CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
1GKZ_1 4JFK_1 7OZL_1 Letter Amino acid
24 8 25 S Serine
1 1 3 W Tryptophan
23 7 26 A Alanine
42 9 21 L Leucine
27 8 20 I Isoleucine
17 16 13 K Lycine
13 4 11 Y Tyrosine
21 9 20 V Valine
8 4 25 N Asparagine
27 7 5 D Aspartic acid
26 3 4 H Histidine
9 2 9 M Methionine
15 6 15 F Phenylalanine
4 2 4 C Cysteine
25 15 12 G Glycine
19 10 16 E Glutamic acid
20 6 19 P Proline
22 6 32 T Threonine
31 3 16 R Arginine
14 2 9 Q Glutamine 

1GKZ_1|Chain A|[3-METHYL-2-OXOBUTANOATE DEHYDROGENASE [LIPOAMIDE]] KINASE|RATTUS NORVEGICUS (10116)
>4JFK_1|Chain A|Peptidyl-prolyl cis-trans isomerase FKBP5|Homo sapiens (9606)
>7OZL_1|Chain A|Capsid protein VP1|Human enterovirus 70 (strain J670/71) (31915)
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 \(w=f(c)\)
1GKZ , Knot 164 388 0.84 40 213 367 
STSATDTHHVELARERSKTVTSFYNQSAIDVVAEKPSVRLTPTMMLYSGRSQDGSHLLKSGRYLQQELPVRIAHRIKGFRSLPFIIGCNPTILHVHELYIRAFQKLTDFPPIKDQADEAQYCQLVRQLLDDHKDVVTLLAEGLRESRKHIEDEKLVRYFLDKTLTSRLGIRMLATHHLALHEDKPDFVGIICTRLSPKKIIEKWVDFARRLCEHKYGNAPRVRINGHVAARFPFIPMPLDYILPELLKNAMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGGGIAHKDLDRVMDYHFTTAEASTQDPRISPLFGHLDMHSGGQSGPMHGFGFGLPTSRAYAEYLGGSLQLQSLQGIGTDVYLRLRHIDGREESFRIHHHHHH
4JFK , Knot 65 128 0.82 40 104 125 
GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEICHLLCKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
7OZL , Knot 132 305 0.82 40 187 292 
ATTQIGEIVKTVANTVESEIKAELGVIPSLNAVETGATSNTEPEEAIQTRTVINMHGTAECLVENFLGRSALVCMRSFEYKNHSTSTSSIQKNFFIWTLNTRELVQIRRKMELFTYLRFDTEITIVPTLRLFSSSNVSFSGLPNLTLQAMYVPTGARKPSSQDSFEWQSACNPSVFFKINDPPARLTIPFMSINSAYANFYDGFAGFEKKATVLYGINPANTMGNLCLRVVNSYQPVQYTLTVRVYMKPKHIKAWAPRAPRTMPYTNILNNNYAGRSAAPNAPTAIVSHRSTIKTMPNDINLTTA

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 \(c\).

\(|P_{f(1GKZ_1)}(2) \setminus P_{f(4JFK_1)}(2)|=151\), \(|P_{f(4JFK_1)}(2) \setminus P_{f(1GKZ_1)}(2)|=42\). 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 1:0001000001011000000100100001101110010101010111001000010011001001000111011001011001111110010110100101011001001111000100100001100110000011011101100000010000110011000100011101110001110000101111100010100110011011001000001011010101011101111111100111011001101010001001001101110110001011101000111110001001100010010100001010111101010011001110111111100010100111010100101110010101001010000101000000
Pair \(Z_2\) Length of longest common subsequence
1GKZ_1,4JFK_1 193 3
1GKZ_1,7OZL_1 170 3
4JFK_1,7OZL_1 165 4

Newick tree

 
[
	1GKZ_1:93.57,
	[
		7OZL_1:82.5,4JFK_1:82.5
	]:11.07
]

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 \((0.85)(0.8)(\frac{516 }{\log_{20} 516}-\frac{128}{\log_{20}128})=114.\)
Status Protein1 Protein2 d d1/2
Query variables 1GKZ_1 4JFK_1 144 95.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]