CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2RRK_1 7CLL_1 1NBM_1 Letter Amino acid
6 33 29 D Aspartic acid
15 41 48 L Leucine
3 11 31 K Lycine
9 18 17 P Proline
2 26 26 T Threonine
2 9 16 Y Tyrosine
9 34 41 V Valine
20 62 49 A Alanine
10 48 49 G Glycine
3 3 0 W Tryptophan
0 10 13 N Asparagine
7 13 5 H Histidine
8 24 39 I Isoleucine
3 8 10 M Methionine
6 18 33 S Serine
9 11 24 Q Glutamine
1 1 2 C Cysteine
15 31 32 E Glutamic acid
3 12 14 F Phenylalanine
9 23 32 R Arginine 

2RRK_1|Chain A|CTP pyrophosphohydrolase|Escherichia coli (83333)
>7CLL_1|Chains A, B, C, D|Enolase|Mycobacterium tuberculosis (1773)
>1NBM_1|Chains A, B, C|F1-ATPASE|Bos taurus (9913)
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 \(w=f(c)\)
2RRK , Knot 66 140 0.77 38 102 134 
GPLGSMKMIEVVAAIIERDGKILLAQRPAQSDQAGLWEFAGGKVEPDESQRQALVRELREELGIEATVGEYVASHQREVSGRIIHLHAWHVPDFHGTLQAHEHQALVWCSPEEALQYPLAPADIPLLEAFMALRAARPAD
7CLL , Knot 170 436 0.79 40 203 406 
MHHHHHHMPIIEQVRAREILDSRGNPTVEVEVALIDGTFARAAVPSGASTGEHEAVELRDGGDRYGGKGVQKAVQAVLDEIGPAVIGLNADDQRLVDQALVDLDGTPDKSRLGGNAILGVSLAVAKAAADSAELPLFRYVGGPNAHILPVPMMNILNGGAHADTAVDIQEFMVAPIGAPSFVEALRWGAEVYHALKSVLKKEGLSTGLGDEGGFAPDVAGTTAALDLISRAIESAGLRPGADVALALDAAATEFFTDGTGYVFEGTTRTADQMTEFYAGLLGAYPLVSIEDPLSEDDWDGWAALTASIGDRVQIVGDDIFVTNPERLEEGIERGVANALLVKVNQIGTLTETLDAVTLAHHGGYRTMISHRSGETEDTMIADLAVAIGSGQIKTGAPARSERVAKYNQLLRIEEALGDAARYAGDLAFPRFACETK
1NBM , Knot 205 510 0.83 38 229 476 
QKTGTAEVSSILEERILGADTSVDLEETGRVLSIGDGIARVHGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDKLIKEGDIVKRTGAIVDVPVGEELLGRVVDALGNAIDGKGPIGSKARRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDAFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAAQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLTELLKQGQYSPMAIEEQVAVIYAGVRGYLDKLEPSKITKFENAFLSHVISQHQALLGKIRTDGKISEESDAKLKEIVTNFLAGFEA

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 \(c\).

\(|P_{f(2RRK_1)}(2) \setminus P_{f(7CLL_1)}(2)|=32\), \(|P_{f(7CLL_1)}(2) \setminus P_{f(2RRK_1)}(2)|=133\). 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 1:11110101101111110001011110011000011110111101010000001110010001110101100110000010101101011011010101010000111100100110011111011110111110110110
Pair \(Z_2\) Length of longest common subsequence
2RRK_1,7CLL_1 165 4
2RRK_1,1NBM_1 167 4
7CLL_1,1NBM_1 122 4

Newick tree

 
[
	2RRK_1:89.13,
	[
		7CLL_1:61,1NBM_1:61
	]:28.13
]

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 \((0.85)(0.8)(\frac{576 }{\log_{20} 576}-\frac{140}{\log_{20}140})=126.\)
Status Protein1 Protein2 d d1/2
Query variables 2RRK_1 7CLL_1 154 101.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]