CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7HCG_1 7ARP_1 4UHJ_1 Letter Amino acid
5 9 2 F Phenylalanine
22 13 7 V Valine
16 12 4 N Asparagine
9 10 14 D Aspartic acid
3 3 4 Q Glutamine
6 11 9 H Histidine
7 6 1 Y Tyrosine
2 9 9 R Arginine
3 0 0 C Cysteine
13 17 6 G Glycine
6 9 7 I Isoleucine
5 7 4 P Proline
15 25 10 A Alanine
6 18 10 E Glutamic acid
13 19 7 K Lycine
2 8 5 M Methionine
19 33 26 L Leucine
11 13 5 S Serine
6 14 5 T Threonine
0 2 1 W Tryptophan 

7HCG_1|Chains A, B|Non-structural protein 3|Severe acute respiratory syndrome coronavirus 2 (2697049)
>7ARP_1|Chains A, B|(S)-2-haloacid dehalogenase|Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij) (63186)
>4UHJ_1|Chains A, B, C|TRANSCRIPTIONAL REGULATORY PROTEIN CPXR|ESCHERICHIA COLI (83333)
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 \(w=f(c)\)
7HCG , Knot 80 169 0.81 38 119 162 
SMVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFL
7ARP , Knot 102 238 0.78 38 144 219 
MGSSHHHHHHGSSAKVKKPELLIFDVNETLLDMGPLENAINESLNSEHAFSLWFRTLLHYSLTETLTGNYVDFGTIGKATLKMTMRKFGKNLSEDRLDAILGNIKKLPAHEDVKEGLKMLKEAQIKLVALSNSNGKLLNAQLQFAGLADYFDAIFSVEAVGRYKPELASYRAVLETMKVPAENTMMVAAHGWDILGAKRAGLRTAFVAREGHAIYPLDGTPELEAKTVLEVARTLLKN
4UHJ , Knot 63 136 0.75 38 91 126 
MNKILLVDDDRELTSLLKELLEMEGFNVIVAHDGEQALDLLDDSIDLLLLDVMMPKKNGIDTLKALRQTHQTPVIMLTARGSELDRVLGLELGADDYLPKPFNDRELVARIRAILRRSHWSEQKLAAALEHHHHHH

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 \(c\).

\(|P_{f(7HCG_1)}(2) \setminus P_{f(7ARP_1)}(2)|=60\), \(|P_{f(7ARP_1)}(2) \setminus P_{f(7HCG_1)}(2)|=85\). 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 1:0110010101010001010010110010010101110110101001111111100100011010000011001110111001101001100010111101001001011001000100001111111011111101100101010010001011110001000110011
Pair \(Z_2\) Length of longest common subsequence
7HCG_1,7ARP_1 145 3
7HCG_1,4UHJ_1 146 3
7ARP_1,4UHJ_1 139 6

Newick tree

 
[
	7HCG_1:73.80,
	[
		7ARP_1:69.5,4UHJ_1:69.5
	]:4.30
]

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 \((0.85)(0.8)(\frac{407 }{\log_{20} 407}-\frac{169}{\log_{20}169})=70.8\)
Status Protein1 Protein2 d d1/2
Query variables 7HCG_1 7ARP_1 87 74.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]