CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8XKV_1 3ANI_1 3TEI_1 Letter Amino acid
53 26 18 G Glycine
62 18 17 S Serine
47 20 14 T Threonine
41 17 13 F Phenylalanine
39 13 20 P Proline
11 11 3 W Tryptophan
78 38 43 L Leucine
58 25 27 A Alanine
43 22 24 D Aspartic acid
8 4 7 C Cysteine
31 13 12 Q Glutamine
81 30 20 E Glutamic acid
8 10 13 H Histidine
59 26 28 I Isoleucine
25 31 19 Y Tyrosine
58 17 18 R Arginine
30 24 19 N Asparagine
55 28 23 K Lycine
16 9 9 M Methionine
52 16 15 V Valine 

8XKV_1|Chain A|Probable inactive ATP-dependent zinc metalloprotease FTSHI 4, chloroplastic|Arabidopsis thaliana (3702)
>3ANI_1|Chain A|Putative uncharacterized protein gbs1889|Streptococcus agalactiae (216495)
>3TEI_1|Chain A|Mitogen-activated protein kinase 1|Homo sapiens (9606)
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 \(w=f(c)\)
8XKV , Knot 323 855 0.85 40 298 777 
MTFYISSSLTPTHFSKPLNPSNTLFPSQFRGSLSSFVRRRKPTEAKLSSKFNLFPSRRNGLITCCSTSSFESTESSVSQEEDAESNRLFEKLRETERERLSNMEELERKANVQLERQLVMASDWSRTLLTMRGKLKGTEWDPETSHRINFSDFMKLLDSNSVQYMEYSNYGQTISVILPYYKDGEPLGEEEDSKKEIIFRRHIVDRMPIDGWNDVWKKLHQQIVNVEVFNVDVVPAEVYTTVATFVVWSMRLALFVSLYVWIDSITRPIYAKLIPCDLGTPTKKIRQPLKRQALGSLGKSRAKFISAEEKTGVTFDDFAGQEYIKRELQEIVRILKNDEEFQNKGIYCPKGVLLHGPPGTGKTLLAKAIAGEAGLPFFAANGTDFVEMFVGVAASRVKDLFASSRSYAPSIIFIDEIDAIGSKRGGPDIGGGGAEREQGLLQILTEMDGFKVTTSQVLVIGATNRLDILDPALLRKGRFDKIIRVGLPSKDGRLAILKVHARNKFFRSEDEKEELLQEVAENTEDFTGAELQNVLNEAGILTARKDLDYIGREELLEALKRQKGTFETGQEDSTEVPEELKLRLAYREAAVAVLACYLPDQYRPISETDINSIRSQPNMRYSETSGRVFARKSDYVNSIIRACAPRVVEEEMFGIENLCWISAKSTLEASQRAEFLILQTGMTAFGKAYYRNQRDLVPNLVPKLEALRDEYMRFAVEKCSSILQEYQSALEEITDVLLEKGEIKADEIWNIYNTAPRIPQKPVRPVDEYGALIYAGRWGIHGVSLPGRVTFSPGNIGFATFGAPRPMETQIISDDTWKLVDEIWDKKVEEIKAEAVIQIEEEKKKPQILMATHFF
3ANI , Knot 171 398 0.85 40 239 383 
MMKIKPVKVESIENPKRFLNSRLLTKIEVEEAIEKALKQLYINIDYFGEEYPTPATFNNIYKVMDNTEWTNGFWTGCLWLAYEYNQDKKLKNIAHKNVLSFLNRINNRIALDHHDLGFLYTPSCTAEYRINGDVKALEATIKAADKLMERYQEKGGFIQAWGELGYKEHYRLIINCLLNIQLLFFAYEQTGDEKYRQVAVNHFYASANNVVRDDSSAFHTFYFDPETGEPLKGVTRQGYSDESSWARGQAWGIYGIPLSYRKMKDYQQIILFKGMTNYFLNRLPEDKVSYWDLIFTDGSGQPRDTSATATAVCGIHEMLKYLPEVDPDKETYKYAMHTMLRSLIEQYSNNELIAGRPLLLHGVYSWHSGKGVDEGNIWGDYYYLEALIRFYKDWELYW
3TEI , Knot 159 362 0.86 40 236 350 
GSMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLAFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLAQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS

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 \(c\).

\(|P_{f(8XKV_1)}(2) \setminus P_{f(3ANI_1)}(2)|=105\), \(|P_{f(3ANI_1)}(2) \setminus P_{f(8XKV_1)}(2)|=46\). 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 1:101010001010010011010001110010101001100001001010001011100001110000000100000010000010000110010000000100100100010101000111100100011010101010010100000101001101100001001000001001011110000101110000000011100011001110110011001000110101101011110100011011110101111101011100100110101110011010001001100011101100010110100001101001110001000100110110000010001100101111011110100111011110111111110100110111111100100111000001101111001011100011101111110000111011001011010000111111000101101111001010011011110001011110101000110000000011001100000101101001100111101000100110001101100001010010000001100101011000111111100110000110000100100010100000010111000001001101011011000111100101101000101000101111001101110100000001110111010110000101110000011000001100100111001010100110100011011001101100011110110111011011101010110111101111011000110000101100110001001010111010000001011110011
Pair \(Z_2\) Length of longest common subsequence
8XKV_1,3ANI_1 151 4
8XKV_1,3TEI_1 140 4
3ANI_1,3TEI_1 153 4

Newick tree

 
[
	3ANI_1:77.89,
	[
		8XKV_1:70,3TEI_1:70
	]:7.89
]

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 \((0.85)(0.8)(\frac{1253 }{\log_{20} 1253}-\frac{398}{\log_{20}398})=222.\)
Status Protein1 Protein2 d d1/2
Query variables 8XKV_1 3ANI_1 282 206
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]