Anyway, alas, three of the major candidates for the US election have names that do not use traditional amino acid abbreviations so I am stuck with analyzing Sarah Palin. But that is OK because of her professed aversion to evolution and support to Creationism (and since sequence analysis is inherently an evolutionary study).
So - I took here name and went to the NCBI Blast page and did some searches. And what came up? Well, here are some of the top hits from the blastp searches (which I used to compare the pretend peptide "SARAHPALIN" with all the peptides in the non redundant collection at Genbank).
>ref|XP_001545292.1|hypothetical protein BC1G_16161 [Botryotinia fuckeliana B05.10]
gb|EDN25226.1|
Length=383
GENE ID: 5425746 BC1G_16161 | hypothetical protein
[Botryotinia fuckeliana B05.10]
Score = 26.9 bits (56), Expect = 189
Identities = 8/9 (88%), Positives = 8/9 (88%), Gaps = 0/9 (0%)
Query 1 SARAHPALI 9
SARA PALI
Sbjct 209 SARAQPALI 217
>ref|YP_061725.1|
gb|AAT88620.1|
Length=451
GENE ID: 2939000 thrA | homoserine dehydrogenase
[Leifsonia xyli subsp. xyli str. CTCB07] (10 or fewer PubMed links)
Score = 26.9 bits (56), Expect = 189
Identities = 8/9 (88%), Positives = 8/9 (88%), Gaps = 0/9 (0%)
Query 1 SARAHPALI 9
SAR HPALI
Sbjct 267 SARVHPALI 275
>ref|ZP_02031476.1| hypothetical protein PARMER_01474 [Parabacteroides merdae ATCC
43184]
gb|EDN87136.1| hypothetical protein PARMER_01474 [Parabacteroides merdae ATCC
43184]
Length=299
Score = 26.1 bits (54), Expect = 340
Identities = 7/8 (87%), Positives = 8/8 (100%), Gaps = 0/8 (0%)
Query 3 RAHPALIN 10
RAHPAL+N
Sbjct 170 RAHPALVN 177
>ref|XP_567332.1|
JEC21]
ref|XP_773201.1|
B-3501A]
gb|EAL18554.1|
B-3501A]
gb|AAW45815.1|
JEC21]
Length=437
GENE ID: 3254188 CNJ01520 | hypothetical protein
[Cryptococcus neoformans var. neoformans JEC21] (10 or fewer PubMed links)
Score = 26.1 bits (54), Expect = 340
Identities = 8/9 (88%), Positives = 8/9 (88%), Gaps = 0/9 (0%)
Query 1 SARAHPALI 9
SAR HPALI
Sbjct 415 SARQHPALI 423
>ref|YP_001626035.1|
gb|ABY24621.1|
Length=386
GENE ID: 5822379 RSal33209_2898 | citrate synthase
[Renibacterium salmoninarum ATCC 33209]
Score = 25.7 bits (53), Expect = 456
Identities = 9/11 (81%), Positives = 9/11 (81%), Gaps = 2/11 (18%)
Query 1 SARAHP--ALI 9
SARAHP ALI
Sbjct 218 SARAHPYAALI 228
>ref|YP_001817256.1|
PB90-1]
gb|ACB73656.1|
PB90-1]
Length=936
GENE ID: 6208547 Oter_0366 | integral membrane sensor hybrid histidine kinase
[Opitutus terrae PB90-1]
Score = 25.2 bits (52), Expect = 611
Identities = 7/7 (100%), Positives = 7/7 (100%), Gaps = 0/7 (0%)
Query 3 RAHPALI 9
RAHPALI
Sbjct 256 RAHPALI 262
>ref|YP_001757871.1|
kinase [Methylobacterium radiotolerans JCM 2831]
gb|ACB27188.1|
kinase [Methylobacterium radiotolerans JCM 2831]
Length=331
GENE ID: 6141303 Mrad2831_5232 | putative anti-sigma regulatory factor,
serine/threonine protein kinase [Methylobacterium radiotolerans JCM 2831]
Score = 25.2 bits (52), Expect = 611
Identities = 7/8 (87%), Positives = 8/8 (100%), Gaps = 0/8 (0%)
Query 2 ARAHPALI 9
ARAHPAL+
Sbjct 299 ARAHPALV 306
>ref|ZP_01466013.1| hydrolase, TatD family [Stigmatella aurantiaca DW4/3-1]
gb|EAU63211.1| hydrolase, TatD family [Stigmatella aurantiaca DW4/3-1]
Length=209
Score = 25.2 bits (52), Expect = 611
Identities = 7/7 (100%), Positives = 7/7 (100%), Gaps = 0/7 (0%)
Query 3 RAHPALI 9
RAHPALI
Sbjct 79 RAHPALI 85
>ref|YP_001558323.1|
gb|ABX41584.1|
Length=357
GENE ID: 5743305 Cphy_1206 | glycosyl transferase group 1
[Clostridium phytofermentans ISDg]
Score = 25.2 bits (52), Expect = 611
Identities = 8/10 (80%), Positives = 8/10 (80%), Gaps = 0/10 (0%)
Query 1 SARAHPALIN 10
S RAHP LIN
Sbjct 113 SERAHPLLIN 122
There does not appear to be a perfect match in the NCBI NR protein database. But take a close look at the #1 scoring hit. That is right, it is from and organism called Botryotinia fuckeliana. No comment on the appropriateness of this name, but it does contain a term I will probably use a lot if she gets elected.
Of course, anybody who has heard me blather on and on about evolution knows that I am always talking about how blast top hits are not a good measure of relatedness per se (see my NAR paper where I first talked about this in 1995). So - I decided to build a tree of Sarah Palin. I used the NCBI Distance Tree option which you can do from blast searches.
Since most likely you cannot see that in enough detail - here is a zoom in.
That one did not come through on the Blog so well either so I decided to output the tree in Newick format and then I searched for a program that could draw a better figure on the web (we have tools in my lab to do this but I am trying to do this all on the web as an exercise). And I found a web site that makes drawtree available. And I plugged in the Newick format and it made a nicer one.
Though making trees from really short sequences is not ideal, in this tree, Sarah Palin is shown to be at the root of a branch including a protein from the parasitic nematode Brugia malayi. So if we take an evolutionary interpretation it seems that this causative agent of filariasis (well, a protein from this agent) is descended from SarahPalin. In other words, she seems to be ancestral to this parasite.
So in conclusion - by similarity - SarahPalin is closest to a plant pathogen with an unusual name. And by phylogeny SarahPalin is ancestral to a parasitic nematode. Sounds about right.
That is fantastic! Widely forwarded already...
ReplyDeleteWait wait wait!
ReplyDeleteIn Parabacterioides merdae, the species name 'merdae' came from the french word 'merde', which is… crap (basically, the place in which you find this bacteria…)
Sequence alignment is so powerful!
You just cannot make this stuff up
ReplyDeleteClearly we can not vote into office someone who may have the power to regulate chromosomal condensation. Especially when she is already under investigation for abuse of power.
ReplyDeleteI can't believe I missed that. She IS condescending.
ReplyDeleteWhen I was a PhD student, my advisor was to speak of her work at a meeting of Israeli and Palestinian scientists & students. As the audience was very broad, the talks were to be very non-specific. So what's a bioinformatics lab to do? We decided it would be fun to look for PEACE in SwissProt. The top hit was... wait for it... the receptor for sperm coat protein in the human zona pellucida. The zona pellucida is the outer membrane of the oocyte.
ReplyDeleteMake love, not war!
Unbelievable. Sarah Palin is closely related to B. fukeliana? Too funny to be made up.
ReplyDeleteDid you search her kids' names to see if they are related to her? Maybe they aren't...
Priceless!!! I think this should become standard practice for anyone standing for office. In fact, lets propose that anyone with non-standard names come up with an appropriate spelling of their choice so that such an analysis can be performed.
ReplyDeleteI have to admit I sat in my chair and sniggered for half and hour after reading this. I then linked anyone I knew who was online at the time...no one else got it.
ReplyDeleteAny palindromic sequences?
ReplyDeleteI think we may have to redefine "palindromic" as "sequences that are indicative of very ancestral states" or something like that
ReplyDeleteI may write a new post on this --- but the best blast hit for "MCCAINPALIN" is ....
ReplyDelete>gb|ACE82429.1| polyprotein [Hepatitis C virus subtype 1a]
Length=3011
Score = 26.1 bits (54), Expect = 339
Identities = 8/10 (80%), Positives = 9/10 (90%), Gaps = 1/10 (10%)
_____Query 1 MCCAINPALI 10
____________MC AI+PALI
___Sbjct 877 MC-AIHPALI 885
Botryotinia fuckeliana (Botrytis cinerea) is a spoilage agent for wine grapes and also purposely encouraged to generate the Noble rot in the production of grapes for Sauterne style wines. Given her political orientation I can't figure out if this revelation means she is inherently for, or against, alcohol consumption. Maybe she's a pit bull with lipstick who likes dessert wines.
ReplyDeleteThankfully, someone changed the name to fuckeliana. Or my blog would not have gotten as much attention. I think given Palin's image, she is more likely to be a beer drinker than a wine drinker (nothing against her personally at all -- I am more on the beer than wine side of things too). And despite really not liking her politics, I cannot help liking some aspects of Palin's persona. Maybe her microbial connection is what does it, given that I still generally refuse to study "macrobes" and don;t like a lot of them ;-)
ReplyDeleteAwesome, just awesome! Thanks!
ReplyDelete*sigh* I can't wait to see the McCain attack ad about liberal anti-palin bias in evolutionists that comes from this post.
ReplyDeleteTrying to just report the facts here Shawna (with a little commentary here and there). If I could have searched using Obama I would have but he has letters in his full name that I could not use.
ReplyDeleteGood stuff, I agree, and quite funny. I do have to point out though that Sarah Palin, being an extant organism, is not "ancestral" to Brugia malayi. Instead, Sarah Palin and Brugia malayi descended from a common ancestor. I only point this out because we should get our evolutionary biology correct, and because it is perhaps even funnier. I wonder what the common ancestor looked like?
ReplyDeleteFinally Mark. Finally someone saw that. I put that there on purpose hoping that some other bloggers would call me to task on it. But alas everyone kept focusing on "fuckeliana". Imagine that. Yes, indeed, as a modern organism SARAHPALIN cannot be ancestral to other modern organisms.
ReplyDeleteI would hardly call her a modern organism.
ReplyDeleteKaren - how about "An organism living in modern times" or "An organism living in modern times that has not evolved much since it shared a common ancestor with parasitic nematodes"
ReplyDelete