SEA-PHAGES | Genome Curation

Link to this post \| posted 17 Jun, 2022 13:31
debbie	Hi all, As of today, June 17, 2022, there are 88 Cluster EE genomes in our records. They are closely related genomes that contain only ~28 genes. In an effort to make the records congruent, my students and I have reviewed ~75 of them and revised 71 of the records. The template we used is attached here, along with a list of 71 records that we touched. We spent an abundant amount of time on the helix-turn-helix DNA binding proteins at the right end of the genome. We investigated 'types' of helix-turn-helix choices and decided the best path is to call them helix-turn-helix DNA binding proteins. August 23, 2022 - I just received word that the genomes that we sent to GenBank have been processed. This cluster just might have congruent calls! Edited 23 Aug, 2022 16:13 74Kb 12Kb

Link to this post | posted 17 Jun, 2022 13:31

Hi all,
As of today, June 17, 2022, there are 88 Cluster EE genomes in our records. They are closely related genomes that contain only ~28 genes. In an effort to make the records congruent, my students and I have reviewed ~75 of them and revised 71 of the records. The template we used is attached here, along with a list of 71 records that we touched. We spent an abundant amount of time on the helix-turn-helix DNA binding proteins at the right end of the genome. We investigated 'types' of helix-turn-helix choices and decided the best path is to call them helix-turn-helix DNA binding proteins.
August 23, 2022 - I just received word that the genomes that we sent to GenBank have been processed. This cluster just might have congruent calls!

Edited 23 Aug, 2022 16:13

Link to this post \| posted 23 Aug, 2022 16:20
viknesh	A for effort and yAy for a cluster that with congruent calls! debbie Hi all, As of today, June 17, 2022, there are 88 Cluster EE genomes in our records. They are closely related genomes that contain only ~28 genes. In an effort to make the records congruent, my students and I have reviewed ~75 of them and revised 71 of the records. The template we used is attached here, along with a list of 71 records that we touched. We spent an abundant amount of time on the helix-turn-helix DNA binding proteins at the right end of the genome. We investigated 'types' of helix-turn-helix choices and decided the best path is to call them helix-turn-helix DNA binding proteins. August 23, 2022 - I just received word that the genomes that we sent to GenBank have been processed. This cluster just might have congruent calls! Thanks Vic! debbie Edited 23 Aug, 2022 18:40

Link to this post | posted 23 Aug, 2022 16:20

viknesh

A for effort and yAy for a cluster that with congruent calls!

debbie
Hi all,
As of today, June 17, 2022, there are 88 Cluster EE genomes in our records. They are closely related genomes that contain only ~28 genes. In an effort to make the records congruent, my students and I have reviewed ~75 of them and revised 71 of the records. The template we used is attached here, along with a list of 71 records that we touched. We spent an abundant amount of time on the helix-turn-helix DNA binding proteins at the right end of the genome. We investigated 'types' of helix-turn-helix choices and decided the best path is to call them helix-turn-helix DNA binding proteins.
August 23, 2022 - I just received word that the genomes that we sent to GenBank have been processed. This cluster just might have congruent calls!

Thanks Vic!
debbie

Edited 23 Aug, 2022 18:40

Link to this post \| posted 02 Mar, 2024 21:55
ClaireRinehart	Debbie, I was using the GenBank submission of Luxx (cluster EE) to evaluate the annotations of our student's practice genomes that are based on Luxx. I found that gene 18 had a -34 gap start called instead of the -4 that we originally called. Start Stop Length Gap Spacer Z-score Final Score Codon Forward 14090 14578 489 -259 6 0.875 -8.104 GTG Forward 14315 14578 264 -34 16 1.587 -6.724 GTG Forward 14327 14578 252 -22 10 1.637 -5.522 GTG Forward 14345 14578 234 -4 16 2.066 -5.760 GTG Forward 14426 14578 153 77 6 1.917 -6.007 ATG Forward I read the Cluster EE forum notes and see that Luxx was modified to bring the group into "conformity". I would like to learn what would justify gene 18 start being called at 14315 other than the fact that the other 84 genomes in Starterator use that site? Thanks, I am still learning. Claire Edited 02 Mar, 2024 22:42

Link to this post | posted 02 Mar, 2024 21:55

ClaireRinehart

Debbie,
I was using the GenBank submission of Luxx (cluster EE) to evaluate the annotations of our student's practice genomes that are based on Luxx. I found that gene 18 had a -34 gap start called instead of the -4 that we originally called.

Start  Stop  Length  Gap  Spacer  Z-score  Final Score  Codon  Forward
14090  14578    489 -259       6    0.875       -8.104         GTG   Forward
14315  14578    264  -34      16    1.587       -6.724         GTG   Forward
14327  14578    252  -22      10    1.637       -5.522         GTG   Forward
14345  14578    234   -4      16    2.066       -5.760         GTG   Forward
14426  14578    153   77       6    1.917       -6.007         ATG   Forward

I read the Cluster EE forum notes and see that Luxx was modified to bring the group into "conformity". I would like to learn what would justify gene 18 start being called at 14315 other than the fact that the other 84 genomes in Starterator use that site?

Thanks,
I am still learning.
Claire

Edited 02 Mar, 2024 22:42

Link to this post \| posted 02 Mar, 2024 22:24
ClaireRinehart	Debbie, I have additionally found Luxx gene 21 and 22 starts have been changed to bring this genome into "conformity" with the other EE genomes. Looking at the data I again disagree with these changes. Please educate me on the rationale. Thanks, Claire Rinehart Luxx Gene 21 (reverse gene) Starterator calls start 15583, which has a very poor Z- and Final Score but captures all of the coding capacity. Start 15577 is just six bases shorter and has a viable Z- and Final score, while capturing most all of the coding capacity. The best scoring start is at 15520 with excellent Z- and Final Scores but looses 63 bases of coding capacity found in the tail region of the typical plot, but into the peak region of the atypical plot. My choice is start 15577. Starterator Info for manual annotations of cluster EE: •Start number 3 was manually annotated 1 time for cluster EE. •Start number 5 was manually annotated 9 times for cluster EE. •Start number 6 was manually annotated 78 times for cluster EE. •Start number 7 was manually annotated 2 times for cluster EE. •Start number 10 was manually annotated 2 times for cluster EE. •Start number 12 was manually annotated 5 times for cluster EE. •Start number 14 was manually annotated 1 time for cluster EE. •Start number 15 was manually annotated 2 times for cluster EE. Gene: Luxx_21 Start: 15583, Stop: 15083, Start Num: 6 Candidate Starts for Luxx_21: (2, 15784), (Start: 5 @15595 has 9 MA's), (Start: 6 @15583 has 78 MA's), (Start: 7 @15577 has 2 MA's), (9, 15559), (Start: 10 @15553 has 2 MA's), (Start: 12 @15520 has 5 MA's), (16, 15475), (17, 15439), (18, 15424), (19, 15397), (20, 15385), (22, 15343), (23, 15319), (25, 15289), (28, 15259), (29, 15250), (30, 15229), (31, 15226), (33, 15202), (38, 15118 ), Ribosomal binding scores: Direction Start Stop Length Gap Spacer Z-score Final Score Codon Reverse 15784 15083 702 -122 14 2.391 -4.856 ATG Reverse 15595 15083 513 67 7 0.6 -8.437 GTG Reverse 15583 15083 501 79 12 0.503 -7.945 ATG Reverse 15577 15083 495 85 10 1.201 -6.398 ATG Reverse 15559 15083 477 103 10 0.549 -7.710 ATG Reverse 15553 15083 471 109 10 1.201 -6.398 ATG Referse 15520 15083 438 142 13 2.987 -3.155 ATG Luxx Gene 22 (reverse gene) (reverse gene) Starterator calls the start at 15893. As you can see below, start 15893 has one of the poorest Z- and Final Scores. A better choice would be 15923 or 15818. In looking at the coding capacity below, Start 15818 would give up a large portion of coding capacity. However, start 15923 would even capture the atypical coding capacity and is my start of choice. Starterator Gene: Luxx_22 Start: 15893, Stop: 15663, Start Num: 5 Candidate Starts for Luxx_22: (3, 15935), (4, 15923), (Start: 5 @15893 has 100 MA's), (6, 15818 ), (7, 15809), (8, 15791), (10, 15740), (11, 15728 ), Ribosomal binding scores: Direction Start Stop Length Gap Spacer Z-Score Final Score Reverse 15935 15663 273 468 15 1.495 -6.714 Reverse 15923 15663 261 480 15 2.237 -5.221 Reverse 15893 15663 231 510 15 0.936 -7.839 Reverse 15818 15663 156 585 9 2.137 -4.595 Reverse 15809 15663 147 598 18 2.137 -6.122 Edited 03 Mar, 2024 10:55

Link to this post | posted 02 Mar, 2024 22:24

ClaireRinehart

Debbie,
I have additionally found Luxx gene 21 and 22 starts have been changed to bring this genome into "conformity" with the other EE genomes. Looking at the data I again disagree with these changes.
Please educate me on the rationale.
Thanks,
Claire Rinehart

Luxx Gene 21 (reverse gene)
Starterator calls start 15583, which has a very poor Z- and Final Score but captures all of the coding capacity. Start 15577 is just six bases shorter and has a viable Z- and Final score, while capturing most all of the coding capacity. The best scoring start is at 15520 with excellent Z- and Final Scores but looses 63 bases of coding capacity found in the tail region of the typical plot, but into the peak region of the atypical plot. My choice is start 15577.

Starterator
Info for manual annotations of cluster EE:
•Start number 3 was manually annotated 1 time for cluster EE.
•Start number 5 was manually annotated 9 times for cluster EE.
•Start number 6 was manually annotated 78 times for cluster EE.
•Start number 7 was manually annotated 2 times for cluster EE.
•Start number 10 was manually annotated 2 times for cluster EE.
•Start number 12 was manually annotated 5 times for cluster EE.
•Start number 14 was manually annotated 1 time for cluster EE.
•Start number 15 was manually annotated 2 times for cluster EE.

Gene: Luxx_21 Start: 15583, Stop: 15083, Start Num: 6
Candidate Starts for Luxx_21:
(2, 15784), (Start: 5 @15595 has 9 MA's), (Start: 6 @15583 has 78 MA's), (Start: 7 @15577 has 2 MA's), (9, 15559), (Start: 10 @15553 has 2 MA's), (Start: 12 @15520 has 5 MA's), (16, 15475), (17, 15439), (18, 15424), (19, 15397), (20, 15385), (22, 15343), (23, 15319), (25, 15289), (28, 15259), (29, 15250), (30, 15229), (31, 15226), (33, 15202), (38, 15118 ),

Ribosomal binding scores:
Direction  Start   Stop  Length  Gap  Spacer  Z-score  Final Score  Codon
Reverse    15784  15083   702   -122    14        2.391    -4.856         ATG
Reverse    15595  15083   513      67      7         0.6         -8.437         GTG
Reverse    15583  15083   501      79    12         0.503    -7.945         ATG
Reverse    15577  15083   495      85    10         1.201    -6.398         ATG
Reverse    15559  15083   477    103    10         0.549    -7.710         ATG
Reverse    15553  15083   471    109    10         1.201    -6.398         ATG
Referse    15520  15083   438    142    13         2.987    -3.155         ATG

Luxx Gene 22 (reverse gene) (reverse gene)
Starterator calls the start at 15893. As you can see below, start 15893 has one of the poorest Z- and Final Scores. A better choice would be 15923 or 15818. In looking at the coding capacity below, Start 15818 would give up a large portion of coding capacity. However, start 15923 would even capture the atypical coding capacity and is my start of choice.

Starterator
Gene: Luxx_22 Start: 15893, Stop: 15663, Start Num: 5
Candidate Starts for Luxx_22:
(3, 15935), (4, 15923), (Start: 5 @15893 has 100 MA's), (6, 15818 ), (7, 15809), (8, 15791), (10, 15740), (11, 15728 ),

Ribosomal binding scores:
Direction  Start   Stop  Length  Gap  Spacer  Z-Score  Final Score
Reverse    15935  15663    273    468    15     1.495     -6.714
Reverse    15923  15663    261    480    15     2.237     -5.221
Reverse    15893  15663    231    510    15     0.936     -7.839
Reverse    15818  15663    156    585      9     2.137      -4.595
Reverse    15809  15663    147    598    18     2.137     -6.122

Edited 03 Mar, 2024 10:55

Link to this post \| posted 03 Mar, 2024 11:03
debbie	Thank Claire, After reviewing your data, i am beginning to believe that conformity is not all that its cracked up to be! I agree with your assessment of gene 18 in Luxx. the 4-base overlap is much more convincing than the bigger overlap. We used alpha-fold to fold the longer version of 18 and the lysin, and no structures were observed to be helpful. So while the data may not change for a while, I agree that the start choice that Claire points out (the 4 base overlap) is a better choice. For genes 21 and 22, I like the original 'conformity' calls because of coding potential evaluations. So call upon your best gene evaluation skills and make your best call. Please draw attention to these genes in your cover letter, so that the QCer can also evaluate. Anyone want to do some bench work?!! Best, debbie

Link to this post | posted 03 Mar, 2024 11:03

debbie

Thank Claire,
After reviewing your data, i am beginning to believe that conformity is not all that its cracked up to be!
I agree with your assessment of gene 18 in Luxx. the 4-base overlap is much more convincing than the bigger overlap. We used alpha-fold to fold the longer version of 18 and the lysin, and no structures were observed to be helpful. So while the data may not change for a while, I agree that the start choice that Claire points out (the 4 base overlap) is a better choice.

For genes 21 and 22, I like the original 'conformity' calls because of coding potential evaluations. So call upon your best gene evaluation skills and make your best call.

Please draw attention to these genes in your cover letter, so that the QCer can also evaluate.

Anyone want to do some bench work?!!

Best,
debbie

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