SEA-PHAGES | membrane protein

Link to this post \| posted 27 Jul, 2017 20:29
ClaireRinehart	I was updating PECAAN's Function field automatch list today and found that the "membrane protein" notation has been dropped. We added the TMHMM transmembrane predictor to PECAAN in response to Debbie indicating that there were several membrane proteins located in a specific region of the Arthobacter genomes. We found these same membrane proteins in our Arthrobacter phage and thought that it would be nice to have this as a PECAAN feature. Knowing that a protein is predicted to be located in the membrane is useful to identifying some functions such as holins while at other times it is not known how this feature contributes to the function but may be found fairly consistently, such as in tape measure proteins. I would like to see this general function feature returned to the approved list, perhaps as "predicted membrane protein" because it brings a lot of functional potential to the annotation table that "hypothetical protein" just does not.

Link to this post | posted 27 Jul, 2017 20:29

I was updating PECAAN's Function field automatch list today and found that the "membrane protein" notation has been dropped. We added the TMHMM transmembrane predictor to PECAAN in response to Debbie indicating that there were several membrane proteins located in a specific region of the Arthobacter genomes. We found these same membrane proteins in our Arthrobacter phage and thought that it would be nice to have this as a PECAAN feature. Knowing that a protein is predicted to be located in the membrane is useful to identifying some functions such as holins while at other times it is not known how this feature contributes to the function but may be found fairly consistently, such as in tape measure proteins. I would like to see this general function feature returned to the approved list, perhaps as "predicted membrane protein" because it brings a lot of functional potential to the annotation table that "hypothetical protein" just does not.

Link to this post \| posted 31 Jul, 2017 15:12
welkin	Hi Claire, I think we can add it back. We will just have to make a note that it should only be used if a more specific assignment can't be justified.

Link to this post \| posted 31 Jul, 2017 15:33
ClaireRinehart	Thanks Welkin. I added "membrane protein" back into the PECAAN approved function list. Dex added a new feature to PECAAN in the drop-down that is used to select gene numbers. If there is a green check before the gene number then you know that the designated function is in the approved list. If a red x is showing before the gene number then the designated function is not a member of the approved function list. This saved me an hour last week when I was reviewing functions and their conformation to the approved function list.

Link to this post | posted 31 Jul, 2017 15:33

ClaireRinehart

Thanks Welkin. I added "membrane protein" back into the PECAAN approved function list.

Dex added a new feature to PECAAN in the drop-down that is used to select gene numbers. If there is a green check before the gene number then you know that the designated function is in the approved list. If a red x is showing before the gene number then the designated function is not a member of the approved function list. This saved me an hour last week when I was reviewing functions and their conformation to the approved function list.

Link to this post \| posted 01 Aug, 2017 03:05
jparker	Just a thought, but I usually think of these as transmembrane "domains" rather than proteins. What is the cutoff for labeling something a particular kind of protein, compared to a protein with a particular domain? I attached a screenshot of the TMHMM output for Emma_35 (Pham 12413 - which appears to be conserved in F1 and BD clusters). So, we are going with "predicted membrane protein"? 57Kb

Link to this post \| posted 15 May, 2019 16:12
smolloy123	Hi Welkin or others, I am QCing Trax, a DU phage. Following the lysin A genes, there are two genes that each have 1 transmembrane domain. The first gene (gp37 on phamearator) is called holin on other DU phage. I know that we are not calling genes with single TMDs "membrane proteins." I also had it in my head that holins have at least 2 TMDs. Do I call these hypothetical? Do I call one of them a holin because of being adjacent to lysin As? Based on the rules that I know I would call these hypothetical. Thanks! Sally

Link to this post | posted 15 May, 2019 16:12

smolloy123

Hi Welkin or others,
I am QCing Trax, a DU phage. Following the lysin A genes, there are two genes that each have 1 transmembrane domain. The first gene (gp37 on phamearator) is called holin on other DU phage.

I know that we are not calling genes with single TMDs "membrane proteins."

I also had it in my head that holins have at least 2 TMDs.

Do I call these hypothetical? Do I call one of them a holin because of being adjacent to lysin As?

Based on the rules that I know I would call these hypothetical.

Thanks!
Sally

Link to this post \| posted 15 May, 2019 17:05
ClaireRinehart	Sally, We have the TMHMM transmembrane prediction function built into PECAAN, but whenever I find such a call in TMHMM I verify it with a couple of programs, SOSUI and TOPCONS. I really like the TOPCONS output because if it does not call a membrane domain then it is almost assured that it is not a membrane protein. We hope to add these additional verification programs into PECAAN this summer. Thanks, Claire

Link to this post | posted 15 May, 2019 17:05

ClaireRinehart

Sally,
We have the TMHMM transmembrane prediction function built into PECAAN, but whenever I find such a call in TMHMM I verify it with a couple of programs, SOSUI and TOPCONS. I really like the TOPCONS output because if it does not call a membrane domain then it is almost assured that it is not a membrane protein. We hope to add these additional verification programs into PECAAN this summer.
Thanks,
Claire

Link to this post \| posted 15 May, 2019 18:14
smolloy123	smolloy123 Hi Welkin or others, I am QCing Trax, a DU phage. Following the lysin A genes, there are two genes that each have 1 transmembrane domain. The first gene (gp37 on phamearator) is called holin on other DU phage. I know that we are not calling genes with single TMDs "membrane proteins." I also had it in my head that holins have at least 2 TMDs. Do I call these hypothetical? Do I call one of them a holin because of being adjacent to lysin As? Based on the rules that I know I would call these hypothetical. Thanks! Sally Also, these TMDs were confirmed in other programs e.g.TMpred (can't ever get SOSUI to work)

Link to this post | posted 15 May, 2019 18:14

smolloy123

smolloy123
Hi Welkin or others,
I am QCing Trax, a DU phage. Following the lysin A genes, there are two genes that each have 1 transmembrane domain. The first gene (gp37 on phamearator) is called holin on other DU phage.

I know that we are not calling genes with single TMDs "membrane proteins."

I also had it in my head that holins have at least 2 TMDs.

Do I call these hypothetical? Do I call one of them a holin because of being adjacent to lysin As?

Based on the rules that I know I would call these hypothetical.

Thanks!
Sally

Also, these TMDs were confirmed in other programs e.g.TMpred (can't ever get SOSUI to work)

Link to this post \| posted 15 May, 2019 18:26
debbie	Sally, Technically, we can call a single TMD if 2 programs find it. I would not be opposed to calling them both Hypothetical Proteins. I just looked at these in phamerator. These 2 genes are found in a region of high nucleotide pairwise similarity (the purple color inbetween). However, the first of these 2 genes is a member of 3 different phams. Are they all calling different things, or is this a case of small genes not meeting alignment cut-offs to make it into the same pham? debbie

Link to this post | posted 15 May, 2019 18:26

debbie

Sally,
Technically, we can call a single TMD if 2 programs find it.
I would not be opposed to calling them both Hypothetical Proteins.
I just looked at these in phamerator. These 2 genes are found in a region of high nucleotide pairwise similarity (the purple color inbetween). However, the first of these 2 genes is a member of 3 different phams. Are they all calling different things, or is this a case of small genes not meeting alignment cut-offs to make it into the same pham?
debbie

Link to this post \| posted 15 May, 2019 21:41
smolloy123	Hi Debbie, Thanks, I aligned the first gene from Trax with the corresponding genes in Neville and Octobien14. They align overall well but mostly for about 2/3 of the sequence on the C-terminus side. Neville is shorter (or at least was called shorter) and the other two don't align well at the N-terminus. I think they don't make the Pham cut because they are too short. I will call them both hypothetical Thanks for your input so I can finish off my last genome! Cheers Sally

Link to this post | posted 15 May, 2019 21:41

smolloy123

Hi Debbie,
Thanks, I aligned the first gene from Trax with the corresponding genes in Neville and Octobien14. They align overall well but mostly for about 2/3 of the sequence on the C-terminus side. Neville is shorter (or at least was called shorter) and the other two don't align well at the N-terminus. I think they don't make the Pham cut because they are too short.

I will call them both hypothetical smile

Thanks for your input so I can finish off my last genome!
Cheers
Sally

Recent Activity

membrane protein