CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
1WZF_1 4FWS_1 6MDY_1 Letter Amino acid
8 24 10 H Histidine
10 12 20 K Lycine
4 12 16 P Proline
15 30 22 V Valine
7 19 11 N Asparagine
14 22 13 D Aspartic acid
0 4 6 C Cysteine
4 11 10 M Methionine
9 14 13 F Phenylalanine
2 3 2 W Tryptophan
8 8 7 Y Tyrosine
14 23 9 R Arginine
9 8 11 Q Glutamine
14 37 21 G Glycine
5 32 14 I Isoleucine
11 32 22 S Serine
9 17 9 T Threonine
26 39 23 A Alanine
19 25 18 E Glutamic acid
27 43 25 L Leucine 

1WZF_1|Chains A, B|Heme oxygenase|Corynebacterium diphtheriae (1717)
>4FWS_1|Chain A|Propionate kinase|Salmonella typhimurium (99287)
>6MDY_1|Chains A, B, C, D|2-dehydro-3-deoxyphosphooctonate aldolase|Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (272624)
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 \(w=f(c)\)
1WZF , Knot 98 215 0.81 38 138 209 
MTTATAGLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGKGL
4FWS , Knot 167 415 0.80 40 210 389 
MRGSHHHHHHGMASNEFPVVLVINCGSSSIKFSVLDVATCDVLMAGIADGMNTENAFLSINGDKPINLAHSNYEDALKAIAFELEKRDLTDSVALIGHRIAHGGELFTQSVIITDEIIDNIRRVSPLAPLHNYANLSGIDAARHLFPAVRQVAVFDTSFHQTLAPEAYLYGLPWEYFSSLGVRRYGFHGTSHRYVSRRAYELLDLDEKDSGLIVAHLGNGASICAVRNGQSVDTSMGMTPLEGLMMGTRSGDVDFGAMAWIAKETGQTLSDLERVVNKESGLLGISGLSSDLRVLEKAWHEGHERARLAIKTFVHRIARHIAGHAASLHRLDGIIFTGGIGENSVLIRQLVIEHLGVLGLTLDVEMNKQPNSHGERIISANPSQVICAVIPTNEEKMIALDAIHLGNVKAPVEFA
6MDY , Knot 124 282 0.82 40 175 271 
MAHHHHHHMRLCGFEAGLDKPLFLIAGPCVIESEELALETAGYLKEMCSQLNIPFIYKSSFDKANRSSISSYRGPGFEKGLSILEKVKSQIGVPVLTDVHEDTPLFEVSSVVDVLQTPAFLCRQTNFIQKVAAMNKPVNIKKGQFLAPWEMKHVIAKAKAQGNEQIMACERGVSFGYNNLVSDMRSLVIMRETGCPVVYDATHSVQLPGGNNGVSGGQREFIPALARAAVAVGISGLFMETHPDPDKALSDGPNSWPLDKMKQLLESLKAADEVYKKYSTDF

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 \(c\).

\(|P_{f(1WZF_1)}(2) \setminus P_{f(4FWS_1)}(2)|=41\), \(|P_{f(4FWS_1)}(2) \setminus P_{f(1WZF_1)}(2)|=113\). 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 1:10010111110100001010001000011001101011110100100011110011001101101011100110111001011100100101000100010101111001001001000101111110001001101011011101100001101011110010111010100000000100101000000011001001111000111011011
Pair \(Z_2\) Length of longest common subsequence
1WZF_1,4FWS_1 154 3
1WZF_1,6MDY_1 157 4
4FWS_1,6MDY_1 163 6

Newick tree

 
[
	6MDY_1:80.99,
	[
		1WZF_1:77,4FWS_1:77
	]:3.99
]

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 \((0.85)(0.8)(\frac{630 }{\log_{20} 630}-\frac{215}{\log_{20}215})=117.\)
Status Protein1 Protein2 d d1/2
Query variables 1WZF_1 4FWS_1 149 112.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]