SEA-PHAGES | All posts created by kaylafast

Link to this post \| posted 28 Feb, 2019 21:53
kaylafast	cdshaffer These are not mutually exclusive results. Looking at the internal structure for RecA, {I used this link: [Rec A page at UniProt]} I can see that RecA includes a AAA-ATPase like domain. So both term apply, it's just a question of specificity. To me RecA is a much better description of a function than a general ATPase fold seen in diverse cellular activities {see this}. So if you have a good match to RecA across most of RecA I would say use RecA. If, on the other hand, the match is simply to the AAA ATPase as found in RecA I would go with the less specific AAA-ATPase. A detailed look at which parts of RecA is aligning to your protein by looking at the actual HHPred alignment should answer that question. Thanks very much!

Link to this post | posted 28 Feb, 2019 21:53

cdshaffer
These are not mutually exclusive results. Looking at the internal structure for RecA, {I used this link: [Rec A page at UniProt]} I can see that RecA includes a AAA-ATPase like domain. So both term apply, it's just a question of specificity.

To me RecA is a much better description of a function than a general ATPase fold seen in diverse cellular activities {see this}. So if you have a good match to RecA across most of RecA I would say use RecA. If, on the other hand, the match is simply to the AAA ATPase as found in RecA I would go with the less specific AAA-ATPase. A detailed look at which parts of RecA is aligning to your protein by looking at the actual HHPred alignment should answer that question.

Thanks very much!

Posted in: Functional Annotation → R cluster Candle pham 4972 function

Link to this post \| posted 27 Feb, 2019 17:08
kaylafast	We are trying to decide which of 3 functional assignments is most appropriate for an R cluster phage [Candle gp68 (stop 5381/pham 4972)]. I see support for all three, though the last is not an approved function. Our evidence for each functional assignment is below. AAA-ATPase AAA-ATPase, Nilo gp72 and 10+ others, phagesDB, 1:1, % alignment = 100%, e = e-164 AAA domain, HHPred, PF13479.6, % probability = 99.81% , % alignment = 79%, e = 3.6e-21 RecA-like DNA recombinase RecA-like DNA recombinase, Riparian gp72 and 10+ others, phagesDB, 1:1, % alignment = 100%, e = e-164 Protein RecA, HHPred, 4PPF_A, Mycobacterium tuberculosis, % probability = 98.87%, % alignment = 86.3%, e = 3.9E-10 nucleotide binding protein (not on official function list) nucleotide binding protein, Zenon gp72 and 6 others, phagesDB, 1:1, 100% alignment, e = e-164 ATP-binding,HHPred, 2ZTS_C, Pyrococcus horikoshii, % probability = 98.87%, % alignment = 90.3%, e = 8.7e-10 Other HHPred hits RecA protein Recombination, Radioresistance, DNA-repair, ATPase, DNA-binding; 1XP8_A; Deinococcus radiodurans; % probability = 98.85%; % alignment = 85.9%; e = 3.9e-10 Protein RecA, DNA-binding protein, ATP-dependent DNA protein; 5JRJ_A; Herbaspirillum seropedicae; % probability = 98.83%, % alignment = 86.3%; e = 4.3e-10

Link to this post | posted 27 Feb, 2019 17:08

kaylafast

We are trying to decide which of 3 functional assignments is most appropriate for an R cluster phage [Candle gp68 (stop 5381/pham 4972)]. I see support for all three, though the last is not an approved function. Our evidence for each functional assignment is below.

AAA-ATPase
AAA-ATPase, Nilo gp72 and 10+ others, phagesDB, 1:1, % alignment = 100%, e = e-164
AAA domain, HHPred, PF13479.6, % probability = 99.81% , % alignment = 79%, e = 3.6e-21

RecA-like DNA recombinase
RecA-like DNA recombinase, Riparian gp72 and 10+ others, phagesDB, 1:1, % alignment = 100%, e = e-164
Protein RecA, HHPred, 4PPF_A, Mycobacterium tuberculosis, % probability = 98.87%, % alignment = 86.3%, e = 3.9E-10

nucleotide binding protein (not on official function list)
nucleotide binding protein, Zenon gp72 and 6 others, phagesDB, 1:1, 100% alignment, e = e-164
ATP-binding,HHPred, 2ZTS_C, Pyrococcus horikoshii, % probability = 98.87%, % alignment = 90.3%, e = 8.7e-10

Other HHPred hits
RecA protein Recombination, Radioresistance, DNA-repair, ATPase, DNA-binding; 1XP8_A; Deinococcus radiodurans; % probability = 98.85%; % alignment = 85.9%; e = 3.9e-10

Protein RecA, DNA-binding protein, ATP-dependent DNA protein; 5JRJ_A; Herbaspirillum seropedicae; % probability = 98.83%, % alignment = 86.3%; e = 4.3e-10

Posted in: Functional Annotation → R cluster Candle pham 4972 function

Link to this post \| posted 01 Nov, 2018 15:31
kaylafast	Debbie Jacobs-Sera Kayla, I have been looking closely at the Cluster B1 phages. I concur with the genes being polynucleotide kinase and terminase. There is no evidence that a small terminase is present in the genome……yet. debbie Thanks!

Posted in: Functional Annotation → Waleliano (B4) Functions (2875-3465 & 3458-5206)

Link to this post \| posted 31 Oct, 2018 20:27
kaylafast	I am looking at 2 genes in Waleliano (B4) and trying to determine the correct functions. They are gp4 (2875-3465) and gp5 (3458-5206). I feel like the functions should be either terminase, small subunit and terminase, large subunit or polynucleotide kinase and terminase. My evidence for each case is below. Help appreciated! 2875-3465 F: terminase, small subunit SIF-BLAST: terminase, small subunit, phagesDB and NCBI, BrownCNA gp4, AKY02717.1, 100%, e-111 SIF-HHPred: no terminase matches SIF-Syn: terminase small subunit, downstream "terminase" and portal protein,BrownCNA and Hangman F: polynucleotide kinase SIF-BLAST: adenylate kinase, phagesDB and NCBI, PhrankReynolds gp1, AWN05584.2, 50%, 7e-42 SIF-HHPred: polynucleotide kinase, HHPred, Bacteriophage T4, d1ly1a_, %78.1, 99.32% SIF-Syn: NKF 3458-5206 F: terminase large subunit SIF-BLAST: terminase large subunit, phagesDB and NCBI, Hangman gp5, AXH47369.1, 99%, e=0.0 SIF-HHPred: terminase large subunit, HHPred, bacteriophage T4, 3CPE_A, 86.3%, 100 SIF-Syn: terminase large subunit, downstream portal protein, BrownCNA and Hangman F: terminase SIF-BLAST: terminase, phagesDB and NCBI, ChrisnMich gp4, AEJ94575.1, 98%, e=0 SIF-HHPred: phage terminase, HHPred, PF03354.14, 76.7%, 99.6% SIF-Syn: terminase, downstream portal protein, BrownCNA and Hangman

Link to this post | posted 31 Oct, 2018 20:27

kaylafast

I am looking at 2 genes in Waleliano (B4) and trying to determine the correct functions. They are gp4 (2875-3465) and gp5 (3458-5206). I feel like the functions should be either
terminase, small subunit and terminase, large subunit
or
polynucleotide kinase and terminase.

My evidence for each case is below. Help appreciated!

2875-3465
F: terminase, small subunit
SIF-BLAST: terminase, small subunit, phagesDB and NCBI, BrownCNA gp4, AKY02717.1, 100%, e-111 SIF-HHPred: no terminase matches
SIF-Syn: terminase small subunit, downstream "terminase" and portal protein,BrownCNA and Hangman

F: polynucleotide kinase
SIF-BLAST: adenylate kinase, phagesDB and NCBI, PhrankReynolds gp1, AWN05584.2, 50%, 7e-42
SIF-HHPred: polynucleotide kinase, HHPred, Bacteriophage T4, d1ly1a_, %78.1, 99.32%
SIF-Syn: NKF

3458-5206
F: terminase large subunit
SIF-BLAST: terminase large subunit, phagesDB and NCBI, Hangman gp5, AXH47369.1, 99%, e=0.0 SIF-HHPred: terminase large subunit, HHPred, bacteriophage T4, 3CPE_A, 86.3%, 100
SIF-Syn: terminase large subunit, downstream portal protein, BrownCNA and Hangman

F: terminase
SIF-BLAST: terminase, phagesDB and NCBI, ChrisnMich gp4, AEJ94575.1, 98%, e=0
SIF-HHPred: phage terminase, HHPred, PF03354.14, 76.7%, 99.6%
SIF-Syn: terminase, downstream portal protein, BrownCNA and Hangman

Posted in: Functional Annotation → Waleliano (B4) Functions (2875-3465 & 3458-5206)

Link to this post \| posted 28 Aug, 2018 21:05
kaylafast	Debbie Jacobs-Sera Kayla, I think everything looks as I would expect. Do you think it is all correct now? debbie So far I think we are back on track. I'll chunk the suspicious components. Thanks Debbie and Vic!

Posted in: Phage Discovery/Isolation → D29 plaques barely visible on M. smeg

Link to this post \| posted 28 Aug, 2018 20:53
kaylafast	P2FF streak from stock #2 Incubation: 37 degrees C, 24 hrs 1.51Mb

Posted in: Phage Discovery/Isolation → D29 plaques barely visible on M. smeg

Link to this post \| posted 28 Aug, 2018 20:52
kaylafast	Control streak plate Incubation 37 degrees C, 24 hrs 1.64Mb

Posted in: Phage Discovery/Isolation → D29 plaques barely visible on M. smeg

Link to this post \| posted 28 Aug, 2018 20:51
kaylafast	Viknesh Sivanathan kaylafast P2FF streak from stock #1 Incubation: 37 degrees C, 2 days (1 day photo unavailable) I would be suspicious of this streak plate (and the culture from which the streak was setup). There appears to be more growth than expected. Go ahead and test your latest culture, but also setup streak plates (and mock streaks) from your glycerol stocks. Let me know what you see. You can then go ahead and setup cultures. The spot test after 24 hrs using my newest M. smeg. P2FF (from stock #2) has definitely provided stronger clearings. This plate includes D29, phage buffer, and 2 other smeg phages from last year. After 24 hrs the streak with no bacteria shows no growth, and the new P2FF after 24 hrs has some growth. I did also start streak plates today using 3 different glycerol stocks. Edited 28 Aug, 2018 20:54 1.55Mb

Link to this post | posted 28 Aug, 2018 20:51

kaylafast

Viknesh Sivanathan
kaylafast
P2FF streak from stock #1
Incubation: 37 degrees C, 2 days (1 day photo unavailable)

I would be suspicious of this streak plate (and the culture from which the streak was setup). There appears to be more growth than expected. Go ahead and test your latest culture, but also setup streak plates (and mock streaks) from your glycerol stocks. Let me know what you see. You can then go ahead and setup cultures.

The spot test after 24 hrs using my newest M. smeg. P2FF (from stock #2) has definitely provided stronger clearings. This plate includes D29, phage buffer, and 2 other smeg phages from last year. After 24 hrs the streak with no bacteria shows no growth, and the new P2FF after 24 hrs has some growth.

I did also start streak plates today using 3 different glycerol stocks.

Edited 28 Aug, 2018 20:54

Posted in: Phage Discovery/Isolation → D29 plaques barely visible on M. smeg

Link to this post \| posted 27 Aug, 2018 16:13
kaylafast	My newest M. smeg P2FF should be ready today so I can do another streak plate, spot test with D29, and the streak with no bacteria.

Posted in: Phage Discovery/Isolation → D29 plaques barely visible on M. smeg

Link to this post \| posted 27 Aug, 2018 15:59
kaylafast	P1FF streak from stock #2 Incubation: 37 degrees C, ~1 day Edited 27 Aug, 2018 16:10 2.23Mb

Posted in: Phage Discovery/Isolation → D29 plaques barely visible on M. smeg

Recent Activity

All posts created by kaylafast