SEA-PHAGES | MPMEs--which one?

Link to this post \| posted 14 Mar, 2018 14:46
welkin	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 14 Mar, 2018 14:46

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
c.sunnen	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 21 May, 2018 13:54

c.sunnen

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
welkin	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
cdshaffer	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): `Query 1 MFPITDTRREMTTMPTTEHGSDVQHLSPEHRDRAWRDRFNARWHYDYGGWIRTRPQDEAS 60 MFPITDTRREMTTMPTTEHGSDVQHLSPEHRDRAWRDRFNARWHYDYGGWIRTRPQDEAS Sbjct 1 MFPITDTRREMTTMPTTEHGSDVQHLSPEHRDRAWRDRFNARWHYDYGGWIRTRPQDEAS 60 Query 61 TFALIPTKHYGPFTEDHSCPACLVVHPPEDCPVLSGNTDML———————VVFD-YDTSPNK 112 TFALIPTKHYGPFTEDHSCPACLVVHPPEDCPVLSGNTD+ +FD +D+ P Sbjct 61 TFALIPTKHYGPFTEDHSCPACLVVHPPEDCPVLSGNTDIFGTTSSGPTIFDSFDSGPGG 120 Query 113 A 113 Sbjct 121 V 121` 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 Edited 05 Jun, 2018 19:45

Link to this post | posted 05 Jun, 2018 14:46

cdshaffer

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):

Query  1    MFPITDTRREMTTMPTTEHGSDVQHLSPEHRDRAWRDRFNARWHYDYGGWIRTRPQDEAS  60
            MFPITDTRREMTTMPTTEHGSDVQHLSPEHRDRAWRDRFNARWHYDYGGWIRTRPQDEAS
Sbjct  1    MFPITDTRREMTTMPTTEHGSDVQHLSPEHRDRAWRDRFNARWHYDYGGWIRTRPQDEAS  60

Query  61   TFALIPTKHYGPFTEDHSCPACLVVHPPEDCPVLSGNTDML———————VVFD-YDTSPNK  112
            TFALIPTKHYGPFTEDHSCPACLVVHPPEDCPVLSGNTD+         +FD +D+ P
Sbjct  61   TFALIPTKHYGPFTEDHSCPACLVVHPPEDCPVLSGNTDIFGTTSSGPTIFDSFDSGPGG  120

Query  113  A  113

Sbjct  121  V  121

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

Edited 05 Jun, 2018 19:45

Link to this post \| posted 07 Jun, 2018 12:28
welkin	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
ball.1766	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). Score Expect Method Identities Positives Gaps 163 bits(412) 8e-50 Compositional matrix adjust. 74/110(67%) 85/110(77%) 0/110(0%) Query 14 MPTTEHGSDVQHLSPEHRDRAWRDRFNARWHYDYGGWIRTRPQDEASTFALIPTKHYGPF 73 M + G+D+ HLS EHRDRAWRDRFNARWH+DYGGWIRTRPQD+ASTFALIP + YGPF Sbjct 1 MKASTQGTDIPHLSSEHRDRAWRDRFNARWHHDYGGWIRTRPQDDASTFALIPDERYGPF 60 Query 74 TEDHSCPACLVVHPPEDCPVLSGNTDMLVVFDYDTSPNKAQADTADDDPR 123 EDHSCP CL +H P++CPVLS + DYDT+P QADTA DD R Sbjct 61 VEDHSCPYCLAIHQPQECPVLSRYAGRAIASDYDTTPKNTQADTAADDLR 110 Edited 05 Jul, 2018 13:01

Link to this post | posted 05 Jul, 2018 02:35

ball.1766

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).

Score	Expect	Method	Identities	Positives	Gaps
163 bits(412)	8e-50	Compositional matrix adjust.	74/110(67%)	85/110(77%)	0/110(0%)
Query  14   MPTTEHGSDVQHLSPEHRDRAWRDRFNARWHYDYGGWIRTRPQDEASTFALIPTKHYGPF  73
            M  +  G+D+ HLS EHRDRAWRDRFNARWH+DYGGWIRTRPQD+ASTFALIP + YGPF
Sbjct  1    MKASTQGTDIPHLSSEHRDRAWRDRFNARWHHDYGGWIRTRPQDDASTFALIPDERYGPF  60

Query  74   TEDHSCPACLVVHPPEDCPVLSGNTDMLVVFDYDTSPNKAQADTADDDPR  123
             EDHSCP CL +H P++CPVLS      +  DYDT+P   QADTA DD R
Sbjct  61   VEDHSCPYCLAIHQPQECPVLSRYAGRAIASDYDTTPKNTQADTAADDLR  110

Edited 05 Jul, 2018 13:01

Link to this post \| posted 05 Jul, 2018 20:14
welkin	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
dbolliva	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 Edited 18 Jul, 2018 19:12

Link to this post | posted 18 Jul, 2018 19:11

dbolliva

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

Edited 18 Jul, 2018 19:12

Link to this post \| posted 14 Jan, 2019 17:52
washj	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
welkin	Hi Jackie, I think this still counts at MPME1. Best, Welkin

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