CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4WKW_1 7NHJ_1 6YCJ_1 Letter Amino acid
27 7 42 A Alanine
18 12 37 E Glutamic acid
13 13 13 H Histidine
20 25 35 L Leucine
10 11 11 N Asparagine
9 17 20 I Isoleucine
14 14 32 P Proline
12 10 22 T Threonine
6 7 10 W Tryptophan
5 6 13 Y Tyrosine
14 18 26 D Aspartic acid
2 5 3 C Cysteine
14 24 31 G Glycine
9 9 6 K Lycine
10 10 20 S Serine
10 17 27 R Arginine
6 11 9 Q Glutamine
6 6 8 M Methionine
7 8 14 F Phenylalanine
16 16 30 V Valine 

4WKW_1|Chains A, B|Uncharacterized protein|Mycobacterium leprae (561304)
>7NHJ_1|Chain A|N6-adenosine-methyltransferase catalytic subunit|Homo sapiens (9606)
>6YCJ_1|Chain A|Aromatic O-demethylase, cytochrome P450 subunit|Amycolatopsis sp. (strain ATCC 39116 / 75iv2) (385957)
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 \(w=f(c)\)
4WKW , Knot 102 228 0.81 40 159 218 
MAHHHHHHMGTLEAQTQGPGSMPEKASVKYQADLWFDPLCPWCWITSRWILEVEKVRDVEVHFHVMSLAILNENREDLTENYLENITKAWGPARVVIAAEQANGASVLDPLYTAMGIRIHNEDNKNLDEVIKRSLADTGLPAELAAAAQSNAYDDALRESHHAGMDPVGDDVGTPTVHVNGVAFFGPVLSKIPRGEEAGKLWDASLTLAAYPHFFELKRTRTEPPQFA
7NHJ , Knot 113 246 0.84 40 167 234 
MGHHHHHHSSGRENLYFQGALTQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
6YCJ , Knot 168 409 0.82 40 219 390 
GPMTTTERPDLAWLDEVTMTQLERNPYEVYERLRAEAPLAFVPVLGSYVASTAEVCREVATSPDFEAVITPAGGRTFGHPAIIGVNGDIHADLRSMVEPALQPAEVDRWIDDLVRPIARRYLERFENDGHAELVAQYCEPVSVRSLGDLLGLQEVDSDKLREWFAKLNRSFTNAAVDENGEFANPEGFAEGDQAKAEIRAVVDPLIDKWIEHPDDSAISHWLHDGMPPGQTRDREYIYPTIYVYLLGAMQEPGHGMASTLVGLFSRPEQLEEVVDDPTLIPRAIAEGLRWTSPIWSASARISTKPVTIAGVDLPAGTPVMLSYGSANHDTGKYEAPSQYDLHRPPLPHLAFGAGNHACAGIYFANHVMRIALEELFEAIPNLERDTREGVEFWGWGFRGPTSLHVTWEV

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 \(c\).

\(|P_{f(4WKW_1)}(2) \setminus P_{f(7NHJ_1)}(2)|=82\), \(|P_{f(7NHJ_1)}(2) \setminus P_{f(4WKW_1)}(2)|=90\). 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 1:110000001101010001110110010100010111011011011000111010010010101011011110000001000010010011111011111001011011011001111010000000100110001100111101111100010001100000111011100110101010111111111001101001101101010111010110100000011011
Pair \(Z_2\) Length of longest common subsequence
4WKW_1,7NHJ_1 172 6
4WKW_1,6YCJ_1 160 4
7NHJ_1,6YCJ_1 168 3

Newick tree

 
[
	7NHJ_1:86.61,
	[
		4WKW_1:80,6YCJ_1:80
	]:6.61
]

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 \((0.85)(0.8)(\frac{474 }{\log_{20} 474}-\frac{228}{\log_{20}228})=71.1\)
Status Protein1 Protein2 d d1/2
Query variables 4WKW_1 7NHJ_1 88 87
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]