CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3UIG_1 5JUW_1 1PNJ_1 Letter Amino acid
3 7 1 W Tryptophan
13 32 4 A Alanine
7 22 6 D Aspartic acid
4 12 2 Q Glutamine
19 35 10 E Glutamic acid
5 19 5 I Isoleucine
16 40 6 K Lycine
4 26 5 S Serine
5 19 3 N Asparagine
11 30 7 L Leucine
3 13 1 M Methionine
10 25 3 P Proline
7 21 4 T Threonine
6 27 4 R Arginine
7 26 12 G Glycine
4 11 1 H Histidine
6 3 0 C Cysteine
11 13 2 F Phenylalanine
0 15 7 Y Tyrosine
2 25 3 V Valine 

3UIG_1|Chains A, B|Baculoviral IAP repeat-containing protein 5|Homo sapiens (9606)
>5JUW_1|Chain A|Histone-lysine N-methyltransferase, H3 lysine-79 specific|Homo sapiens (9606)
>1PNJ_1|Chain A|PHOSPHATIDYLINOSITOL 3-KINASE P85-ALPHA SUBUNIT SH3 DOMAIN|Bos taurus (9913)
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 \(w=f(c)\)
3UIG , Knot 69 143 0.79 38 106 135 
GMGAPTLPPAWQPFLKDHRISTFKNWPFLEGCACTPERMAEAGFIHCPTENEPDLAQCFFCFKELEGWEPDDDPIEEHKKHSSGCAFLSVKKQFEELTLGEFLKLDRERAKNKIAKETNNKKKEFEETAKKVRRAIEQLAAMD
5JUW , Knot 181 421 0.86 40 238 406 
GMGEKLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTTQPMKLNTRPSTGLLRHILQQVYNHSVTDPEKLNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKGSVSWTGKPVSYYLHTIDRTILENYFSSLKNPKLREEQEAARRRQQRESKSNAATPTKGPEGKVAGPADAPMDSGAEEEKAGAATVKKPSPSKARKKKLNKKGRKMAGRKRGRPKKMNTA
1PNJ , Knot 45 86 0.77 38 75 84 
GSMSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEAKPEEIGWLNGYNETTGERGDFPGTYVEYIGRKKISP

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 \(c\).

\(|P_{f(3UIG_1)}(2) \setminus P_{f(5JUW_1)}(2)|=35\), \(|P_{f(5JUW_1)}(2) \setminus P_{f(3UIG_1)}(2)|=167\). 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 1:11111011111011100001001001111010100100110111100100001011001101001011010001100000000101110100010010110110100001000110000000001000100100110011110
Pair \(Z_2\) Length of longest common subsequence
3UIG_1,5JUW_1 202 3
3UIG_1,1PNJ_1 137 3
5JUW_1,1PNJ_1 211 5

Newick tree

 
[
	5JUW_1:11.50,
	[
		3UIG_1:68.5,1PNJ_1:68.5
	]:44.00
]

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 \((0.85)(0.8)(\frac{564 }{\log_{20} 564}-\frac{143}{\log_{20}143})=122.\)
Status Protein1 Protein2 d d1/2
Query variables 3UIG_1 5JUW_1 158 104
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]