SEA-PHAGES | All posts created by powelleann

Link to this post \| posted 15 Feb, 2024 20:46
powelleann	The start of KentuckyRacer Gene 84 was changed from 62351 to 62378 due to having more 1:1 alignment with similar phage in BLAST on PhagesDB and BLAST on NCBI. Starterator also called this start with 52 MAs. After running BLAST on both NCBI and PhagesDB, two different functions were identified. On PhagesDB all hits called for RecA-like DNA recombinase with 1:1 alignment with more than 10 Streptomyces phage. However, on NCBI BLAST top hits called for UvsX-like recombinase with more than 10 Streptomyces phage. One of the top hits was with Streptomyces StarPlatinum with 99.40% identity, 99% query coverage, e-value of 0.0, and 1:1 alignment. However, the Official SEAPHAGES function list does not make UvsX-like recombinase an approved function. After running the protein sequence through HHPred, top hits also called for RecA. One hit from Mycobacterium tuberculosis for RecA had a 100% probability, e-value of 3.5e-36, and 98.8% coverage. Our question is which function should we go with because NCBI and Phage DB have different functions? Lanae Canen and Gabby Carter

Link to this post | posted 15 Feb, 2024 20:46

The start of KentuckyRacer Gene 84 was changed from 62351 to 62378 due to having more 1:1 alignment with similar phage in BLAST on PhagesDB and BLAST on NCBI. Starterator also called this start with 52 MAs.
After running BLAST on both NCBI and PhagesDB, two different functions were identified. On PhagesDB all hits called for RecA-like DNA recombinase with 1:1 alignment with more than 10 Streptomyces phage. However, on NCBI BLAST top hits called for UvsX-like recombinase with more than 10 Streptomyces phage. One of the top hits was with Streptomyces StarPlatinum with 99.40% identity, 99% query coverage, e-value of 0.0, and 1:1 alignment. However, the Official SEAPHAGES function list does not make UvsX-like recombinase an approved function.
After running the protein sequence through HHPred, top hits also called for RecA. One hit from Mycobacterium tuberculosis for RecA had a 100% probability, e-value of 3.5e-36, and 98.8% coverage.
Our question is which function should we go with because NCBI and Phage DB have different functions?

Lanae Canen and Gabby Carter

Posted in: Annotation → RecA-like recombinase or UvsX-like recombinase for KentuckyRacer 62351-62378

Link to this post \| posted 15 Feb, 2024 17:54
powelleann	We are annotating the phage KentuckyRacer and have come across a section where there is two genes that directly overlap in Phamerator. Start site for the first gene is 65377 and stop 65658, and a 0 base pair gap, this gene has the longest ORF this is gene 95. No coding potential on GeneMark was found. Coding potential was discovered in another overlapping reading frame. The other gene included has a start site 65390 and stop 65638 and a gap of 13 bp and is gene 96. Gene 96 was not included in DNA master. When compared to the Phamerator map, the other phages IchabodCrane and MindFlayer share the pham number 87029 (16) as KentuckyRacer_96. Gene 95 pham number is 1536 (70). We are unsure of how to determine which is the correct gene. Thank you. Riley Bryant Anna Elpers

Link to this post | posted 15 Feb, 2024 17:54

powelleann

We are annotating the phage KentuckyRacer and have come across a section where there is two genes that directly overlap in Phamerator. Start site for the first gene is 65377 and stop 65658, and a 0 base pair gap, this gene has the longest ORF this is gene 95. No coding potential on GeneMark was found. Coding potential was discovered in another overlapping reading frame. The other gene included has a start site 65390 and stop 65638 and a gap of 13 bp and is gene 96. Gene 96 was not included in DNA master. When compared to the Phamerator map, the other phages IchabodCrane and MindFlayer share the pham number 87029 (16) as KentuckyRacer_96. Gene 95 pham number is 1536 (70). We are unsure of how to determine which is the correct gene.
Thank you.

Riley Bryant Anna Elpers

Posted in: Annotation → 2 genes in same place of Cluster BE phage, Kentucky Racer

Link to this post \| posted 23 Mar, 2022 18:55
powelleann	While checking gaps in our JPandJE draft genome we noticed two potentially overlapping DNA Primase ORFs, both in the reverse direction. The first was called by Glimmer the second was not, but there is coding potential present in the Genemark graph. The first extends from 31440 to 30808 and is 633bp long (Pham 15206). The second extends from 31681 to 31292 and is about 390 bp long (Pham 100144). There are 1:1 phagesdb BLAST matches for both of these sequences. They were also both annotated as DNA primase in Immanuel3 (genes 57 and 5. The overlap if both are included is 149 bp. We are not sure whether to include the second DNA primase molecule.Please let me know. Thank you in advance. Ann Powell

Link to this post | posted 23 Mar, 2022 18:55

powelleann

While checking gaps in our JPandJE draft genome we noticed two potentially overlapping DNA Primase ORFs, both in the reverse direction. The first was called by Glimmer the second was not, but there is coding potential present in the Genemark graph. The first extends from 31440 to 30808 and is 633bp long (Pham 15206). The second extends from 31681 to 31292 and is about 390 bp long (Pham 100144). There are 1:1 phagesdb BLAST matches for both of these sequences. They were also both annotated as DNA primase in Immanuel3 (genes 57 and 5 smile

. The overlap if both are included is 149 bp.

We are not sure whether to include the second DNA primase molecule.Please let me know.

Thank you in advance.

Ann Powell

Posted in: Gene or not a Gene → Two overlapping DNA Primases in JPandJE

Link to this post \| posted 13 Jan, 2022 18:29
powelleann	Thank you so much for the information.

Posted in: Notes and Final Files → Notes format when using DNA Master

Link to this post \| posted 13 Jan, 2022 16:53
powelleann	My class is using DNA Master to annotate our first genome this semester. I noticed that we no longer need to enter notes in the specified format in the notes area of DNA Master. Is there a spreadsheet format or file type that you would like us to use? Please let me know. Thanks.

Posted in: Notes and Final Files → Notes format when using DNA Master

Link to this post \| posted 13 Jan, 2022 16:52
powelleann	My class is using DNA Master to annotate our first genome this semester. I noticed that we no longer need to enter notes in the specified format in the notes area of DNA Master. Is there a spreadsheet format or file type that you would like us to use? Please let me know. Thanks.

Posted in: Notes and Final Files → Notes format when using DNA Master

Link to this post \| posted 21 Jan, 2020 17:32
powelleann	Hello, I am sorry I forgot this. What is the password for students to access the DNA Master Prefernces Gene Prediction? Thanks, Ann Powell

Posted in: DNA Master → Password for DNA master Preferences Gene Prediction

Link to this post \| posted 01 Mar, 2019 19:59
powelleann	Thank you for the suggestions!

Posted in: Functional Annotation → Lysin A and Holin in BI1 cluster Streptomyces phage

Link to this post \| posted 28 Feb, 2019 19:34
powelleann	In our annotation of Streptomyces phage Esketit (cluster BI1), we have been unable to locate a Lysin A gene, but we have found a gene coding for LysM-Like endolysin. We also noted that similar phage (OylmpicHelado and Spectropatronm) are also missing this gene. Please advise us on how to proceed before we submit the genome. In addition, our holin is much longer than the typical holin length. Ours is about 360 aa whereas the length is usually about 110 aa. Only the first part of our product actally matches (HHpred) with holin function. We have found no other holin in the genome. We were wondering if it is possible to have a longer holin or a holin that is continuous with another protein sequence added on to the terminal portion of the functional holin?. Thanks, Ann

Link to this post | posted 28 Feb, 2019 19:34

powelleann

In our annotation of Streptomyces phage Esketit (cluster BI1), we have been unable to locate a Lysin A gene, but we have found a gene coding for LysM-Like endolysin. We also noted that similar phage (OylmpicHelado and Spectropatronm) are also missing this gene. Please advise us on how to proceed before we submit the genome.

In addition, our holin is much longer than the typical holin length. Ours is about 360 aa whereas the length is usually about 110 aa. Only the first part of our product actally matches (HHpred) with holin function. We have found no other holin in the genome. We were wondering if it is possible to have a longer holin or a holin that is continuous with another protein sequence added on to the terminal portion of the functional holin?.

Thanks,

Ann

Posted in: Functional Annotation → Lysin A and Holin in BI1 cluster Streptomyces phage

Link to this post \| posted 04 Jun, 2018 18:16
powelleann	Hello, Is there any way to get a large cluster C1 phage genome to annotate on a MacBook Pro (using WINE). Most of the time, I can open the file but when I try to show ORFs in a frames view I run out of memory or get various error messages. Another time I was able to generate the ORFs in Frames, but then could not get RBS scores when I selected a gene (again an error message). I will be using this computer during the upcoming faculty workshop, so any help would be much appreciated. Ann

Link to this post | posted 04 Jun, 2018 18:16

powelleann

Hello,

Is there any way to get a large cluster C1 phage genome to annotate on a MacBook Pro (using WINE). Most of the time, I can open the file but when I try to show ORFs in a frames view I run out of memory or get various error messages. Another time I was able to generate the ORFs in Frames, but then could not get RBS scores when I selected a gene (again an error message).

I will be using this computer during the upcoming faculty workshop, so any help would be much appreciated.

Ann

Posted in: DNA Master → Annotating Cluster C1 phage onn Macbook Pro

Recent Activity

All posts created by powelleann