Interior viral origin in pol via selkov

The residue study of active site flap, reverse transcriptase thumb domain in HIV pol identity.
by Mark McGary 5/17/2014

Few organizational motief’s in protein are as complex and difficult to assess as the intricate fold region of HIV pol. However, this interesting problem is modeled by the selkov technique and multiplex link assay.
Here, the observer needs to understand every passage in selkov determinant is poised within questions such as…..”Can I foresee mutation adventure within the assay? and….. “What specific observations are coherent?” Observationally, ready to sieze upon alignment and prophensity of multi species regard…..as to “What makes sense”.

Using the multivariant species….selkov view, the assay chain of events via reverse transcriptase thumb domain…as an active site flap… leads to tetraymena thermophila and papio anubis. *diguanyla cyclase, and the interesting pathogen sets of vibro, coriobacter g, ecor, streptococcus….within a replication related sequence data of hitherto impenetrable domain.
Here, one must take the view of an adventure in protein. Guided by selkov results.
As observationally coherent, the baboon residue as aligned within the HIV pol regionality are in the author’s humble opinion, unique towards the HIV ORF.
Here is a view of the ape-homo sapiens intersection in residue premised of substance within the transcriptional impact,
XP_003899201 2535 IHQFSTMIDDIKATQTDIKLSRYTAGSASPTPTFKTRKHRDFRSSDFSRSSRGSLNGGNRVNNAKNKRTNNENNKKESRN 2614 ETW57687 1075 WETFAPSIWNGMICALTYKDNSET-GPKGKAP—-KQNKDLKEKLWDNDGNKPKNG-NDYNSVTLKDENSGAQPNQTPS 1148 XP_001302210 540 VKQIMTVVHIDSNSLNEIDTIKVFVDICSKLIQDLDQKVRPILGFAGKVVEIPSQIGEYIDGLLKREEEKIEVIKKENSL 619 XP_002815313 1 ———————————————————————-MAVAAALTGL 10 EAX05237 510 IHQFSTMIDDIKATQTDIKLSRYTAGSASPTPTFKTRKHRDFRSSDFSRSSRGSLNGGNRVNNAKNKRTNNENNKKESRN 589 XP_003899201 2615 KNS ———-LGRSERRTSKVSRKGSKDVVDHMT IHMDDSDSITVSEQSEPSAECWQNMYKLLN——- 2671 ETW57687 1149 TTS[7]FVVRPPYFryLEEWGETFCRERRKRLRKIRGECT –KDGGKTKKCSGDGEYCEEIFSKKYNVLQDLSWSCA 1227 XP_001302210 620 KIK ELNSKLAD–VKQTNEALNDKLRKIAFELRTVF-[2]LEKTRKQNSALTEQLEVA—-TDRIEIEKGENTKIQ 688 XP_002815313 11 QAE[7]DYLSDPIT–IECGHNFCRSCIQQSWMDLQELFP[8]QEGHFRSNTQLGRMIEIAKLLQSTKSNKRKQEETTLC 97 EAX05237 590 KNS ———-LGRSERRTSKVSRKGSKDVVDHMT IHMDDSDSITVSEQSEPSAECWQNMYKLLN——- 646 XP_003899201 2672 —–FYSLISDPTGILEKSSETFGPAGVRSPTEPTCKVVFENEQDNSSLTKTQRKRSL-VTSEPQHvtlIVFGIGMVNR 2745 ETW57687 1228 KPCRLYKTWIEKKRTEFEEQKKAYGDQKQNCKEESKGA—QSNKDSNGVCGTLEKTCN-TAKD——FLQKLGPCSK 1297 XP_001302210 689 ERQNQYVSVIKSLQSEVKRQEALLK-ERQEVNERRIEQMLENERQLRFDEVDALKRKQKaELSELQN—-QVGRKREKL 763 XP_002815313 98 EKHNQPLSVFCKEDLMVLCPLCTQPPDHQGHHVRPIEKAAIHYRKRFCSYIQPLKK—-QLADLQK—-LISTQSKKP 169 EAX05237 647 —–FYSLISDPTGILEKSSETFGPAGVRSPTEPTCKVVFENEQDNSSLTKTQRKRSL-VTSEPQHvtlIVFGIGMVNR 720 XP_003899201 2746 THLEADIGGLTME–SELKRIHGS-FTLKEKMKDVLHQKMTE TCATAHIG—————-GVNIVLLEGIT 2803 ETW57687 1298 NNSGDDKKG—E–DEIKF———DDDKTFQHTNLCD PCSKFNVNCKENGNcTDVQGNTctGTTVITAENFK 1360 XP_001302210 764 SEIKVSLQKLREE-kEETEHALKMkITELEQENESTI-RMAE[3]VLCKSRIEELMQLN-TELEGKV–KSLALLSQRNS 838 XP_002815313 170 LELREMVENQRQElsSEFEHLNQF—-LDREQQAVLSRLAE[6]QKLSANITAFSNYS-ATLKSQL–SKVVELSELSE 245 EAX05237 721 THLEADIGGLTME–SELKRIHGS-FTLKEKMKDVLHQKMTE TCATAHIG—————-GVNIVLLEGIT 778
Plasmodium and trich. v. joining the viewpoint to observe pathogenesis descriptors as potentially conserved residue.
The underlying foment and decay indicators addative in insult….as active site flap regards completing the commensual additions to interior HIV evasion and conservation mechanism of sheer formatible uptake post corynebacter envelope transition, premised. Active residues of thermophyllic organism also contribute to active chemistries. As well as a curious mechanism observed in citrus residue linked decay.
Why the typical alignment tools do not adequately grapple with mutation adventure are regards of what view the observer determines via result. Here are the pathways observed incomplete, but which futher a more robust view of the HIV interior mechanisms, species insult and uptake, and provide interesting premise to treatment modality beyond the typical scope of sequence data toward a single species, single locus by assay of interior motiefs of actual conserved mutation. With the clear objective of a larger view in mutation, I trace the steps of adequate inquiry. The method of selkov as a multiplex view is rather an additional advance to the toolbar, but very useful indeed in large block assay of interior gene, specific to mutation adventure via species within the envelope domain of viral ORF.

To begin, I should introduce the reader to the parallel in sargauro cactus virus and HIV pol.
That is to ask….., “If the parallel in a single species is found coherent, would not more emerge with parallel method?
*exact blast challenge:
CLVEEKKITEHDLKVEVTLDHEHEDGDKRTCKKVGVVRLTFRKTMLANARLHEANRAGRTAS
results:
gb|AAB36707.1| replication-related protein [Saguaro cactus virus]” class=”deflnDesc” id=”deflnDesc_1″ onclick=”DisplayAlignFromDescription(this);” href=”#alnHdr_9629191″ ind=”1″ seqid=”9629191″ gi=”9629191″ seqfsta=”gi|9629191″ accs=”ref|NP_044383.1|” len=”31″ hsp=”1″ stat=”disp”replication-related protein [Saguaro cactus virus] >gb|AAB36707.1| replication-related protein [Saguaro cactus virus] 101 101 100% 1e-22 100% NP_044383.1 Select seq ref|NP_044382.1|
gb|AAB36710.1| SCVP86 [Saguaro cactus virus]” class=”deflnDesc” id=”deflnDesc_2″ onclick=”DisplayAlignFromDescription(this);” href=”#alnHdr_9629194″ ind=”2″ seqid=”9629194″ gi=”9629194″ seqfsta=”gi|9629194″ accs=”ref|NP_044382.1|” len=”31″ hsp=”1″ stat=”disp”SCVP86 [Saguaro cactus virus] >gb|AAB36710.1| SCVP86 [Saguaro cactus virus] 101 101 100% 2e-22 100% NP_044382.1 Select seq gb|ABB79924.1|
putative polymerase-associated protein [Pelargonium flower break virus] 51.1 51.1 70% 1e-05 74% ABB79924.1 Select seq gb|ABB79925.1|
RNA-dependent RNA polymerase [Pelargonium flower break virus] 51.1 51.1 70% 1e-05 74% ABB79925.1 Select seq ref|NP_945124.1|
emb|CAD55836.1| p27 protein [Pelargonium flower break virus]” class=”deflnDesc” id=”deflnDesc_5″ onclick=”DisplayAlignFromDescription(this);” href=”#alnHdr_39163633″ ind=”5″ seqid=”39163633″ gi=”39163633″ seqfsta=”gi|39163633″ accs=”ref|NP_945124.1|” len=”23″ hsp=”1″ stat=”disp”p27 protein [Pelargonium flower break virus] >emb|CAD55836.1| p27 protein [Pelargonium flower break virus] 50.7 50.7 70% 1e-05 74% NP_945124.1 Select seq ref|NP_945123.1|
emb|CAD55835.1| p86 protein [Pelargonium flower break virus]” class=”deflnDesc” id=”deflnDesc_6″ onclick=”DisplayAlignFromDescription(this);” href=”#alnHdr_39163632″ ind=”6″ seqid=”39163632″ gi=”39163632″ seqfsta=”gi|39163632″ accs=”ref|NP_945123.1|” len=”23″ hsp=”1″p86 protein [Pelargonium flower break virus] >emb|CAD55835.1| p86 protein [Pelargonium flower break virus] 50.7 50.7 70% 2e-05 74% NP_945123.1 Select seq ref|NP_945122.1|
emb|CAD55834.1| p99 protein [Pelargonium flower break virus]” class=”deflnDesc” id=”deflnDesc_7″ onclick=”DisplayAlignFromDescription(this);” href=”#alnHdr_39163631″ ind=”7″ seqid=”39163631″ gi=”39163631″ seqfsta=”gi|39163631″ accs=”ref|NP_945122.1|” len=”23″ hsp=”1″p99 protein [Pelargonium flower break virus] >emb|CAD55834.1| p99 protein [Pelargonium flower break virus] 50.7 50.7 70% 2e-05 74% NP_945122.1 Select seq ref|YP_008378652.1|
gb|ACT36595.1| P28 [Calibrachoa mottle virus]” class=”deflnDesc” id=”deflnDesc_8″ onclick=”DisplayAlignFromDescription(this);” href=”#alnHdr_529154248″ ind=”8″ seqid=”529154248″ gi=”529154248″ seqfsta=”gi|529154248″ accs=”ref|YP_008378652.1|” len=”33″ hsp=”1″P28 [Calibrachoa mottle virus] >gb|ACT36595.1| P28 [Calibrachoa mottle virus] 46.0 46.0 93% 4e-04 61% YP_008378652.1 Select seq ref|YP_008378651.1|
gb|ACT36594.1| P87 [Calibrachoa mottle virus]” class=”deflnDesc” id=”deflnDesc_9″ onclick=”DisplayAlignFromDescription(this);” href=”#alnHdr_529154247″ ind=”9″ seqid=”529154247″ gi=”529154247″ seqfsta=”gi|529154247″ accs=”ref|YP_008378651.1|” len=”33″ hsp=”1″P87 [Calibrachoa mottle virus] >gb|ACT36594.1| P87 [Calibrachoa mottle virus] 46.0 46.0 93% 5e-04 61% YP_008378651.1 Select seq ref|YP_004191790.1|
gb|ADV15467.1| p27 [Honeysuckle ringspot virus]” class=”deflnDesc” id=”deflnDesc_10″ onclick=”DisplayAlignFromDescription(this);” href=”#alnHdr_320202720″ ind=”10″ seqid=”320202720″ gi=”320202720″ seqfsta=”gi|320202720″ accs=”ref|YP_004191790.1|” len=”31″ hsp=”1″p27 [Honeysuckle ringspot virus] >gb|ADV15467.1| p27 [Honeysuckle ringspot virus] 36.3 36.3 93% 0.72 58% YP_004191790.1

Now with a multispecies view, inclusive of reptile, let us further examine the interesting observational motief presented above with a view to intersection with precursor elements.
The exact blast challenge, NCBI, NIH. Below:
CLVEEKKITEHDLKVEVTLDHEHEDGRKCTKKGVVVLRFTKRMTATANLREHHAARRGTSQ

Extracted species results, from larger output as larger interesting study notes:
Below:
XP_006485460.1
PREDICTED: pentatricopeptide repeat-containing protein At5g04780-like [Citrus sinensis] CAI56756.1
hypothetical protein [Homo sapiens] ABM88765.1
erythrocyte membrane protein 1 [Plasmodium falciparum] BAG10419.1
KIAA1109 protein [synthetic construct] ABC59821.1
fragile site-associated protein [Homo sapiens] NP_056127.2
uncharacterized protein KIAA1109 [Homo sapiens] >ref|XP_005263344.1| PREDICTED: uncharacterized protein KIAA1109 isoform X6 [Homo sapiens] >sp|Q2LD37.2|K1109_HUMAN RecName: Full=Uncharacterized protein KIAA1109; AltName: Full=Fragile site-associated protein XP_005263343.1
PREDICTED: uncharacterized protein KIAA1109 isoform X5 [Homo sapiens] XP_005263342.1
PREDICTED: uncharacterized protein KIAA1109 isoform X4 [Homo sapiens] XP_005263339.1
PREDICTED: uncharacterized protein KIAA1109 isoform X1 [Homo sapiens] >ref|XP_005263340.1| PREDICTED: uncharacterized protein KIAA1109 isoform X2 [Homo sapiens] >ref|XP_005263341.1| PREDICTED: uncharacterized protein KIAA1109 isoform X3 [Homo sapiens] YP_002941222.1
ferric uptake regulator, Fur family [Kosmotoga olearia TBF 19.5.1] >ref|WP_015868863.1| Fur family transcriptional regulator [Kosmotoga olearia] >gb|ACR80218.1| ferric uptake regulator, Fur family [Kosmotoga olearia TBF 19.5.1] WP_002706615.1
CheW domain protein [Treponema saccharophilum] >gb|EIC00436.1| CheW domain protein [Treponema saccharophilum DSM 2985] XP_003896839.1
PREDICTED: thiamin pyrophosphokinase 1-like [Papio anubis] WP_009594072.1
hypothetical protein [Paenibacillus sp. HGF5] >gb|EGG34075.1| leucine rich repeat protein [Paenibacillus sp. HGF5] XP_005314453.1
PREDICTED: E3 ubiquitin-protein ligase RNF43-like isoform X2 [Chrysemys picta bellii]
Here, the data as a mined result has become observational from HIV-1 pol origin to a multispecies view, coherent in potential mechanisms and observational to the viral replication related protein. This is the viewpoint that might suggest an adequate index case assignment to the HIV virus particulars to pol origin. One must discard the pathogen set and full assess the primate to determine best further assessment regard, but happily, the set includes operant conservation of primate to gather a sense of where the pathogen insult must reside…and where multispecies….a firm understanding that the computational alogrythm has indeed aligned actual proteins in whatever regard as multispecies in origin….and must therefore be robust. The sheer power of this alignment can easily be overwhelming without regard to refinement in further selection. Here the application of additional selkov toolbar findings are additive to inquiry towards pathogenesis and mutation adventure as observed conserved and potential of insult…..and replication.

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