SEA-PHAGES | Functional assignments in B2 phage Rhinoforte

Link to this post \| posted 02 May, 2017 21:06
lblumer	The following are a few functions we have identified in Phage Rhinoforte that are not in the approved list. I read your responses to Jackie and note that none of these duplicate her questions. ORF 2: queuine tRNA-ribosyltransferase, Blastp Phamerator, e=0.0, Glass gp2 ORF 6: GTP cyclohydrolase, Blastp Phamerator, e=e-108, LizLemon gp6 ORF 8: peroxide stress protein YaaA, HHPred, prob=99.81 e=2.3e-20, E. coli (HHPred coverage with this match is only 75% of the query sequence.) ORF 18: membrane protein, Blastp Phamerator, e=1e-18, Attis gp21 Not certain that this is the same as membrane protein Band-7-like that is in the list for Functional Assignments. ORF 42: tail fiber protein, Blastp NCBI, e=3e-08, Mediterranean phage uvMED (Should this just be called a minor tail protein?) Thanks. Larry I have attached the Rhinoforte DNA Master file for reference. 48Kb

Link to this post | posted 02 May, 2017 21:06

The following are a few functions we have identified in Phage Rhinoforte that are not in the approved list. I read your responses to Jackie and note that none of these duplicate her questions.

ORF 2: queuine tRNA-ribosyltransferase, Blastp Phamerator, e=0.0, Glass gp2

ORF 6: GTP cyclohydrolase, Blastp Phamerator, e=e-108, LizLemon gp6

ORF 8: peroxide stress protein YaaA, HHPred, prob=99.81 e=2.3e-20, E. coli
(HHPred coverage with this match is only 75% of the query sequence.)

ORF 18: membrane protein, Blastp Phamerator, e=1e-18, Attis gp21
Not certain that this is the same as membrane protein Band-7-like that is in the list for Functional Assignments.

ORF 42: tail fiber protein, Blastp NCBI, e=3e-08, Mediterranean phage uvMED (Should this just be called a minor tail protein?)

Thanks.

Larry

I have attached the Rhinoforte DNA Master file for reference.

Link to this post \| posted 05 May, 2017 15:06
welkin	Hi Larry, I moved you to a new thread so it would be easier to find for other people annotating B2 phages. In general, each new function question should be a new thread. For your questions: ORF 2: queuine tRNA-ribosyltransferase, Blastp Phamerator, e=0.0, Glass gp2 yes, go ahead. we should put it on the big list. ORF 6: GTP cyclohydrolase, Blastp Phamerator, e=e-108, LizLemon gp6 yes, go ahead with this one too. ORF 8: peroxide stress protein YaaA, HHPred, prob=99.81 e=2.3e-20, E. coli (HHPred coverage with this match is only 75% of the query sequence.) No. ORF 18: membrane protein, Blastp Phamerator, e=1e-18, Attis gp21 Not certain that this is the same as membrane protein Band-7-like that is in the list for Functional Assignments. The Attis protein was labeled as a membrane protein after it was examined with TMHMM. If you get a similar output, go ahead and call this one a membrane protien too. It is not the same as the Band 7 proteins. ORF 42: tail fiber protein, Blastp NCBI, e=3e-08, Mediterranean phage uvMED (Should this just be called a minor tail protein?) This one is kind of scrawny to be a tail fiber. Let's hold off until we have some bench data. Thanks Larry!

Link to this post | posted 05 May, 2017 15:06

welkin

Hi Larry, I moved you to a new thread so it would be easier to find for other people annotating B2 phages. In general, each new function question should be a new thread.

For your questions:
ORF 2: queuine tRNA-ribosyltransferase, Blastp Phamerator, e=0.0, Glass gp2
yes, go ahead. we should put it on the big list.

ORF 6: GTP cyclohydrolase, Blastp Phamerator, e=e-108, LizLemon gp6
yes, go ahead with this one too.

ORF 8: peroxide stress protein YaaA, HHPred, prob=99.81 e=2.3e-20, E. coli
(HHPred coverage with this match is only 75% of the query sequence.)

No.

ORF 18: membrane protein, Blastp Phamerator, e=1e-18, Attis gp21
Not certain that this is the same as membrane protein Band-7-like that is in the list for Functional Assignments.

The Attis protein was labeled as a membrane protein after it was examined with TMHMM. If you get a similar output, go ahead and call this one a membrane protien too. It is not the same as the Band 7 proteins.

ORF 42: tail fiber protein, Blastp NCBI, e=3e-08, Mediterranean phage uvMED (Should this just be called a minor tail protein?)
This one is kind of scrawny to be a tail fiber. Let's hold off until we have some bench data.

Thanks Larry!

Link to this post \| posted 12 May, 2017 19:26
lblumer	Thanks Welkin, I ran TMHMM on the product of ORF 18 and four distinct TMHs were predicted with probabilities of 0.9 and greater. I will go ahead and call this function the same as Attis. Thanks for the direction to TMHMM and the comments on this group.

Link to this post \| posted 12 May, 2017 20:10
lblumer	One more question: ORF 66 of Rhinoforte has the best Blastp matches to HTH DNA binding domain (or protein) but I understand that this is not a specific function, although it is in our accepted list. This same gene product also matches RNase E, e=2e-35, Bane1 gp 69 with 81% query coverage. Bane1 is the best match with this function identified. Is RNase E an accepted function?

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Functional assignments in B2 phage Rhinoforte