CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
1CQG_1 9EKE_1 3UPK_1 Letter Amino acid
12 4 48 A Alanine
3 4 13 N Asparagine
10 12 31 E Glutamic acid
6 3 38 L Leucine
3 2 16 P Proline
7 7 16 S Serine
1 6 5 Y Tyrosine
0 2 24 R Arginine
7 11 21 D Aspartic acid
5 3 11 Q Glutamine
12 7 20 K Lycine
1 0 3 W Tryptophan
11 7 37 V Valine
1 6 4 C Cysteine
5 4 41 G Glycine
4 9 32 I Isoleucine
5 3 30 T Threonine
1 9 8 H Histidine
2 2 10 M Methionine
9 3 11 F Phenylalanine 

1CQG_1|Chain A|THIOREDOXIN|Homo sapiens (9606)
>9EKE_1|Chains A, C[auth B]|Salivary anti-complement protein|Lutzomyia longipalpis (7200)
>3UPK_1|Chain A|UDP-N-acetylglucosamine 1-carboxyvinyltransferase|Enterobacter cloacae (550)
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 \(w=f(c)\)
1CQG , Knot 56 105 0.82 38 85 103 
MVKQIESKTAFQEALDAAGDKLVVVDFSATWCGPAKMIKPFFHSLSEKYSNVIFLEVDVDDAQDVASEAEVKATPTFQFFKKGQKVGEFSGANKEKLEATINELV
9EKE , Knot 53 104 0.79 38 82 94 
SEDCENIFHDNAYLLKLDCEAGRVDPVEFDDISDEEIYEITVDVGVSSEDQEKVAKIIRECIAQVSTQDCTKFSEIYDCYMKKKICNYYPENMGSGHHHHHHHH
3UPK , Knot 171 419 0.82 40 203 380 
MDKFRVQGPTRLQGEVTISGAKNAALPILFAALLAEEPVEIQNVPKLKDIDTTMKLLTQLGTKVERDGSVWIDASNVNNFSAPYDLVKTMRASIWALGPLVARFGQGQVSLPGGCAIGARPVDLHIFGLEKLGAEIKLEEGYVKASVNGRLKGAHIVMDKVSVGATVTIMSAATLAEGTTIIENAAREPEIVDTANFLVALGAKISGQGTDRITIEGVERLGGGVYRVLPDRIETGTFLVAAAISGGKIVCRNAQPDTLDAVLAKLREAGADIETGEDWISLDMHGKRPKAVTVRTAPHPAFPTDMQAQFTLLNLVAEGTGVITETIFENRFMHVPELIRMGAHAEIESNTVICHGVEKLSGAQVMATDLRASASLVLAGCIAEGTTVVDRIYHIDRGYERIEDKLRALGANIERVKGE

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 \(c\).

\(|P_{f(1CQG_1)}(2) \setminus P_{f(9EKE_1)}(2)|=63\), \(|P_{f(9EKE_1)}(2) \setminus P_{f(1CQG_1)}(2)|=60\). 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 1:110010000110011011100111101010101110110111001000000111101010010011001010101010110010011010110000101010011
Pair \(Z_2\) Length of longest common subsequence
1CQG_1,9EKE_1 123 3
1CQG_1,3UPK_1 184 3
9EKE_1,3UPK_1 185 3

Newick tree

 
[
	3UPK_1:10.42,
	[
		1CQG_1:61.5,9EKE_1:61.5
	]:38.92
]

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 \((0.85)(0.8)(\frac{209 }{\log_{20} 209}-\frac{104}{\log_{20}104})=34.0\)
Status Protein1 Protein2 d d1/2
Query variables 1CQG_1 9EKE_1 43 42.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]