SEA-PHAGES | Is this really not a Minor Tail Protein?

Link to this post \| posted 30 May, 2023 05:45
fbaliraine	We are annotating this large protein (999 aa) down the tape measure, in is draft gp 35 in both phages Dulcita and Diminimus (28791-29789 bp) in subcluster M1. It’s sequence is below: MASFTPIVPVRSNRPLELQRGNTLRYRYTLSGNKTFPAGTSAVLTVSNTYGQVVGAFIGTVAGKTIEFVEGPEISDTLARTDTWTLSVTYPGETHPTMLEQGQIIRVEAPFPDQPAMSPEFEGVRYEYHFGTPGFVKDPSWRILNGHPRVYDNSFRSLPNAVSSGSLFGGDLTFFDDVCMLWFAPLATDIVRLTYNTIRPIDNSNGEVWTIICSNYDATNWAGFHHKQVFGIGSWDDDEISVVTGTGPTTFTKRETESYDTVNNQAYTAEYNPVSNTYSLYVGTSLEPLISWTDETNVVEHGEGERYVGFGFKSALLYAGVQVSDWYIANTPZ Notably, it mostly hits hypothetical proteins in phagesDB, although it hits minor tail proteins of the same phages such as PegLeg & Reindeer in NCBI (which happen to show hypothetical proteins in phagesDB). In HHPred, it hits gene 31 of Mycobacterium phage D29 and phage L5, which upon inspection in the phagesDB gene list, that gene is a minor tail protein, and the HH probabilities for both phages are 99.85% & 99.86% respectively, with the hit in UniProt note about Protein existence, being "Predicted" (In some case for other proteins, UniProt states, "Evidence at protein level". According to the Resource Guide, minor tail proteins genes are big genes down the tape measure and usually not more than 5. We think that this would make the 5th big gene after the tape measure. We also know that we can use synteny only to call minor tail proteins, “You can call minor tail proteins for the 'big' genes downstream of the tape measure protein. there is usually not more than 5.” To use synteny, ALL the following three conditions must be met: (1) of the correct size , (2) adjacent to other structural genes of known, verifiable function and (3) the only possible option for that function in the genome (https://seaphagesbioinformatics.helpdocsonline.com/article-90). Given that D29 is a well-studied prototypic phage, we are inclined to call this large gene a minor tail protein, but since many hits in phagesDB are to Hypothetical proteins, we would like to cross-check to be sure that we are not missing something. On the other hand, there is a smaller (459 aa) draft gene 30 in Diminimus and Ducita downstream the tape measure which hits many minor tail proteins in phagesDB and is between two large, minor tail proteins but we would contend that this should be a Hypothetical Protein given its small size. Its sequence is: MPPLNVHPPDPNHPKGMAWVLGVGMVDPRPGNNPNQPMAIVQSWEPTSELWWKLGLRWHPELAEVWAVGGGQFEIAQIVNEKPEAQEMSLEEGAAEVLEYIGKEHPEYAEMLQQIHNAGSDVERIKLVKQFDGEIKRLMTLMKYVSTKPAEEZ Except something has changed lately, the following forum posts (4464 & 4546) suggest not calling small proteins minor tail proteins (https://seaphages.org/forums/topic/4464/; https://seaphages.org/forums/topic/4546/) In summary, we are thinking of calling the large (999 aa) gene (draft gp 35) a minor tail protein and the smaller (459 aa) gene (draft gp 30) a hypothetical protein. See attached phamerator map. What’s your verdict? Fred Edited 30 May, 2023 17:41 115Kb

Link to this post | posted 30 May, 2023 05:45

We are annotating this large protein (999 aa) down the tape measure, in is draft gp 35 in both phages Dulcita and Diminimus (28791-29789 bp) in subcluster M1. It’s sequence is below:

MASFTPIVPVRSNRPLELQRGNTLRYRYTLSGNKTFPAGTSAVLTVSNTYGQVVGAFIGTVAGKTIEFVEGPEISDTLARTDTWTLSVTYPGETHPTMLEQGQIIRVEAPFPDQPAMSPEFEGVRYEYHFGTPGFVKDPSWRILNGHPRVYDNSFRSLPNAVSSGSLFGGDLTFFDDVCMLWFAPLATDIVRLTYNTIRPIDNSNGEVWTIICSNYDATNWAGFHHKQVFGIGSWDDDEISVVTGTGPTTFTKRETESYDTVNNQAYTAEYNPVSNTYSLYVGTSLEPLISWTDETNVVEHGEGERYVGFGFKSALLYAGVQVSDWYIANTPZ

Notably, it mostly hits hypothetical proteins in phagesDB, although it hits minor tail proteins of the same phages such as PegLeg & Reindeer in NCBI (which happen to show hypothetical proteins in phagesDB).

In HHPred, it hits gene 31 of Mycobacterium phage D29 and phage L5, which upon inspection in the phagesDB gene list, that gene is a minor tail protein, and the HH probabilities for both phages are 99.85% & 99.86% respectively, with the hit in UniProt note about Protein existence, being "Predicted" (In some case for other proteins, UniProt states, "Evidence at protein level". According to the Resource Guide, minor tail proteins genes are big genes down the tape measure and usually not more than 5. We think that this would make the 5th big gene after the tape measure. We also know that we can use synteny only to call minor tail proteins, “You can call minor tail proteins for the 'big' genes downstream of the tape measure protein. there is usually not more than 5.” To use synteny, ALL the following three conditions must be met: (1) of the correct size , (2) adjacent to other structural genes of known, verifiable function and (3) the only possible option for that function in the genome (https://seaphagesbioinformatics.helpdocsonline.com/article-90).

Given that D29 is a well-studied prototypic phage, we are inclined to call this large gene a minor tail protein, but since many hits in phagesDB are to Hypothetical proteins, we would like to cross-check to be sure that we are not missing something.

On the other hand, there is a smaller (459 aa) draft gene 30 in Diminimus and Ducita downstream the tape measure which hits many minor tail proteins in phagesDB and is between two large, minor tail proteins but we would contend that this should be a Hypothetical Protein given its small size. Its sequence is:

MPPLNVHPPDPNHPKGMAWVLGVGMVDPRPGNNPNQPMAIVQSWEPTSELWWKLGLRWHPELAEVWAVGGGQFEIAQIVNEKPEAQEMSLEEGAAEVLEYIGKEHPEYAEMLQQIHNAGSDVERIKLVKQFDGEIKRLMTLMKYVSTKPAEEZ

Except something has changed lately, the following forum posts (4464 & 4546) suggest not calling small proteins minor tail proteins (https://seaphages.org/forums/topic/4464/; https://seaphages.org/forums/topic/4546/)

In summary, we are thinking of calling the large (999 aa) gene (draft gp 35) a minor tail protein and the smaller (459 aa) gene (draft gp 30) a hypothetical protein. See attached phamerator map.

What’s your verdict?

Fred

Edited 30 May, 2023 17:41

Link to this post \| posted 30 May, 2023 13:00
debbie	Fred, I would think that the hits to the Bacillus and E.coli phages are just as compelling. I would call this a minor tail protein. debbie

Link to this post \| posted 30 May, 2023 17:39
fbaliraine	Thank you Debbie. This clarifies things about this gene since it has previously been called NKF as evident from the phagesDB hits. We are now calling this large gene (gp 35 in Dulcita and Diminimus and other homologous subclcuster M1 phage genes in the same region) as minor tail protein, and the small gene (gp 30) as NKF. Fred Edited 30 May, 2023 17:40

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Is this really not a Minor Tail Protein?