Link to this post | posted 16 Aug, 2023 15:53

smolloy123

We are now calling lysin B in cluster CQ genomes. CQ genomes carry the same lysin B gene found in cluster A15 and CU genomes. PReviously in the CQs this gene was assigned the function of serine hydrolase. But this sequence aligns to the same crystal structures (2czq cutinase and 1qoz acetyl xylan esterase) as the D29 lysin B (see Payne, K., Sun, Q., Sacchettini, J. and Hatfull, G.F., 2009. Mycobacteriophage Lysin B is a novel mycolylarabinogalactan esterase. Molecular microbiology, 73(3), pp.367-381.) Attached is a Pham map of CQ genomes Cucurbita aligned to Culver with the lysin B genes highlighted in a pink box. Note that Cucurbita has assigned the function serine hydrolase. 2.18Mb

Link to this post | posted 03 Aug, 2023 19:49

smolloy123

There is not enough evidence to support calling the tail assembly chaperone programmed ribosomal frame (PRF) in the cluster O phages. A +2 programmed ribosomal frameshift was called in most cluster O mycobacteriophage (e.g. CatDawg gp52 and 53) and they are reported in the cluster O mycobacteriophage paper (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118725). The "slippery sequence" that was identified (GAAAAGT), however, is not canonical and we really don't have any evidence that this is a slippery sequence. See the Bioinformatics guide for more information on what the canonical slippery sites are. Also, the second gene (gpGT) (e.g. MadKillah gp51 or CatDawg gp53), does not have HHPred alignments to tail assembly chaperone proteins. Because it also does not have a slippery sequence, this protein should be called "Hypothetical Protein." The first gene (gpG; MadKillah gp50) does have HHpred alignment to tail assembly chaperones and therefore should be called a tail assembly chaperone.

Link to this post | posted 07 Jun, 2023 14:58

smolloy123

From the SEA Faculty at the 2023 Faculty meeting: In many DN phages, the gene found between the portal and scaffolding protein should be called a capsid maturation protease. Historically, this gene has been called a MuF-like minor capsid protein, which as described in the approved function list can no longer be called. When you run HHPRED, you will likely find hits to MuF, but not hits to proteases. However, many of these genes have hits that have high similarity and probability to gp15 in D29 in Uniprot (Hit O6420. This can be done by selecting Uniprot as one of your algorithms in HHPRED. Because we know gp15 in D29 is a capsid maturation protease, having a strong hit to this protein allows you to call this a capsid maturation protease.

Link to this post | posted 07 Jun, 2023 14:58

smolloy123

From the SEA Faculty at the 2023 Faculty meeting: In many DN phages, the gene found between the portal and scaffolding protein should be called a capsid maturation protease. Historically, this gene has been called a MuF-like minor capsid protein, which as described in the approved function list can no longer be called. When you run HHPRED, you will likely find hits to MuF, but not hits to proteases. However, many of these genes have hits that have high similarity and probability to gp15 in D29 in Uniprot (Hit O6420. This can be done by selecting Uniprot as one of your algorithms in HHPRED. Because we know gp15 in D29 is a capsid maturation protease, having a strong hit to this protein allows you to call this a capsid maturation protease.

Link to this post | posted 07 Jun, 2023 14:56

smolloy123

A follow up on Debbie's post on TACs in cluster DNs written by SEA faculty at the 2023 Faculty member: Not all cluster DN phage genomes have two tail assembly chaperones (TAC) that can be called and a programmed ribosomal frameshift (PRF) that can be called. An example of a DN phage with a non-canonical -1 programmed translational frameshift (CCCGGAA) is Horus gp 15 and gp 16 and the PRF should not be called. If no PRF can be called and there is no HHpred evidence supporting a TAC function assignment then only one TAC chaperone should be called. An example of a DN phage with a canonical -1 programmed translational frameshift (GGGGGAA) is found in Oday TAC gp14. Although there is no HHpred evidence for a TAC in Oday gp15, because the canonical slippery site is present in gp14, gp15 is called a TAC.

Link to this post | posted 08 Jul, 2022 17:34

smolloy123

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UMaine is a land, sea and space grant university, and maintains a leadership role as the University of Maine System's flagship institution. UMaine is the state's public research university and a Carnegie R1 top-tier research institution, dedicated to providing excellent teaching, research and service for Maine, the nation and the world. More information about UMaine is at umaine.edu. The University of Maine offers a wide range of benefits for employees including, but not limited to, tuition benefits (employee and dependent), comprehensive insurance coverage including medical, dental, vision, life insurance, and short and long term disability as well as retirement plan options. As a former NSF ADVANCE institution, the University of Maine is committed to diversity in our workforce and to dual-career couples. UMaine is located in beautiful Central Maine. Many employees report that a primary reason for choosing to come to UMaine is quality of life. Numerous cultural activities, excellent public schools, safe neighborhoods, high quality medical care, little traffic, and a reasonable cost of living make the greater Bangor area a wonderful place to live. Learn more about what the Bangor region has to offer here. Employees in the University of Maine System are required to comply with UMS COVID protocols which currently include, but are not limited to, being vaccinated, obtaining a qualified vaccination exemption, and/or participating in regular COVID testing. Further information can be found here. Qualifications: Required: A doctoral degree in molecular biology, microbiology, biomedical sciences, or closely related area by date of hire. Demonstrated experience in teaching undergraduates in molecular biology, microbiology, biomedical sciences, or closely-related discipline. Evidence of commitment to pedagogical development. Experience mentoring students in the laboratory setting. Effective written and oral communication skills. Evidence of organizational and time management skills. Evidence of successful performance in collaborative environments. Potential to contribute to the University of Maine’s commitment to an inclusive and diverse student body that includes first-generation and socioeconomically-disadvantaged students and those from groups that are under-represented in biomedical sciences. Preferred: Demonstrated approaches to evidence-based and inclusive teaching. Evidence of familiarity with safety standards for laboratory instruction. Evidence of strong potential for research in phage-bacterial host interactions. Other Information: Materials must be submitted via "Apply For Position" below. 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Link to this post | posted 28 Apr, 2022 23:40
smolloy123	Wow wonderful ideas and thanks for the speedy responses! I like the idea of adding a note that specifies that both domains must be included in the alignment. Thanks everyone!!!

Link to this post | posted 28 Apr, 2022 14:52
smolloy123	I am going to answer my own post and suggest simply metallopeptidase. There are five different functions (DNA binding protein. HTH DNA binding domain, metalloprotease, metallopeptidase, peptidase) assigned to this homolog in phagesdb and it would be good if we could settle on one!

Link to this post | posted 28 Apr, 2022 14:52
smolloy123	I am going to answer my own post and suggest simply metallopeptidase. There are five different functions (DNA binding protein. HTH DNA binding domain, metalloprotease, metallopeptidase, peptidase) assigned to this homolog in phagesdb and it would be good if we could settle on one!

Link to this post | posted 28 Apr, 2022 14:49

smolloy123

Hi All, I am calling a gene in a singleton phage Finkle (gp42 on Phamerator and and between integrase and Immunity repressor). I noted that in AY cluster specific tips Debbie states that the gene that hits IrrE only aligns to the HTH DNA binding domain and therefore call it such. The gene I am looking at is found in a long list of phage across both Gordonia clusters and prophage clusters (CY, CZ, DN, F, MabA, P). But this protein in HHpred has high quality alignment to IrrE and includes the peptidase region (with the HEXXH motif) and the HTH DNA binding domain. Given its location between the integrase and immunity repressor my guess is that this is something like the ImmA antirepressor. But since we can't use guesses for function assignment what do we call this? metallopeptidase helix-turn-helix DNA binding protein? That is too long a name. Please send suggestions. Also the HHpred data is attached!