CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3CZP_1 5FTK_1 4IPC_1 Letter Amino acid
19 13 2 Y Tyrosine
48 65 6 A Alanine
9 32 9 N Asparagine
47 68 7 E Glutamic acid
6 20 5 M Methionine
22 31 2 F Phenylalanine
17 40 9 S Serine
49 58 7 R Arginine
34 62 3 D Aspartic acid
23 26 6 Q Glutamine
10 10 2 H Histidine
34 47 5 K Lycine
20 43 7 P Proline
2 12 2 C Cysteine
28 63 9 G Glycine
47 69 14 L Leucine
16 3 0 W Tryptophan
27 53 11 V Valine
26 59 11 I Isoleucine
16 32 6 T Threonine 

3CZP_1|Chains A, B|Putative polyphosphate kinase 2|Pseudomonas aeruginosa PAO1 (208964)
>5FTK_1|Chains A, B, C, D, E, F|TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE|HOMO SAPIENS (9606)
>4IPC_1|Chain A|Replication protein A 70 kDa DNA-binding subunit|Homo sapiens (9606)
Protein code \(c\) LZ-complexity \(\mathrm{LZ}(w)\) Length \(n=|w|\) \(\frac{\mathrm{LZ}(w)}{n /\log_{20} n}\) \(p_w(1)\) \(p_w(2)\) \(p_w(3)\) Sequence \(w=f(c)\)
3CZP , Knot 199 500 0.82 40 227 457 
GHMFESAEVGHSIDKDTYEKAVIELREALLEAQFELKQQARFPVIILINGIEGAGKGETVKLLNEWMDPRLIEVQSFLRPSDEELERPPQWRFWRRLPPKGRTGIFFGNWYSQMLYARVEGHIKEAKLDQAIDAAERFERMLCDEGALLFKFWFHLSKKQLKERLKALEKDPQHSWKLSPLDWKQSEVYDRFVHYGERVLRRTSRDYAPWYVVEGADERYRALTVGRILLEGLQAALATKERAKRQPHAAPLVSSLDNRGLLDSLDLGQYLDKDAYKEQLAAEQARLAGLIRDKRFRQHSLVAVFEGNDAAGKGGAIRRVTDALDPRQYHIVPIAAPTEEERAQPYLWRFWRHIPARRQFTIFDRSWYGRVLVERIEGFCAPADWLRAYGEINDFEEQLSEYGIIVVKFWLAIDKQTQMERFKEREKTPYKRYKITEEDWRNRDKWDQYVDAVGDMVDRTSTEIAPWTLVEANDKRFARVKVLRTINDAIEAAYKKDKGA
5FTK , Knot 295 806 0.81 40 279 705 
MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFGSFRFPSGNQGGAGPSQGSGGGTGGSVYTEDNDDDLYG
4IPC , Knot 63 123 0.82 38 102 118 
GSHMVGQLSRGAIAAIMQKGDTNIKPILQVINIRPITTGNSPPRYRLLMSDGLNTLSSFMLATQLNPLVEEEQLSSNCVCQIHRFIVNTLKDGRRVVILMELEVLKSAEAVGVKIGNPVPYNE

Let \(P_w(n)\) be the set of distinct subwords (intervals) in a word \(w\). Let \(p_w(n)\) be the cardinality of \(P_w(n)\). Let \(f(c)\) be the sequence in FASTA with 4-symbol Protein Data Bank code \(c\).

\(|P_{f(3CZP_1)}(2) \setminus P_{f(5FTK_1)}(2)|=50\), \(|P_{f(5FTK_1)}(2) \setminus P_{f(3CZP_1)}(2)|=102\). Let \( Z_k(x,y)=|P_x(k)\setminus P_y(k)|+|P_y(k)\setminus P_x(k)| \) be a LZ76 style (set of subwords) Jaccard distance numerator for \(P(k)\).Hydrophobic-polar version of Sequence 1:10110010110010000000111010011101010100010111111101101110100101100110101101001101000010011010110011101001111101000110101010100101001101100100110001111101110100001000101100010001010110100001000110010011000000011101101100000110110111011011110000100010111110010001110010110010001000011100101111100001000011111010011101111001001101000011111110000010101101100111000101100010101110010110111011010101001000100011111011111000001001000000100000100001000001000101110110000001111011010000110101100100110110000011
Pair \(Z_2\) Length of longest common subsequence
3CZP_1,5FTK_1 152 4
3CZP_1,4IPC_1 187 5
5FTK_1,4IPC_1 207 3

Newick tree

 
[
	4IPC_1:10.09,
	[
		3CZP_1:76,5FTK_1:76
	]:29.09
]

Let d be the Otu--Sayood distance d.
Let d1 be the Otu--Sayood distance d1. (This makes the 4TYN sequence AAAAAA a close match...)
A roughly speaking expected distance is \((0.85)(0.8)(\frac{1306 }{\log_{20} 1306}-\frac{500}{\log_{20}500})=206.\)
Status Protein1 Protein2 d d1/2
Query variables 3CZP_1 5FTK_1 262 210
Was not able to put for d
Was not able to put for d1

In notation analogous to [Theorem 16, Kjos-Hanssen, Niraula and Yoon (2022)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]