CDS complement (1 - 564) /note=Glimmer and GeneMark gave different start sites, but the Glimmer start site was chosen because it has the better Z score, is the most annotated in Starterator, and leaves less of a gap between that gene and the next. /note=HHPRED showed a probability of 79.3 for being a rob transcription factor, however the percent coverage was low at 25.6684. The other phages with the most synteny all called this a hypothetical protein. Deep TMHMM was run to see if it could be a membrane protein, but this protein most likely operates inside, not outside. CDS complement (648 - 1457) /note=Glimmer & Genemark called 1457as start, only has an overlap of 2, the start has all the coding potential for the gene, 36% frequency DNA primase/polymerase on Phagesdb. Match with Phagesdb Blast with CrunchyBoi, PineapplePluto, and HitchHiker for DNA primase/polymerase. /note= /note=Glimmer and Genemark stop sight match the stop sight on Starterator. The start sight is 1460 and the stop sight is 2863. This makes this a relatively short gene. Looking at the pham maps comparing Crunchyboi, Birdfeeder, Hitchhiker, and Tictac we see that it was retained as a gene. Due to this, this is likely a gene. There is no known function, however, NCBI Blast found a match for a hypothetical protein similar to one in Birdfeeder_3, LilyLou_3, Crunchyboi_4, and Hitchhiker_4 and their functions were DNA Helicase or a DNA Primase. Because of this I believe that Tictac 3s function might be either DNA Helicase or a DNA Primase. CDS complement (1460 - 2863) /note=Glimmer and Genemark start sight match. The start sight is 2863 and the stop sight is 1460. This genes lentgh is 1404 Base Pairs. Looking at the pham maps comparing Crunchyboi, Birdfeeder, Hitchhiker, and Tictac we see that it was retained as a gene. Due to this, this is likely a gene. There is no known function, however, NCBI Blast found a match for a hypothetical protein similar to one in Birdfeeder_3, LilyLou_3, Crunchyboi_4, and Hitchhiker_4 and their functions were DNA Helicase or a DNA Primase. Because of this I believe that Tictac 3s function might be either DNA Helicase or a DNA Primase. CDS complement (2910 - 3092) /note=Start site matches Pham report suggestions, Genemark start, and Glimmer start. When looking at possible reading frames this start site matched well with GM coding capacity. This start site has the best gap and spacer scores, longest gene length, and best Z score. While the gap is a longer than we would like, this start site is the one with the smallest gap and the longest coding potential. Phages DB blast search showed multiple phages with matching genes listed as NKF, HHPRED did not have any high probability matches. CDS complement (3147 - 4397) /note=For Tictac gene 24, Slimmer and GeneMark both agree that the start is at 4397. There are 34manual annotations found in starterator that support the start site. There were significant hits on HHpred and NCBI BLAST that identified the function as DNA helicase. So, we can determine this has a high probability of being DNA helicase gene. CDS complement (4387 - 5163) /note=Looking at both the GlimmerStart, GeneMark, and Starterator, they all suggested that the start codon be at 5163 base pairs and stop at 4387. In Starterator, it had over nine manual annotations stating this was the start codon in Tictac for this specific gene. This is a reverse gene and has a total of 777 base pairs, making it a considerable gene due to its length. I decided not to pick the longest open reading frame because it has a 143 overlap of base pairs between this gene and gene 7. This choice also has high peaks in GeneMark for coding potential and the best statistics that fully allow it to be considered a gene. When I looked at PhagesDB, the best compatible phages that had similar genes to this one were Crunchyboi, PineapplePluto, HitchHiker, YellowPanda, and TinyTimothy. I would consider this the only gene that is in this region and not any other one due to the spacing and overlap. Finding the predicted function was unsuccessful in both PhagesDB and HHpred. They both predicted in this gene and the other bacteriophages that it is an unknown function/hypothetical protein, which means we have not been able to know its full functionality within the bacteriophage. All I know is that it has some function inside of the bacteriophage; I`m just not sure what it is. So, I`ll be stating its function as a hypothetical protein. CDS complement (5156 - 5485) /note=When looking at both the Glimmer and Genemark, it marked the start codon at 5485. I decided to pick the suggested start since it had 330 base pairs and was the longest gene candidate. A gene is categorized for the length of over 120 base pairs, causing it to be almost two times the required length to be long enough for a gene. There was a slight concern of the overlap of base pairs which was 31 to be exact. The reason why that was considered to be overlooked on this matter is so we don`t remove any important functionality of the gene in its coding potential. When looking at DNAMaster and Genemark, the model presented a peak, representing an area of potential coding. Based on the information in PECAAN, the phages with this similar gene are Crunchyboi, PineapplePluto, and HitchHiker. With the overlaps within this specific gene, this is the only one in this particular region where the predicted function could be a WhiB family transcription factor CDS complement (5455 - 6006) /note=Glimmer and Genemark both agree on the same start site, 6006. This start site produces the second longest open reading frame with 552 base pairs. There is an overlap of 11 and a spacer of 12. PhagesDB`s protein blast showed a 1e-64 similarity to birdfeeder_8 which is an Ruv-C-like resolvase. HHpred confirms this gene codes for an Ruv-C-like resolvase. CDS complement (5996 - 6319) /note=This is a gene and it starts at 6,319 and it stops a 5,996. NrdH-like glutaredoxin, is what I was able to find was what gene 10 is from everything that I looked at this was the one that appeared the most on hhpred it had a 99.24% match to glutaredoxin. I also blasted this gene and the first couple of results were glutaredoxin so I made the decision that this gene is glutaredoxin. CDS complement (6372 - 6581) /note=Based off of the information on the blast it looks like the all of the ones that are similar do not have a known function such as CrunchyBoi, PineapplePluto, and Hitchhiker all of their functions are also unknown. On hhpred the highest probability was 70% percent and its function was Unknown. The suggested start was used due to it having the best looking numbers for the start of the gene. CDS complement (6589 - 8838) /note=Function confirmed by HHpred, Phamerator, and PhagesDB blast. Start and stop includes highest coding potential. Start sight confirmed by starterator. CDS complement (8831 - 9064) /note=There was no significant hit in HHpred. No membrane spanning regions shown in DeepTMHMM. GeneMark and Glimmer are the same. CDS complement (9057 - 9329) /note=Blast on DNA Master, Glimmer, GeneMark and Pham Starterator all agree on 9329 being the start coordinate. The sequences it is most similar to on phages Pineapple Pluto and Hitchhiker list the gene as a hypothetical protein. HHpred did not show statistically significant results for coding for any known proteins. It was also run on Deep TMHMM, which showed that it is very likely a protein that works inside. CDS complement (9322 - 10467) /note=Glimmer start site has the most MAs on Starterator, with an overlap of <30 bp, >2 z-score, and a spacer between 4-12. The length is consistent with other Pham members. The protein function has an e-value of 0 on PhagesDB blast. On HHPRED, the e value is 5.3e-17 with the highest probability, similar to NCBI Blast. CDS complement (10445 - 10576) /note=Glimmer and Genemark stop sight match the stop sight on Starterator. The start sight is 10576 and the stop sight is 10445. This makes this a relatively short gene. However, when looking at the pham maps compared Crunchyboi, we see that it was retained as a gene. If this was declared not to be a gene that would leave a gap larger than 50 BP. Due to this, this is likely a gene. There is no known function, however, NCBI Blast found a match for a hypothetical protein similar to one in Pineapple_Pluto_16, Crunchyboi_16, and Hitchhiker_16. CDS complement (10573 - 10704) /note=Glimmer start ATG 10,704 Stop 10,573 Reverse. Length is greater than 120 possibly qualifying it for a gene. Length is sufficient (above 30). Insufficient HHPRED probabilities /note=Other phages have homologous(corresponding) genes in the same location with no known functions. CDS complement (10761 - 11615) /note=This is a gene that starts at 11531 and stops at 10761. For this Gene, according to HHpred, the function that is coded seems to be DNA binding function with that having the highest probability of 97.19%. When I ran blasts on the amino acid sequence many closely related sequences were Unknown functions. The sequence of amino acid for this gene, it aligns closest to Pineapple Pluto phages gene. The Glimmer start/Staterator suggested start/genemark start did not match the actual start. CDS complement (11730 - 12098) /note=Genemark and Glimmer start both show that the start is 11730 and looking at the starterator it also shows that the start Number is 5 because it has 1 mannual annotator. I would say that yes it is long enough to be a gene based on the Genemark and Glimmer start information, it does have coding potential because there are peaks on the Genemark graph. This gene has similar phages which are HitchHiker, yellow panda, and Tiny Timothy while the rest of the phages are drafts. Yes, it is the only gene in the region, I blasted this gene using phagesdb and it depicted to have no function. Hence, it is a hypothetical protein. CDS complement (12098 - 12730) /note=I conclude this is a gene. Both Glimmer and Genemark called this gene and it has coding potential along the length. It is long enough at 633bp and does not overlap with any other gene in this region. This gene has also been called in Crunchyboi, Hitchhiker, and PineapplePluto. The data best support the auto-annotated start at 12730 with 16 manual annotations and no other start has a manual annotation. There are no additional upstream starts, so this is longest ORF and captures all of the coding potential. There is a large gap of 234bp, but there are no other upstream starts that could extend this gene into the gap. This start has a good RBS. The only better RBS score is for a start that would result in a gene of 12bp, which is too small and cuts out much coding potential. There is NKF that can be called based on the evidence, which corresponds to the call for Hitchhiker. HHPred predicts a domain that is similar to a primase-polymerase enzyme domain. CDS complement (12965 - 13234) /note=Glimmer start ATG 13234, Stop: 12965 Reverse(matching) /note=GeneMark Start: 13234 /note=There are 56 other matching genes on other phages using Phages DB. 46.6 HHPRED possibility (insufficient). Gap of 1 Qualifying for gene possibility Length greater than 120 qualifying for a gene. Phages have homologous(corresponding) genes in the same location with NO KNOWN FUNCTION. " CDS complement (13236 - 13589) /note=Start site was chosen because it matched the manual entries for other phage start sites, had good coding potential, gave the longest coding potential, and was the recommended start site for Glimmer and GeneMark. This start site also gives good gap, spacer, z, and final scores. It also is an ATG codon which would be the most likely start codon. While this gene is listed as No Known Function for all other phages similar to it on phages DB, it is likely a membrane protein because DeepTMHHM shows it as having one trans-membrane domain. HHpred also shows that part of the gene has a high probability of matching with cell membrane associated genes. CDS complement (13591 - 13710) /note=I was looking at the Glimmer Start and the GeneMark. It stated the start was at 13710, so I decided to pick the suggested starter since the length was longer and best due to the other option only having 24 base pairs, which is below the recommended amount to be considered a gene. With the suggested start, there are exactly 120 base pairs, meaning it`s considered a gene. When looking into the GeneMark document of TicTac, I can see there being a peak in the complementary sequence higher than 0, showing evidence there is coding potential. Looking at the phages who have this similar gene, which were Crunchyboi and PineapplePluto. Looking further into GeneMark, it didn`t show any other possible overlaps or significant gaps, meaning there isn`t a possibility for another gene to be in this sequence. When looking for a predicted function, both Crunchyboi and PineapplePluto had specified it as a No Known Function (NKF)/Hypothetical Protein. I looked at PhagesDB, and it presented no known function, but for HHpred, it presented contrasting opinions, saying it had a high probability of 89.4 percent that it could be a coiled-coil protein. Since there is no further evidence to conclude this is a coiled-coil protein-coding gene, we will state it as a hypothetical protein, but I am adding the HHpred evidence to give a possibility this is where its domain lies. CDS complement (13710 - 14006) /note=For Tictac gene 24, Glimmer and GeneMark both agree that the start at 14006. There are 23 manual annotations found in starterator that support the start site. The 14006 start also has a 4 bp overlap. Good RBS scores. There were no significant hits on HHpred or NCBI BLAST, so, we can determine that this gene has NKF. CDS complement (14003 - 14290) /note=No significant hits show in HHpred. Blast search shows coding potential, but NKF. PECAAN showed too high of a E-value, not the highest final score and too low of a z-score. Phamerator showed a potential gene match with Crunchy Boi. GeneMark agrees with Glimmer start with the number being 14290. DeepTMHMM inside topology CDS complement (14274 - 14528) /note=The start site has the most MAs on Starterator. The length is >255 despite not being the longest, and has an ATG codon. It has the required gap, spacer, z-score, and final score values. Similar function listed with other phage. The probability on HHPRED is < 90%. DeepTMHMM suggests inside topology. CDS complement (14528 - 14713) /note=This is a gene because it is the right length and has good coding potential. Start site was chosen due to it given the largest coding potential, having the best gap and spacer numbers, the best Z-score and Final score, and it also has the most common start codon of ATG. This start site also was the manually entered start site for all other phages with this gene (10 of them). This was the suggested start site of gene-mark and glimmer start as well. This gene has no known function. No other phage on phages DB have a listed function for this gene. HHpred did not give any high probability matches for this gene and DeepTMHMM shows that this is not a membrane protein. CDS complement (14785 - 15267) /note=Glimmer and Genemark start match starterator start. A large gap exists between genes downstream gene, but a stop codon upstream prevents this gene from starting sooner. It is already long enough to be a gene, and there is not evidence that this gap is part of this gene. Compared to pineapplepluto, this was kept as a gap between the two genes. The data best supports starting at 15267. This gives it the longest gene possible while following gene rules. There is good coding potential in Genemark indicating evidence that this is a gene. There is NKF for this gene. However, on the NCBI blast, there was an indication that this is a hypothetical protein. DeepTMHMM suggests inside topology. CDS complement (15400 - 15543) /note=I was looking at the Glimmer Start and the GeneMark. There was a glimmer start at 15543, but there was no stated GeneMark. The reason why there was no numbered mark showing is because GeneMark believed there was no potential coding in that area, so I`m not entirely sure if it`s truly considered a gene. With that in mind, I still decided to pick the suggested start. There are 144 base pairs, meaning it could be considered a gene since it has more than 120 base pairs. The gap overlapped by only four base pairs, which is considered something more beneficial than harmful. The scores for the Z-score and final score were the best options. Looking at the phages that have this similar gene, Crunchyboi, PineapplePluto, and HitchHiker had the highest e-value score. When looking for a predicted function, those three bacteriophages had specified it as a Hypothetical Protein/Unknown Function. I looked at PhagesDB and HHpred, but I didn`t find any crucial evidence stating it could be something else other than a hypothetical protein. DeepTMHMM suggests inside topology CDS complement (15540 - 15731) /note=There are no similar genes in registered EK1 cluster phages. There is no significant coding potential but the gap between genes would be too large if it was not present. HHpred gives a borderline probability between 88.1 and 92.2 percent probability and 52.4 percent coverage for signal peptidase I. DeepTMHMM suggests inside topology. CDS complement (15728 - 16042) /note=Glimmer and GeneMark gave two different possible start sites, with the GeneMark overlap being -17, and Glimmer being -8. Since -17 is too big of an overlap, and PECAAN`s chosen start was the same as Glimmer, the Glimmer start site at 16042 was chosen. It has a reasonable spacer, as well as the best Z score and final score. In HHPRED, there was no probabilities above a 90%, so it was assumed that this gene codes for a hypothetical protein with no known function. The sequence was also run in Deep TMHMM, which showed that the hypothetical protein would most likely operate inside. CDS complement (16035 - 16247) /note=Glimmer start and Genemark clarified that this is a gene looking at the starting point and that is why I selected it as the suggested start, which was justified by looking at the starterator. It is long enough to be a gene and it does have coding potential, based on the information depicted by phagedb it has similar phages which are pineapplePluto, crunchyboi, HitchHiker, and Pabst. It does not have a predicted function it is a hypothetical protein, I blasted it on NCBI and I observed that the identity percentages of the similar phages as Tictac were lower compared to the coverage percentage therefore I did not select any. Results from Hhpred show that the probability of it being a hypothetical protein is 85%, which is a good percentage, which is why I selected it. I figured it is a membrane protein looking at the results from the DeepTMHMM it shows it has a trans-membrane domain. CDS complement (17158 - 17499) /note=Based of of the information shown in PECAAN and from HHpred and the Blast it was prominently evident that there was no known function the only thing it may have been is a hypothetical protein but it had a low percentage for that. So i decided that there wasn`t a known function. DeepTMHMM suggests inside topology. CDS 18004 - 31464 /note=HHpred provides three potential matches for the end of the gene above 90% probability (WD repeat-containing protein, Signal recognition particle subunit SRP68, PC4 and SFRS1-interacting protein). All matches occur at the C terminus. All of these matches are related to protein-protein interactions. Which might correspond to the potential function of cleaving the cell membrane. It is also by far the longest gene in the genome. However this is a short tail phage which means it can not be a tape measure protein. DeepTMHMM suggests outside topology. CDS 31461 - 33539 /note=The start site is 31461 which Starterator, Glimmer, and genemark agree on. On NCBI blast the amino acid sequence got a 100% match for portal proteins of many of the phage in the Cluster(EK1). On HHpred I got 100% matches for portal protein. CDS 33591 - 35261 /note=HHpred shows no significant evidence of it being a major capsid protein. Blast showed coding potential and gives us an idea of it being a major capsid protein. GeneMark and Glimmer has the same score of 33591, shows the final score being the highest at -2.541. The spacer was at 11, and the z-score was greater than 2 being at 2.921. Phamerator showed a match with another gene on HitchHiker. start site shown on GeneMark was 33591 and the stop being at 35261. The gene directly downstream of the called portal protein. Phage Akoni an EK phage gene 33 was experimentally proven to be a major capsid protein. CDS 35331 - 35495 /note=Based on the information given by Glimmer Start and Genemark Start both agree that it is a gene because it starts at 35531, I selected the suggested starterator because it has a length that is over 120, the final score is good as well as the Z-score even though the gap is over 30 base pairs which is not a good thing. Yes, it is long enough to be a gene because it has more than 120 base pairs, it does have a coding potential, and looking at the Glimmer start and Genemark start graph had peaks. This gene has been called in similar phages which are Crunchyboi, HitchHiker, and Pineapple because they have an e-value higher than 4. Yes, it is the only gene in the region there were no other genes in that region. I blasted this gene on phagesDB and it showed that it has no predicted function, therefore being a hypothetical protein. CDS 35573 - 36421 /note=The start site was agreed on by both Glimmer, GeneMark, and PECAAN. High coding potential in expected region in GeneMark. It also compared to many other phages that called that same gene a minor tail protein. HHPRED also gave high probability for a few different possible tail proteins. CDS 36421 - 38187 /note=36421 Start site on both Glimmer Start and GeneMark, with the longest ORF. Spacer, z-score and final score within range. BLAST suggest minor tail protein, however HHPRED give receptor proteins. DeepTMHMM show outside topology, suggesting tail protein function. CDS 38210 - 39070 /note=I looked at Glimmer Start and Genemark both agree that the start point is 38210 and I selected it as the suggested start cause of the information from the starterator which showed the start number 28 having 42 manual annotators. It has coding potential looking at the genemark, there are no genes in the same region as this one but it has similar phages which are crunchyboi, Pabst, pineapple, corn21, HitchHiker, Lesnorah, and Bluerugrat even though some of the phages have an e-value lower than 4. It has a predicted function which is Endolysin, clarified from both Phagesdb blast and NCBI blast showing a 100% identity with certain phages with a similar function. CDS 39070 - 39561 /note=When blasted on NCBI a 100% match for the amino acid sequence of crunchyboi phage was found. The protein type of the crunchyboi amino acid was a membrane protein. HHPred found that there was a 83.94% probability that this protein was an membrane protein. Starterator report matched suggested start site. This could be a potential Holin gene due to gene 39 being endolysin. CDS 39548 - 39991 /note=HHPred has high probability that the gene is a “shock protein”. There isn’t adequate evidence in the Phagesdb Pham to prove that it is a shock protein. Only one transmembrane domain needs to be found to identify this as a membrane protein. And that is present in DeepTMHMM. So, this gene is currently identified as membrane protein. CDS 39984 - 40217 /note=potential gene is only 234 pairs long, does have lots of coding potential, phamerator doesn`t show any other genes that could be in this region, this start point is the LORF, has the highest Z-score, overlaps by 8, spacer below 12, highest available final score. All results from phages DB show unknown function, no matches from HHPred have a high enough probability to be viable. NCBI blast shows a high probability to match hitchhiker, crunchyboi, and pineapplepluto for membrane proteins. There is enough evidence towards membrane protein that we are going to call it. CDS 40256 - 41536 /note=Genemark shows good coding potential. There are no large gaps between the upstream or the downstream gene. Start sight of 40256 gives the longest possible gene. Compares well on the PHAM maps and the PHAM report. Start also has the best spacer, z-score, and final score. Does not have any known function. NCBI shows that it is a hypothetical protein. It has no transmembrane domains. DeepTMHMM suggests outside topology. CDS 41548 - 42621 /note=Glimmer and Genemark start sight match the start sight on Starterator. The start sight is 41548 and the stop sight is 2863. This makes the base pairs around 1074 in length. Looking at the pham maps comparing Crunchyboi, Birdfeeder, Hitchhiker, and Tictac we see that it was retained as a gene. Due to this, this is likely a gene. There is no known function, even on NCBI Blast Birdfeeder_41, LilyLou_44, Crunchyboi_45, and Hitchhiker_45 showed up as NKF. CDS 42624 - 43412 /note=When I looked into both Glimmer and GeneMark, it presented the same start location at 42,624 base pairs. I decided to pick the suggested starter since it had many great attributes such as; it being the longest open reading frame, gap was only two base pairs, the spacer is over the recommended amount (which is 9-14), but not by too many to consider having it changed to another start cite. The scores and start codons were perfect for this gene. It has coding potential due to looking at the GeneMark graphs, which presented a very high range of coding potential in all 789 base pairs. The phages that are the most correlated with this specific gene are Crunchyboi, PineapplePluto, HitchHiker, and Pabst, with a decent e-value score over e^-4. There could be a possibility it could have another gene, but likely not due to other genes surrounded by it being over 1000 base pairs. I tried looking for a predicted function, but all the ones of PhagesDB predicted it was an unknown function. I was going to suggest it could be a complex viral protein, but when looking at HHpred, it had taken a significant amount of base pairs (almost over 80) out of the possibility. I don`t think it is a complex viral protein due to the fact we would be removing so much crucial functional sequencing in this gene. So, I have decided to put it under the function of a hypothetical protein. I did add that there could be a possibility it could be a virion-associated complex protein, but I did not find any other convincing evidence that it could for sure be this type of protein. CDS 43412 - 46084 /note=The recommended start site was the same on Glimmer, GeneMark, and Starterator. However, there isn`t coding potential at the beginning of the suggested start site. The gap would have been too big if any of the other start sites were used, so we still went with the recommended. /note=Most phages with similar genes called this a hypothetical protein, but HitchHiker called it a minor tail protein. /note=HHPred had hits with high probabilities and high percent coverage for a couple different tail tubular proteins, one was even specific to Podoviridae. CDS 46096 - 46332 /note=GeneMark indicates strong coding potential, with no significant gaps between the upstream or downstream genes. The start site at position 46,096 yields the longest possible gene. This start site also aligns well with PHAM maps and reports.. Additionally, it has the most favorable spacer, z-score, and final score. However, no known function has been identified. NCBI classifies it as a hypothetical protein, and no transmembrane domains are present. CDS 46332 - 47867 /note=length at start point is well beyond minimum length, the spacer is below 12, the gap overlaps by 1, the final score is the largest number available, it is the LORF, does contain the coding potential, however there is not much coding potential found. Has a very high match (~98%) with hitchhiker, pineapplepluto and crunchyboi phages for the function of phosphoesterase. HHPred has high probability, but low coverage so that might need a second opinion. The CDD did not have any likely matches. CDS 47945 - 48868 /note=Glimmer and Genemart start site both match at 47945. There are 39 MA`s for the start site 47945. HHPred and NCBI Blast lack hits with significant probability. So, we can assume that this gene has NKF. NCBI describes this gene as a Hypothetical protein on PECAAN, but no other site supports these results. DeepTMHMM suggests inside topology CDS 48868 - 49566 /note=Glimmer and Gememark start match, and the gap, spacer, z-score, and final score give evidence that the start is 48868. The startorator report also has 23 MA for start sight 48868. This start site also gives it the longest possible gene. There is enough evidence to declare a function. There are no gaps upstream or downstream. There is a 3 BP overlap between the upstream gene. Deep Tm does not indicate that this is a transmembrane protein. CDS 49563 - 50669 /note=Suggested start site with the most MAs on Starterator. The start site is similar on both Glimmer Start and GeneMark. The gene has an acceptable length, an overlap of 4 bp, and spacer region within 4 -12, and has the longest ORF. The start codon is also ATG. HHPRED function probability is less than 90%, and the PhagesBlast give a NKF function, comparing this with other CrunchyBoi. Inside topology. CDS 50763 - 51203 /note=Start site 50763 is the only one listed on Starterator, and is similar on both Glimmer Start and GeneMark. The gap is a bit longer than 50bp, however there isn`t any coding potential between this and the previous gene. PhagesBLAST give NKF, comparing it to other phages, and HHPRED function probabilities are below 90%. DeepTMHMM gives an inside topology. CDS 51206 - 52702 /note=Glimmer and Genemark have different start sights. Starorator also has manual annotations for two different start sights at 51206 and 51266. There is good coding potential in GeneMark. Gene mark shows that there is no overlap at the start site 51206 and does not contain any other coding potential in this region. This start site would also give the gene a longer gene and a smaller gap. The Blast on PhageDB indicates that this is a terminase. HHpred also gave evidence for a Large Terminase Subunit and DNA packaging protein. This is not surprising to see DNA packaging protein because that is a role that terminase plays. There is no transmembrane protein for this gene. CDS 52702 - 53043 /note=This is a gene because it is long enough to be a gene and has good coding potential. This starting site was chosen because it gave the longest coding potential, good gap, spacer, Z, and final scores. It also matched the start sites of this gene in other related phages. It also happens to start with the ATG codon which is the most likely start site. Other related phages with this gene listed it as having no known function. HHpred did give this gene a match with a matrix protein for a monkey virus. DeepTMHHM did not predict this as a membrane protein. CDS 53015 - 53287 /note=This gene was not originally included in the PhagesDB gene list but it was added to fill the gap between the adjacent genes. The region has no coding potential on GeneMark but there is a start and stop codon appropriately spaced in the second direct reading frame to fill the gap between the genes. The start codon chosen creates a 28 base pair overlap with the previous gene which is borderline too large but it has the best Z score largest reading frame and most probable start codon (ATG) as well as being more similar to the start location for the phages that have added homologous genes. Neither HHpred nor blasts searches provided any significant indication of gene function. It has no transmembrane domains. CDS 53349 - 53609 /note=Gene includes full coding potential though coding potential is low. It has the highest coding potential in its region and the gap between genes would be far to large if it was not present. HHpred gives no indications of potential domains with reasonable probability. Blasting searching reveals no know function. No transmembrane coding potential. CDS complement (53598 - 53774) /note=No Coding potential in the region, no sufficient findings on HHPred. Start is selected as 53776 by 9 manual entries on Pham Starterator rather than 53774 but 53776 is not an option.