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MPMEs--which one?
Link to this post | posted 14 Mar, 2018 14:46 | |
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The MPMEs – mycobacteriophage mobile elements— are very small and closely related. So how to tell them apart? If your MPME is IDENTICAL to BPs 58, you have MPME1. If your MPME is IDENTICAL to Fruitloop 71, you have MPME2. IF you are not IDENTICAL to either, let us know! maybe you found a new one!. See Sampson et al for more information. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2833263/ |
Link to this post | posted 21 May, 2018 13:54 | |
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I'm posting here because it seems logical to me to keep this MPME question within this thread. In the F1, NormanBulbieJr, we have a sequence that is only one amino acid different from the MPME1 in BPs_58. For now, I'm calling it MPME1, but perhaps it's a new one? Results below are from phagesdb: >BPs_58, function unknown, 123 Length = 123 Score = 270 bits (690), Expect = 5e-73 Identities = 122/123 (99%), Positives = 122/123 (99%) Query: 1 MFPITDTRREMTTMPTTEHESDVQHLSPEHRDRAWRDRFNARWHYDYGGWIRTRPQDEAS 60 MFPITDTRREMTTMPTTEH SDVQHLSPEHRDRAWRDRFNARWHYDYGGWIRTRPQDEAS Sbjct: 1 MFPITDTRREMTTMPTTEHGSDVQHLSPEHRDRAWRDRFNARWHYDYGGWIRTRPQDEAS 60 Query: 61 TFALIPTKHYGPFTEDHSCPACLVVHPPEDCPVLSGNTDMLVVFDYDTSPNKAQADTADD 120 TFALIPTKHYGPFTEDHSCPACLVVHPPEDCPVLSGNTDMLVVFDYDTSPNKAQADTADD Sbjct: 61 TFALIPTKHYGPFTEDHSCPACLVVHPPEDCPVLSGNTDMLVVFDYDTSPNKAQADTADD 120 Query: 121 DPR 123 DPR Sbjct: 121 DPR 123 |
Link to this post | posted 22 May, 2018 15:34 | |
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Hi Nikki, You are right— one amino acid off means we will stay with MPME1. Thanks! |
Link to this post | posted 05 Jun, 2018 14:46 | |
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It appears many of the O cluster phage have a derivative of MPME1, its clearly not a MPME2 but much more than a single residue difference: Alignment to BPs_58 to JangDynasty gp22 (but several O phage have identical sequence):
This is identical for 99 a.a. then what looks like a spurious BLAST extension, should we also call this MPME1 or add new approved term to somehow indicate a derivative of MPME1 As a follow up, in Cresawn et al PLoS ONE 10(3) they are annotating the "truncated" version with the full MPME1 annotation. I am going to add this to the O specific annotations forum |
Link to this post | posted 07 Jun, 2018 12:28 | |
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As a follow up from Graham: How long is a piece of string?! If [a new MPME] is 1 aa different, that is not enough for it to be MPME3. If it is a truncated version of MPME1, that does not make it MPME3. If there is a new MPME, full length with all of the features, and it is ~75% DNA identity to 1 and 2, then that would be 3. |
Link to this post | posted 05 Jul, 2018 02:35 | |
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While QC'ing Zerg I came across an ORF where other Pham members have been called as MPME1 and 2 (or just MPME protein) but many other members of the pham didn't call a function at all so I am not sure how to proceed. I have included the alignment with Fruitloop 71 but since it is not an identical match I don't know if I should call it MPME2 or if it is a new one (or nothing at all).
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Link to this post | posted 05 Jul, 2018 20:14 | |
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Hi Sarah, How similar is it to MPME1? And does it have the rest of the MPME features? If so, it sounds like you may have MPME 3…. |
Link to this post | posted 18 Jul, 2018 19:11 | |
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In the genome of Girr that I am Qcing it appears that there is a MPME similar to that seen by Sarah in Zerg. The alignment below is with fruitloop 71 and does not align the C-terminus Alignment statistics for match #1 Score Expect Method Identities Positives Gaps 151 bits(382) 3e-54 Compositional matrix adjust. 66/82(80%) 73/82(89%) 0/82(0%) Query 14 MPTTEHGSDVQHLSPEHRDRAWRDRFNARWHHDYGGWIRTRPQDDASTFALIPDERYGPF 73 M + G+D+ HLS EHRDRAWRDRFNARWHHDYGGWIRTRPQDDASTFALIPDERYGPF Sbjct 1 MKASTQGTDIPHLSSEHRDRAWRDRFNARWHHDYGGWIRTRPQDDASTFALIPDERYGPF 60 Query 74 TEDHSCPYCLVVHPPEDCPVLN 95 EDHSCPYCL +H P++CPVL+ Sbjct 61 VEDHSCPYCLAIHQPQECPVLS 82 I also tried with BPs58 uery 1 MFPITDTRREMTTMPTTEHGSDVQHLSPEHRDRAWRDRFNARWHHDYGGWIRTRPQDDAS 60 MFPITDTRREMTTMPTTEHGSDVQHLSPEHRDRAWRDRFNARWH+DYGGWIRTRPQD+AS Sbjct 1 MFPITDTRREMTTMPTTEHGSDVQHLSPEHRDRAWRDRFNARWHYDYGGWIRTRPQDEAS 60 Query 61 TFALIPDERYGPFTEDHSCPYCLVVHPPEDCPVLNWREQEL 101 TFALIP + YGPFTEDHSCP CLVVHPPEDCPVL+ L Sbjct 61 TFALIPTKHYGPFTEDHSCPACLVVHPPEDCPVLSGNTDML 101 Just for fun, here is the alignment between Girr (Query) and Zerg (Subject) Alignment statistics for match #1 Score Expect Method Identities Positives Gaps 163 bits(412) 8e-59 Compositional matrix adjust. 76/88(86%) 80/88(90%) 0/88(0%) Query 14 MPTTEHGSDVQHLSPEHRDRAWRDRFNARWHHDYGGWIRTRPQDDASTFALIPDERYGPF 73 MPTTEHGSDVQHLSPEHRDRAWRDRFNARWH+DYGGWIRTRPQD+ASTFALIP + YGPF Sbjct 1 MPTTEHGSDVQHLSPEHRDRAWRDRFNARWHYDYGGWIRTRPQDEASTFALIPTKHYGPF 60 Query 74 TEDHSCPYCLVVHPPEDCPVLNWREQEL 101 TEDHSCP CLVVHPPEDCPVL+ L Sbjct 61 TEDHSCPACLVVHPPEDCPVLSGNTDML 88 |
Link to this post | posted 14 Jan, 2019 17:52 | |
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Renaissance (G1) gp57 is in the same pham 43215 as MPME1 but it is only identical for the first 114aa. The inverted repeats are at positions 39786-39796 and 40213-40223, and thus 438bp. Consequently, it is 1bp/2bp smaller than MPME1/MPME2. It is more similar to MPME1 than MPME2. Is this a new MPME else what should I call it? |
Link to this post | posted 14 Jan, 2019 18:54 | |
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Hi Jackie, I think this still counts at MPME1. Best, Welkin |