SEA-PHAGES | All posts created by meckardt21

Link to this post \| posted 08 May, 2018 14:44
meckardt21	Welkin Pope Hi Megan, These are certainly minor tail proteins. Some minor tail proteins have enzymatic activity, it can helps the phage recognize the correct host, get through the cell surface, and/or through the cell wall to inject the DNA. The most compelling evidence is synteny– the phage needs a certain number of minor tail proteins to make a tail. This gene is the right size and in the right place, and it is too big to be a lysin domain. Thanks! Welkin Great. Thanks for the help!

Link to this post | posted 08 May, 2018 14:44

Welkin Pope
Hi Megan,
These are certainly minor tail proteins. Some minor tail proteins have enzymatic activity, it can helps the phage recognize the correct host, get through the cell surface, and/or through the cell wall to inject the DNA.
The most compelling evidence is synteny– the phage needs a certain number of minor tail proteins to make a tail. This gene is the right size and in the right place, and it is too big to be a lysin domain.

Thanks!
Welkin

Great. Thanks for the help!

Posted in: Functional Annotation → Minor Tail Protein (Pham 21676) in EA Phages?

Link to this post \| posted 08 May, 2018 14:37
meckardt21	Hi all, I am checking functional calls for our genomes. The genome in question is Andromedas and it is a Microbacterium phage in the cluster EA2. Gene 22 in this genome is the gene in question. PhagesDB and NCBI BLAST suggest minor tail protein as the function, but the HHPred evidence suggests a chitinase/hydrolase function. I don't know what evidence was used in the past to make this functional call in other EA phages, but my guess is it may be based on synteny as this gene is located at a place in the genome where minor tail proteins would be expected. However, due to the HHPred results, I am uncomfortable calling this as a minor tail protein. Additionally, I see in the official function list that the Gordonia phages occasionally have their Lysin A split into 2 parts. This is a Microbacterium phage and not a Gordonia phage, but given that this is the gene before the putative Lysin A (gene 23) in Andromedas's genome and that it is returning this type of hits via HHPred, is it possible that there is a similar situation in these Microbacterium phages? I appreciate any help or advice offered as I finalize these functional calls. This actually impacts 2 of our 3 Microbacterium phage genomes we are working on this semester. I have attached some evidence that I assembled while investigating this gene in PDF format to this message. Thanks in advance! Edited 08 May, 2018 14:40 1021Kb

Link to this post | posted 08 May, 2018 14:37

meckardt21

Hi all,

I am checking functional calls for our genomes. The genome in question is Andromedas and it is a Microbacterium phage in the cluster EA2. Gene 22 in this genome is the gene in question. PhagesDB and NCBI BLAST suggest minor tail protein as the function, but the HHPred evidence suggests a chitinase/hydrolase function. I don't know what evidence was used in the past to make this functional call in other EA phages, but my guess is it may be based on synteny as this gene is located at a place in the genome where minor tail proteins would be expected. However, due to the HHPred results, I am uncomfortable calling this as a minor tail protein.

Additionally, I see in the official function list that the Gordonia phages occasionally have their Lysin A split into 2 parts. This is a Microbacterium phage and not a Gordonia phage, but given that this is the gene before the putative Lysin A (gene 23) in Andromedas's genome and that it is returning this type of hits via HHPred, is it possible that there is a similar situation in these Microbacterium phages?

I appreciate any help or advice offered as I finalize these functional calls. This actually impacts 2 of our 3 Microbacterium phage genomes we are working on this semester.

I have attached some evidence that I assembled while investigating this gene in PDF format to this message.

Thanks in advance!

Edited 08 May, 2018 14:40

Posted in: Functional Annotation → Minor Tail Protein (Pham 21676) in EA Phages?

Link to this post \| posted 26 Apr, 2018 17:11
meckardt21	Debbie Jacobs-Sera Evan, I think these are the tail assembly chaperone genes, but I could not locate the slippery sequence. If you have a suggestion, let me know. Hi Debbie et al., I am checking our annotation of an EA2 phage and have encountered the same issue. My phage is Andromedas and this is in re genes 13/14 on phamerator. By comparing to an EA4 phage I believe I have found the location of where the frameshift should occur, but there is a stop codon at this location. I did not find any other slippery sequences in this region. I have attached some documentation that I assembled while searching. I would love some advice on how to document in my final file. Given the fact that we cannot pinpoint the location of the frameshift, should I leave them as is in the final annotation? Thanks in advance. Edited 26 Apr, 2018 17:22 514Kb

Link to this post | posted 26 Apr, 2018 17:11

meckardt21

Debbie Jacobs-Sera
Evan,
I think these are the tail assembly chaperone genes, but I could not locate the slippery sequence. If you have a suggestion, let me know.

Hi Debbie et al., I am checking our annotation of an EA2 phage and have encountered the same issue. My phage is Andromedas and this is in re genes 13/14 on phamerator. By comparing to an EA4 phage I believe I have found the location of where the frameshift should occur, but there is a stop codon at this location. I did not find any other slippery sequences in this region.

I have attached some documentation that I assembled while searching. I would love some advice on how to document in my final file. Given the fact that we cannot pinpoint the location of the frameshift, should I leave them as is in the final annotation?

Thanks in advance.

Edited 26 Apr, 2018 17:22

Posted in: Frameshifts and Introns → Annotation advise: Frameshift in EA1

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