gene assists with control of transcription and translation, DNA repair, splicing. We inferred this was the function because when blasting the protein sequence of this gene it matched with many other bacteriophage genes that had this function. Another possible function for this gene could`ve have been a terminase small subunit, which plays a role in DNA packaging. However, we didn’t choose this function because when running the protein sequence in HHpred the bacterophages with this function had a low probability score. /note= /note=The function is DNA binding protein and is supported by AS3. BLAST and HHPred also support because the probability is 52% which is a bit low and phamaorator also allowd to compare the gene. The start and stop also match. the gene assists with control of transcription and translation, DNA repair, splicing. /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 370 - 1992 /note=We`ve concluded that this gene exists and it`s function is most likely being a terminase large subunit.. This function means the gene takes part in DNA packaging and acting as a ATP-driven molecular motor. We inferred this was the function because when blasting the protein sequence of this gene it matched with many other bacteriophage genes that had this function. /note= /note=QC by Daniela Jara /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. /note= /note=The function is terminate and is supported by AS3. BLAST and HHPred also support because the probability is 100% which is good and phamaorator also allowd to compare the gene. The start and stop also match. The gene takes part in DNA packaging and acting as a ATP-driven molecular motor. CDS 1989 - 2318 /note=We`ve concluded that this gene exists and it`s function is most likely being a RNA binding protein. This function means the gene takes part in regulating gene expression by controlling various aspects of RNA`s life cycle. We inferred this was the function because when blasting the protein sequence of this gene it matched with many other bacteriophage genes that had this function and HHpred also matched this gene with other phage genes that played a similar role. /note= /note=QC by Daniela Jara /note= /note=The function is RNA biding protein and is supported by AS3. BLAST and HHPred also support because the probability is 96% which is good and phamaorator also allowd to compare the gene. The start and stop also match. CDS 2335 - 4254 /note=We`ve concluded that this gene exists and it`s function is most likely being a portal protein. This function means the gene takes part in facilitating the entry and exit of DNA during viral replication and infection. We inferred this was the function because when blasting the protein sequence of this gene and looking at HHpred there were matches with genes from other phages that played a similar role. /note= /note=QC by Daniela Jara /note= /note=The function is portal protein and is supported by AS3. BLAST and HHPred also support because the probability is 100% which is good and phamaorator also allowd to compare the gene. The start and stop also match. CDS 4280 - 5032 /note=We`ve concluded that this gene exists and it`s function is most likely being a capsid maturation protease. This function means they facilitate the entry and exit of DNA during viral replication and infection. We inferred this was the function because when blasting the protein sequence of this gene and looking at HHpred there were matches with genes from other phages that played a similar role. /note= /note=QC by Daniela Jara /note= /note=The function is capsid maturation protease and is supported by AS3. BLAST and HHPred also support because the probability is 99% which is good and phamaorator also allowd to compare the gene. The start and stop also match. CDS 5115 - 6428 /note=We`ve concluded that this gene exists and it`s function is being a major capsid protein. The function of this gene is to serve as the primary structural building block and facilitate viral entry into host cells. We inferred this was the function because when blasting the protein sequence of this gene and looking at HHpred there were matches with genes from other phages that played a similar role. /note= /note=QC by Daniela Jara /note= /note=The function is major capsid protein and is supported by AS3. BLAST and HHPred also support because the probability is 100% which is good and phamaorator also allowd to compare the gene. CDS 6510 - 6692 /note=We`ve concluded that this gene exists and it`s a hypothetical protein. This gene has a function but it can not yet be determined. We inferred this because when blasting the protein sequence of this gene and looking at HHpred there were matches with genes from other phages that are uncharacterized as well. /note= /note=QC by Daniela Jara /note= /note=This function is NKF because the other AS3 also do not have a function name. BLAST and HHPred do provide enough information to declare a function name. The start and stop do match. CDS 6714 - 7301 /note=We`ve concluded that this gene exists and it`s function is most likely being a RNA binding protein. This function means the gene takes part in regulating gene expression by controlling various aspects of RNA`s life cycle. We inferred this was the function because when blasting the protein sequence of this gene it matched with many other bacteriophage genes that had this function and HHpred also matched this gene with other phage genes that played a similar role. /note= /note=This function is RNA binding protein and is supported by the other AS3. BLAST and HHPred also support because the probabikry is 99% which is very high. Phamerator also compared the genes locations to supporte the function. /note= /note=QC by Daniela Jara CDS 7312 - 7650 /note=The function called is head-to-tail stopper. There were hits in HHpred with a probability of 99.6 and a coverage of 97.3214% Also compared to other genes on the AS3 cluster, it showed a match. /note= /note=This function is head to tail stopper and is supported by the other AS3. BLAST and HHPred also support because the probabikry is 99% which is very high. Phamerator also compared the genes locations to supporte the function. CDS 7655 - 7909 /note=We`ve concluded that this gene exists and it`s a hypothetical protein. This gene has a function but it cannot yet be determined. We inferred this because when blasting the protein sequence of this gene and looking at HHpred there were matches with genes from other phages that are uncharacterized as well. There is also a match with the Family of unknown function on HHPred /note= /note=This function is NKF because the other AS3 also do not have a function name. BLAST and HHPred do provide enough information to declare a function name. The start and stop do match. CDS 7902 - 8342 /note=I chose the function tail terminator 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 terminator. 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 function is tail terminator and is supported by the other AS3. BLAST and HHPred also support because the probabikry is 99% which is very high. Phamerator also compared the genes locations to supporte the function. CDS 8378 - 8959 /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 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=This function is major tail protein and is supported by the other AS3. BLAST and HHPred also support because the probabikry is 99% which is very high. Phamerator also compared the genes locations to supporte the function. CDS 9060 - 9413 /note=BLAST search revealed significant similarity to tail assembly chaperone genes found in other phages, particularly within the same cluster. HHPred supported this identification by showing high probability hits to known tail assembly chaperone proteins, with good coverage and alignment. /note= /note=This function is tail assembly chaperone and is supported by the other AS3. BLAST and HHPred also support because the probabikry is 96% which is very high. Phamerator also placed this gene in the expected genomic context CDS join(9060..9386,9386..9784) /note=BLAST search revealed significant similarity to tail assembly chaperone genes found in other phages, particularly within the AS3 cluster. HHPred supported this identification by showing high probability hits to known tail assembly chaperone proteins, with good coverage and alignment. /note= /note=This function is tail assembly chaperone and is supported by the other AS3. BLAST and HHPred also support because the probabikry is 98% which is very high. Phamerator also placed this gene in the expected genomic context CDS 9788 - 12076 /note=HHPred returned a 99.7 probability with 98.95% coverage, indicating a highly confident and nearly full-length alignment to known tape measure proteins. BLAST results showed strong similarity to tape measure proteins in other phages. Phamerator also placed this gene in the expected genomic context, typically downstream of tail assembly chaperone genes and upstream of minor tail proteins consistent with the organization seen in related phage. /note= /note=This function is tape measure protein and is supported by the other AS3. BLAST and HHPred also support because the probabikry is 99% which is very high. Phamerator also placed this gene in the expected genomic context CDS 12076 - 12921 /note=This function is minor tail protein and is supported by AS3 others. BLAST and HHPred also support it because the probability is 90% which is good. The start and stop signs also match. CDS 12931 - 14175 /note=This function is minor tail protein and is supported by AS3 others. BLAST and HHPred also support it because the probability is 99% which is good. The start and stop signs also match. CDS 14180 - 15139 /note=This function is minor tail protein and is supported by AS3 others. BLAST and HHPred also support it because the probability is 92% which is good. The start and stop signs also match. CDS 15149 - 15772 /note=This function is minor tail protein and is supported by AS3 others. BLAST and HHPred also support it because the probability is 96% which is good. The start and stop signs also match. CDS 15772 - 16194 /note=This function is NKF because the other AS3 also do not have a function name. BLAST and HHPred do provide enough information to declare a function name. The start and stop do match. CDS 16204 - 16494 /note=This function is NKF because the other AS3 also do not have a function name. BLAST and HHPred do provide enough information to declare a function name. The start and stop do match. CDS 16561 - 17622 /note=This function is endolysin and is supported by the other AS3. HHPred probability is 99% which is high. The target goes from 27 to 239 which is also very good. The start and stop signs also match. CDS 17622 - 17945 /note=This gene is a membrane protein which helps cells to communicate, maintain their shape, carry out changes triggered by chemical messengers, and transport and share material. /note= /note=The function is membrane protein and is supported by the there AS3. /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 (18078 - 18209) /note=In BLAST when looking at the alignment of the protein sequence of this gene it matches completely with the DNA binding protein sequence from phage RedFox. Using this information we concluded that the function of this gene may be as a hypothetical protein. This function is unknown. /note= /note=The function is NFK because all the others AS3 also do not have a function assigned. BLAST and HHPred do not show anything to prove it has a function name. /note= /note=BG Note: This hits HTH domain of 8Q4D_D in HHPred, so we think this is a DNA binding protein CDS complement (18206 - 18520) /note=In BLAST when looking at the alignment of the protein sequence of this gene it matches completely with the DNA binding protein sequence from phage RedFox. Using this information we concluded that the function of this gene may be as a hypothetical protein. This function is unknown. /note= /note=The function is NFK because all the others AS3 also do not have a function assigned. BLAST and HHPred do not show anything to prove it has a function name. CDS complement (18517 - 18732) /note=Helix-turn-helix DNA-binding proteins regulate phage gene expression, helping control infection timing, lifecycle decisions, and ensuring successful replication and survival. /note= /note=The function is helix-turn-helix DNA binding domain. It is supported by the other AS3 functions and BLAST and HHPred also support. HHPred probabity is 99% and coverage is 77% which is high and good. CDS complement (18785 - 19504) /note=The function of this protein is currently unknown. It may have a role in phage replication, structure, or host interaction, but no confirmed function has been identified yet. /note= /note=The function name which is NfKF because all the AS3 have the same function.. BLAST and HHPred do not provide enough information but in HHPred the probabiility is 82%which is hight but the AS3 do not provide enough infirmation to give a function name. CDS complement (19926 - 20165) /note=The function name which is NfKF because all the AS3 have the same function.. BLAST and HHPred do not provide enough information but in HHPred the probabiility is 49%which is veryl ow but the AS3 do not provide enough infirmation to give a function name. /note= /note=BG Note: Changed start to 20165 as its a -4 with the preceding gene. Currently, no MAs for this call, but -4 doesn`t happen by coincidence. CDS complement (20162 - 20521) /note=After reviewing the evidence, I assigned this gene as a hypothetical protein, as both annotation groups agreed on the function, with only a minor stop codon typo. BLAST and HHPred hits both aligned to hypothetical proteins, and Phamerator confirmed this function based on comparisons with related genes. Starterator and coding potential analysis also supported the selected start site, reinforcing the final call. /note= /note=I agree with the function name which is NfKF because all the AS3 have the same function.. BLAST and HHPred do not provide enough information but in HHPred the probabiility is 20% which is very low. /note= /note=BG: changed to -4 start CDS complement (20518 - 20871) /note=After reviewing both annotation groups, I followed the group that selected glimmer, as my evidence matched theirs. BLAST and HHPred both strongly supported the function as HNH endonuclease, with high identity and low e-values, and coding potential, Starterator, and synteny analysis also aligned with this call. Based on this combined evidence, I confidently assigned the function as HNH endonuclease. /note= /note=- Checked Justin /note= /note=BG: Changed start to -4 start. /note= /note=The function is HNH endonuclease. The start and stop numbers are accurate. BLAST and HHPred both support the information because HHPred probably is 98% and 60& where both are good. CDS complement (20868 - 21209) /note=After reviewing both annotation groups, I confirmed that both agreed on the function and supporting evidence, so I selected the start site at 21209–20868, which is part of the longest ORF and supported by both Glimmer and Genemark. BLAST and HHPred strongly supported the function as helix-turn-helix DNA-binding domain protein, with high alignment scores and low e-values, and synteny with related phages confirmed this annotation. Based on this combined evidence, I confidently assigned the function as helix-turn-helix DNA-binding domain protein. /note= /note=The function is helix-turn-helix DNA binding domain because all AS3 have the same function. I agree with the start and stop numbers, Blast and HHPred also support this because the probability is 99% and coverage is 84% which both are very high. The target goes from 1 to 103 which is also very good CDS complement (21302 - 21526) /note=After reviewing the data from both annotation groups, I confirmed agreement on the start site 21526–21302, which is part of the longest ORF and supported by both Glimmer and Genemark. BLAST hits, including to SEA_RENNA12_31 and RedFox 32, showed strong alignment but no defined function, and HHPred results also did not assign a known function. Based on this evidence, I assigned the function as hypothetical protein, as no confirmed functional prediction is currently available. /note= /note=The function is NFK. I agree with the start and stop signs being the same. HHPred and Blast did not give much information and in HHPred the probability is 44%which is low but the coverage is 70 which is high but in all other AS3 clusters no function was assigned. This is why the gene is NKF CDS complement (21529 - 21972) /note=After reviewing the data, both annotation groups agreed on the function and selected start site 21972–21529, which is part of the longest ORF and supported by both Glimmer and Genemark. BLAST hits, including to SEA_JUNOI12_32 and Rattail 33, showed strong alignment but did not assign a specific function, and HHPred results were uninformative. Based on this consistent evidence, I assigned the function as hypothetical protein, as no confirmed function could be identified. /note= /note=The function is NFK. I agree with the start and stop signs being the same. HHPred and Blast did not give much information and in HHPred the probability is 78% and the coverage is 73 which is high but in all other AS3 clusters no function was assigned. This is why the gene is NKF CDS complement (22031 - 22210) /note=After reviewing both annotation groups, I confirmed that they agreed on the start site 22210–22031, which is part of the longest ORF and supported by both Glimmer and Genemark. BLAST and HHPred results did not return strong functional hits, but similar annotations in Cluster AS3 phages consistently assigned the function as unknown. Based on this, I assigned the function as unknown, supported by the consistent Cluster AS3 calls and lack of definitive functional evidence. /note= /note=The function is NFK. I agree with the start and stop signs being the same. HHPred and Blast did not give much information and in HHPred the probability is 84% but the coverage is 52 which is okay but in all other AS3 clusters no function was assigned. This is why the gene is NKF CDS complement (22358 - 22618) /note=After reviewing both annotation groups, I confirmed that they agreed on the start site 22618–22358, which is part of the longest ORF and supported by both Glimmer and Genemark. The top HHPred hit showed a probability of 78.4%, but did not confidently assign a known function, and BLAST results were uninformative. Given that this function has been consistently assigned as unknown in all Cluster AS3 phages, I assigned the function as unknown based on this /note= /note=This function is function unknown for all AS3. HHpred the coverage is only 40% which is low. BLAST does not give much information so therefore this gene does not have a function name. CDS complement (22720 - 23913) /note=The function of this gene is identified as tyrosine integrase. The top HHPred hit had a probability of 100%, with more alignments, lower e-value, and greater coverage than any other hits. In Phamerator, this function was also assigned based on comparison with other genes. /note= /note=I agree with the result of this investigation. This was because of the hits on H pred and also how the gene compares to other genes that have the function tyrosine integrase. Francis Mareendran (QC) /note= /note=The function is tyrosine integrase which other AS3 are. HHPred probablility is 100% and targets from 1 to 348 which is good. CDS complement (23906 - 24283) /note=The function of this gene is identified as an immunity repressor. The top HHPred hit had a probability of 98.8%, with more alignments, lower e-value, and higher coverage than all other hits. Additionally, the alternative hits were closely related in function. In Phamerator, this function was also assigned based on comparisons with other genes. /note= /note=H pred gave decent hits for this gene being an immunity repressor. But phamerator didn`t provide any information on what the function of this gene could possible be. Francis Mareendran (QC) /note= /note=I agree with the function being impunity repressors which are proteins that bind to and block other infections. HHpred is 98% which makes the first evidence the best. CDS 24503 - 24772 /note=The function of this gene is identified as helix-turn-helix DNA-binding. The HHPred hit had a probability of 98.9%, with more alignments, lower e-value, and greater coverage than any other hits. Phamerator also supported this function through comparisons with related genes. /note= /note=This gene did share the same characteristics with some of the same size genes in phamerator. It aslo got some hits with BLAST. the evidence does point towards the gene having the helix-turn-helix DNA binding domain. Francis Mareendran (QC) /note= /note=The function is helix-turn-helix- DNA binding where it goes after one DNA. HHPred has two types of evidence that backs it up. /note= /note=BG: Maybe Cro, but not sure we have enough evidence to call it as such yet. CDS 24773 - 25003 /note=The function of this gene is helix-turn-helix DNA Binding. On HHPred, the hit had a probability of 98.9. It also has more alignments than all the other hits, also lower e value and more coverage than any other hits. In phamerator, the function was called compared to other genes. /note= /note=This gene definitely shared a lot of characteristics with the genes in phamerator. Genes with the function Helix-turn Helix DNA binding domain. It also got decent hits on Hpred. This does support the function of the gene. Francis Mareendran (QC) CDS 25000 - 26013 /note=The function of this gene is rece-like exonuclease. On HHPred, the hit had a probability of 99.9. It has a coverage of 59.0504%. In phamerator, the function was called compared to other genes. /note= /note=This gene had connections to this function on phamerator but I didn`t see much evidence of this anywhere else really. This function is a little debateable. Francis Mareendran (QC) CDS 26014 - 26811 /note=The function of this gene is Rec-T-like DNA paring protein. On HHPred, the hit had a probability of 100. It also has more alignments than all the other hits, also lower e value and more coverage than any other hits. In phamerator, the function was called compared to other genes. /note= /note=This gene definitely shows many signs of having that function. This function shows up multiple times on phamerator and had great hit on Hpred. BLAST also provided insight into this function. Francis Mareendran (QC) CDS 26808 - 27407 /note=The function of this gene is DNA Methyltransferase. On HHPred, in 4 conservertive hits that was the function called. It has a probability of 99.9 and a coverage 94.4724%. In phamerator, the function was called compared to other genes. /note= /note=QC by Daniela Jara /note= /note=This gene shows many signs of having this function due to similar sized genes that also have the function DNA methyltransferase. It also got hits on hpred and also a lot of good hits on BLAST. Francis Mareendran (QC) CDS 27169 - 27966 /note=The function of this gene is DNA methyltransferase. On HHPred, the probability compared with what other phages in cluster AS3 called has a more higher probablity and larger sequencing length. It also has more alignments than all the other hits. In phamerator, the function was called compared to other genes. /note= /note=On phamerator this function was definitely visible through the positioning and size of similar genes. This gene`s function also showed up many times on BLAST. This all leads me to agree with this assessment of the gene`s function. Francis Mareendran (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 27963 - 28343 /note=The function of this gene is Helix-turn-helix dna binding protein. On HHPred, the hit had a probability of 98.7. It also has more alignments than all the other hits. In phamerator, the function was called compared to other genes. Also based on the function frequency, this is the function called in the AS3 cluster. /note= /note=Phamerator proves this gene`s function due to the location and sizes of genes close by. BLAST also gives a decent asmount of hits. Francis Mareendran (QC) CDS 28340 - 28810 /note=The function of this gene is RusA-Like resolvase. On HHPred, the hit had a probability of 99.5 and 91.6667% coverage. It has the highest coverage and lowest e value among the other hits. In phamerator, the function was called compared to other genes. Based on the functions frequency in the AS3 cluster this is the function called. /note= /note=This function can be found on phamerator with other genes that are the same size as this gene. BLAST and Hpred also give many hits for this gene as well. I can agree with this assenssment. Francis Mareendran (QC) CDS 28807 - 29586 /note=The function of this gene is helix-turn-helix DNA binding domain. On HHPred, the hit had a probability of 97.7 It also has more alignments than all the other hits. In phamerator, the function was called compared to other genes. Also in the function frequency AS3 clusters pahes calls this function. /note= /note=This function can be very noticable due to the evidence on phamerator for it. As well as hit getting hits on BLAST and Hpred, the evidence here is adequet enough to suggest this gene`s function. Francis Mareendran (QC) CDS 29583 - 30986 /note=The function of this gene is DNA Methylttransferase. On HHPred, the hit had a probability of 99.9, 97.4304 coverage and a smaller e value and high probabiblity than the rest of the hits . In phamerator, the function was called compared to other genes. Also The frequency of function in AS3 is DNA Methylttransferase. /note= /note=Phamertor was a little messy at deciphering what this gene could be. Ecspecuially withhow many genes are in close proximity with each other. But BLAST more than makes up for it, in terms of the amount of hits it got for this function. Francis Mareeendran (QC) CDS 30983 - 31447 /note=We`ve concluded that this gene exists and it`s a hypothetical protein. This gene has a function but it cannot yet be determined. We inferred this because when blasting the protein sequence of this gene and looking at Blast there were matches with genes from other phages that are uncharacterized as well. /note= /note=I`ve come to a different conclusion than this one. I believe that this gene`s function uis DNA methylase because of it`s location and positioning based on Phamerator and the hits I got on BLAST. Francis Mareendran (QC) /note= /note=BG: Strong hit to 1NO1_A in HHPred. Agree with assessment of call done by Atlantica. CDS 31444 - 32034 /note=The function of this gene is Hypothetical protein. On HHPred,, the first hit had a probability of 95.6 and a coverage of 18.8776% which is higher than all the other hits. Also in phamerator, comparing it to other gene of different pham, the hypothetical protein function was called. /note= /note=I agree with what this gene`s function was concluded to be. I didn`t get much out of phamerator but I was bale to find a bunch of hits on BLAST. As well as adequate enough evidence on Hpred. Francis Mareendran (QC) CDS 32189 - 32416 /note=We`ve concluded that this gene exists and it`s a hypothetical protein. This gene has a function but it cannot yet be determined. We inferred this because when blasting the protein sequence of this gene and looking at Blast there were matches with genes from other phages that are uncharacterized as well such as Renna12 and Redfox /note= /note=I agree with the conclusion drawn for this gene`s particular function. This is because I didn`t get anything out of Phamerator. And I got inconsistent results with BLAST and Hpred with this gene`s function. Francis Mareendran (QC). CDS 32481 - 32636 /note=I chose membrane protein because it got a match on HHpred with a probability of 65.4 and a coverage of 33.3333%. Also on deepTMHMM, it shows that it is has a transmembrane domain. And compared to other phages in the AS3 cluster, this was the function called. /note=-Annotation QC check Sarah /note= /note=I agree with this sentiment on this gene`s functiuon. I didn`t get substantial enough eviddence from Phamerator. But BLAST and Hpred both provided enough hits for me to also draw the same conclusion. I overall agree with this assessment. Francis Mareendran (QC). CDS 32633 - 32905 /note=We`ve concluded that this gene exists and it`s a hypothetical protein. This gene has a function but it cannot yet be determined. We inferred this because when blasting the protein sequence of this gene and looking at Blast there were matches with genes from other phages that are uncharacterized as well such as Renna12 ect... /note=Annotation QC check - Sarah CDS 32902 - 33147 /note=We`ve concluded that this gene exists and it`s a hypothetical protein. This gene has a function but it cannot yet be determined. We inferred this because when blasting the protein sequence of this gene and looking at Blast there were matches with genes from other phages that are uncharacterized as well such as Renna12 and PhluffyCoco /note=- Annotation QC check Sarah CDS 33144 - 33515 /note=In HHPred, it had a probability of 99.6 and a coverage of 82.1138%. This gene was also found in other genome in the same cluster with the same matching sequence as this gene. Also in the AS3 cluster this is the known function called for this particular gene /note=Annotation QC check- Sarah CDS 33505 - 34014 /note=I selected the function SSB protein after reviewing results. In HHPred, the top hit had a 100 probability and a coverage of 70.4142%. This gene was also found in other genome in the same cluster with the same matching sequence as this gene. Also in the AS3 cluster this is the function called for this gene. /note= /note=Annotation QC check- Sarah /note=QC by Daniela Jara CDS 34169 - 34903 /note=I selected the function NucT-Like nuclease after reviewing results. In HHPred, the top hit had a 99.43 probability and a coverage of 61.4754%. This gene was also found in other genome in the same cluster with the same matching sequence as this gene. Also it is the hit with most alignments in the genome. /note= /note=- Annotation QC check Sarah /note=QC by Daniela Jara CDS 34903 - 35262 /note=I selected the function terminase small subunit after reviewing results. In HHPred, the top hit had a 99.8 probability and a coverage of 79.8%. This gene was also found in other genome in the same cluster with the same matching sequence as this gene. /note= /note=Annotation QC check - Sarah /note=QC by Daniela Jara CDS 35259 - 35600 /note=We`ve concluded that this gene exists and it`s a hypothetical protein. This gene has a function but it cannot yet be determined. We inferred this because when blasting the protein sequence of this gene and looking at Blast there were matches with genes from Juno112 that are uncharacterized as well. /note= /note=- Annotation QC Sarah /note=QC by Daniela Jara CDS 35603 - 35767 /note=We`ve concluded that this gene exists and it`s a hypothetical protein. This gene has a function but it cannot yet be determined. We inferred this because when blasting the protein sequence of this gene and looking at Blast there were matches with genes from Juno112 that are uncharacterized as well. /note= /note=- Annotation QC check Sarah CDS 35764 - 35886 /note=We`ve concluded that this gene exists and it`s a hypothetical protein. This gene has a function but it cannot yet be determined. We inferred this because when blasting the protein sequence of this gene and looking at Blast there were matches with genes from Juno112 that are uncharacterized as well. /note= /note=- Annotation QC check Sarah CDS 36065 - 36280 /note=We`ve concluded that this gene exists and it`s a hypothetical protein. This gene has a function but it cannot yet be determined. We inferred this because when blasting the protein sequence of this gene and looking at Blast there were matches with genes from Juno112 that are uncharacterized as well. /note= /note=- - Annotation QC check Sarah CDS 36277 - 36594 /note=We`ve concluded that this gene exists and it`s a hypothetical protein. This gene has a function but it cannot yet be determined. We inferred this because when blasting the protein sequence of this gene and looking at Blast there were matches with genes from Juno112 that are uncharacterized as well. /note= /note=- - Annotation QC check Sarah CDS 36591 - 36806 /note=We`ve concluded that this gene exists and it`s a hypothetical protein. This gene has a function but it cannot yet be determined. We inferred this because when blasting the protein sequence of this gene and looking at Blast there were matches with genes from Juno112 that are uncharacterized as well. /note= /note=- - Annotation QC check Sarah CDS 36806 - 37018 /note=We`ve concluded that this gene exists and it`s a hypothetical protein. This gene has a function but it cannot yet be determined. We inferred this because when blasting the protein sequence of this gene and looking at Blast there were matches with genes from Juno112 that are uncharacterized as well. /note= /note=- Annotation QC check Sarah CDS 37018 - 37209 /note=We`ve concluded that this gene exists and it`s a hypothetical protein. This gene has a function but it cannot yet be determined. We inferred this because when blasting the protein sequence of this gene and looking at Blast there were matches with genes from Juno112 that are uncharacterized as well. /note= /note=- - Annotation QC check Sarah CDS 37206 - 37424 /note=We`ve concluded that this gene exists and it`s a hypothetical protein. This gene has a function but it cannot yet be determined. We inferred this because when blasting the protein sequence of this gene and looking at Blast there were matches with genes from Juno112 that are uncharacterized as well. /note= /note=QC by Daniela Jara CDS 37537 - 37644 /note=We`ve concluded that this gene exists and it`s a hypothetical protein. This gene has a function but it cannot yet be determined. We inferred this because when blasting the protein sequence of this gene and looking at Blast there were matches with genes from Juno112 and KHumphery that are uncharacterized as well. /note= /note=QC by Daniela Jara CDS 37634 - 37858 /note=I assigned the function helix-turn-helix DNA binding domain protein to this gene based on multiple lines of evidence. The BLAST results showed strong similarity to annotated genes in other phages, with 85% coverage and an E-value of 8.8e-9, indicating a highly significant match. HHPred reinforced this with a 99% probability. I also verified the gene`s position and synteny using Phamerator, which supported the functional call in the context of related phages. /note= /note=QC by Daniela Jara /note=BG: This gene not called by Glimmer or Genemark, but there is strong coding potential and it fills the space. Other AS3 phage have genes in this region, which is conserved at the nucleotide level. CDS 38102 - 38389 /note=I chose the function HNH endonuclease 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 HNH endonucleases. 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 by Daniela Jara