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I am one ignorant...

Why GAG protein HIV-1 (virus) is in Staphylococcus sp. SS21 and in Klebsiella quasipneumoniae (Bacteria)? These are the links in GenBank:

Staphylococcus sp. SS21
LOCUS       WP_193573829             503 aa            linear   BCT 29-OCT-2020
DEFINITION  hypothetical protein [Staphylococcus sp. SS21].

HIV-1
LOCUS       KU749412                9188 bp    RNA     linear   VRL 08-DEC-2016
DEFINITION  HIV-1 isolate DEMC14PK009 from Pakistan, partial genome.

protein align:

mgarasllsggqldrwerirlrpggkkkyrlkhivwasrelerfavnpgllessegcrkileqlqpslqtgseelrslyntvavlycvqqridvkdtkealekieeeqnkskkkaqqtaadkgnnspvsqnfpivqnlqgqmvhqpisprtlnawvkvveekafspevipmfsalsegatpqdlntmlntvgghqaamqmlketineeaaewdrlhpvhagpvapgqmreprgsdiagttstlqeqigwmtnnpaipvgeiykrwiilglnkivrmysptsildirqgpkepfrdyvdrfyktlraeqasqdvknwmtetllvqnanpdcktilkalgpaatleemmtacqgvggpshkarilaeamsqvtqptnilmqrgnfrtprktvkcfncgkeghiakncraprkkgcwkcgkeghqmkdcserqanflgkiwpshkgrpgnflqnrpeptappappeesfrfgegtttpaqkqepidkdlyplaslkslfgndpssq
|||||| | |  || |||||||||||| | ||| ||||||| ||| ||||||  |||  |  |||| |||| |||||| |||| ||||   | |||||||| ||||||||   || |  |        | | ||||||||||||| |||||||||||| ||||||||||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||| ||| | | ||  ||||||||||||||||||||||| |||||||||||||||||||| |||||||| |||||||| ||||||||||||||| |||| |||||||||||||||| |||| ||||||| |      ||| ||     | |||||||||| | ||||||||||||||||||||||| ||||||||||||||||||||||| |||||||||   ||||| | || || |||  ||   || ||||||| || ||         
MGARASILRGEKLDTWERIRLRPGGKKHYMLKHLVWASRELDRFALNPGLLETLEGCKQIIKQLQPALQTGTEELRSLFNTVATLYCVHAGIPVKDTKEALDKIEEEQNKCQQKAKQ--AEAAAAGKISLNYPIVQNLQGQMVHQAISPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPVAPGQMREPRGSDIAGTTSTLAEQIAWITGNPPVPVGEIYKRWIILGLNKIVRMYSPXSILDIRQGPKEPFRDYVDRFFKTLRAEQATQDVKNWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGVGGPGHKARVLAEAMSQTT--NAIMMQRSNFKGPKRTIKCFNCGKEGHLARNCRAPRKKGCWKCGKEGHQMKDCNERQANFLGKIWPSHKGRPGNFLQSRPEPTAPPA---ESFRF-EETT-PAPKQEQKDK--EPLTSLKSLFGSDPLSQ

The links in GenBank of Klebsiella quasipneumoniae :

LOCUS       WP_199660587             458 aa            linear   BCT 06-JAN-2021
DEFINITION  hypothetical protein, partial [Klebsiella quasipneumoniae].
ACCESSION   WP_199660587
VERSION     WP_199660587.1

protein align:

-----------------------grkkyk-lkhlvwasrelerfalnpgllesaegcqqimeqlqsalgtgseelkslfntvatlwcvhqrieikdtkealdkveevkskqkaqqaqrtqqaaaatgsssqnypivqnaqgqmvhqsmsprtlnawvkvveekafspevipmftalsegatpqdlnmmlnivgghqaamqmlkdtineeaaewdrthpvhagpvapgqireprgsdiagttstlqeqigwmtnnppipvgeiykrwivlglnkivrmyspvsildirqgpkepfrdyvdrffktlraeqatqevknwmtesllvqnanpdcktilrglgpgatleemmtacqgvggpghkarvlaeamsqaqqsnimmqrgnfrg-qrtikcfncgkeghiarnckaprkrgcwkcgkeghqmkdcnerqanflgriwpshkgrpgnfpqsrpeptappaesf-geevtpsprqe-----pvd--kel-----ypp
                       | ||   ||||||||||| ||||||||||  ||| ||  ||| || || ||| ||||||||| |||  |  ||||||||  ||   |   | |   |  ||| |  | ||||||| |||||||  ||||||||||| |||||||||||||||||||||||||| ||| |||||||||||||||||||||||| |||||||||||| ||||||||||||||| ||| | | ||| |||||||||| |||||||||||| ||||||||||||||||||||||||||||||||||||||| ||||||||||||||| |||||||||||||||||||||||||||||||||     ||||| || |  ||||||||||||| |||| |||| |||||||||||||||||||||||| |||||||||||| ||||||||||||||  || || | ||     |    | |   
MGARASILRGEKLDTWERIRLRPGGKKHYMLKHLVWASRELDRFALNPGLLETLEGCKQIIKQLQPALQTGTEELRSLFNTVATLYCVHAGIPVKDTKEALDKIEEEQNK-CQQKAK--QAEAAAAGKISLNYPIVQNLQGQMVHQAISPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPVAPGQMREPRGSDIAGTTSTLAEQIAWITGNPPVPVGEIYKRWIILGLNKIVRMYSPXSILDIRQGPKEPFRDYVDRFFKTLRAEQATQDVKNWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGVGGPGHKARVLAEAMSQ-TTNAIMMQRSNFKGPKRTIKCFNCGKEGHLARNCRAPRKKGCWKCGKEGHQMKDCNERQANFLGKIWPSHKGRPGNFLQSRPEPTAPPAESFRFEETTPAPKQEQKDKEPLTSLKSLFGSDPLSQ

The links in GenBank of hypothetical protein HMV63_24500 [Escherichia coli] and protein align with HIV-1 GAG:

LOCUS       HAJ5901352               246 aa            linear   BCT 11-MAY-2020
DEFINITION  TPA: hypothetical protein HMV63_24500 [Escherichia coli].
ACCESSION   HAJ5901352
VERSION     HAJ5901352.1

-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------mtsnppipvgdiykrwiilglnkivrmyspvsildirqgpkepfrdyvdrffktlraeqatqdvknwmtetllvqnanpdcktilralgpgasleemmtacqgvggpshkarvlaeamsqannanimmqksnfkgprrnvkcfncgkeghiarncraprkrgcwkcgkeghqmkdcterqanflgkiwpshkgrpgnflqsrpeptappaesfkfeettptprqeprdrepltslkslfgsdplsq
                                                                                                                                                                                                                                                        | ||| ||| ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| |||||||||||||| ||||||||||||  || |||| |||||| |  |||||||||||||||||||| ||||||||||||||| |||||||||||||||||||||||||||||||||||| |||||| | ||| | |||||||||||||||||      
MGARASILRGEKLDTWERIRLRPGGKKHYMLKHLVWASRELDRFALNPGLLETLEGCKQIIKQLQPALQTGTEELRSLFNTVATLYCVHAGIPVKDTKEALDKIEEEQNKCQQKAKQAEAAAAGKISLNYPIVQNLQGQMVHQAISPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPVAPGQMREPRGSDIAGTTSTLAEQIAWITGNPPVPVGEIYKRWIILGLNKIVRMYSPXSILDIRQGPKEPFRDYVDRFFKTLRAEQATQDVKNWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGVGGPGHKARVLAEAMSQTTNA-IMMQRSNFKGPKRTIKCFNCGKEGHLARNCRAPRKKGCWKCGKEGHQMKDCNERQANFLGKIWPSHKGRPGNFLQSRPEPTAPPAESFRFEETTPAPKQEQKDKEPLTSLKSLFGSDPLSQ

I remember Blast find result in plant bacteria or virus too

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2 Answers 2

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The interesting numbers of an alignment are coverage (91%) and identity (82.68%) of API70200.1 (the protein encoded in KU749412) against WP_199660587.

There are two cases:

  • technical error: samples were contaminated, which happens not infrequently.
  • biology did something cool: horizontal gene transfer

The former is likely to be present when you have a single sequence where this gene is present and it is not from a complete genome.

The latter, unless it's an ancient transfer, would likely result in flanking regions and genes.

So blasting the gene to the Klebsiella quasipneumoniae proteome, shows there are three hits (two poor). There is no strain name in list, whereas there are three complete genomes of three strains. So the sequence WP_199660587 is a one off and not from a complete genome. Therefore, the clues strongly point towards it being a technical error.

enter image description here

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  • $\begingroup$ so "samples were contaminated," you say manchine that return the sequence do not make difference of DNA (Batteria) and RNA (HIV-1) virus??? possible error in data copy paste $\endgroup$
    – RosLuP
    Jan 9, 2021 at 15:29
  • $\begingroup$ HIV inserts its genome into the nuclear genome by using an enzyme, reverse transcriptase, which copies the RNA as DNA. This same enzyme is used by humans to sequence RNA (the reverse transcribed version is called cDNA). Whereas Nanopore can actually read RNA the required processing for DNA samples is incompatible, so it was either gDNA or cDNA contamination during sample prep. $\endgroup$
    – Matteo Ferla
    Jan 9, 2021 at 15:46
  • $\begingroup$ for me could be one lab escape... it seems the page is for me this science.sciencemag.org/content/266/5193/1981/tab-e-letters the genbank file is LOCUS WP_142766724 415 aa linear BCT 07-JAN-2020 DEFINITION DDE-type integrase/transposase/recombinase, partial [Klebsiella pneumoniae]. $\endgroup$
    – RosLuP
    Jan 10, 2021 at 23:40
  • $\begingroup$ Bacteria are so numerous and so diverse that pretty much all sorts of oddities can happen, such as naked viral cDNA being absorbed and integrated via native recombinases. However, there are all sorts of "oh that's interesting" in environmental bacteria, but the truth is that only stuff that gets made into technology is looked at and that step requires a lot of effort. Say new enzymes, I have speculated the function of scores of enzymes and every time it I or others have placed then in the category "too much effort over publication impact". $\endgroup$
    – Matteo Ferla
    Jan 11, 2021 at 10:50
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for me could be one lab escape...

it seems the page is for me this

  https://science.sciencemag.org/content/266/5193/1981

there is a pay wall so I can not read that... The title is

Crystal structure of the catalytic domain 
of HIV-1 integrase: 
similarity to other polynucleotidyl transferases

i know nothing of argument, but it seems someone unknow for unknow reason infect one bacteria of Klebsiella pneumonia with the virus HIV-1. Someone know what happen if one common bacteria infect with the HIV-1 is diffused? what happen if there is something activate virus replication in the bacteria when the bacteria is in some human?

the genbank file would be:

LOCUS WP_142766724 415 aa linear BCT 07-JAN-2020
DEFINITION DDE-type integrase/transposase/recombinase, partial
 [Klebsiella pneumoniae].

The general speech

We, You don't have the right (or the intelligence) to change 
one iota of any DNA or RNA. Genetic material, if we still 
want to live a few years, must always be read-only, 
never re-written from us because consequences are unknows.
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  • $\begingroup$ Eukaryotic viruses cannot infect bacteria. The cell wall is thick. The membrane has different protein (entrypoints) and then even if you transformed a bacterium with a viral genome on a plasmid it would not express because of promoters and very different codon bias. And... if you made a codon-optimised viral proteome under bacterial promoters and transformed it the assembled viral particles would not be able to get out. $\endgroup$
    – Matteo Ferla
    Jan 11, 2021 at 10:54
  • $\begingroup$ for me not deep enought $\endgroup$
    – RosLuP
    Jan 11, 2021 at 11:45

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