CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2PTG_1 4BKM_1 5BRF_1 Letter Amino acid
28 30 38 G Glycine
3 4 15 H Histidine
3 9 16 M Methionine
12 11 14 F Phenylalanine
8 12 10 Q Glutamine
3 7 8 C Cysteine
12 7 18 I Isoleucine
11 13 13 T Threonine
2 2 3 W Tryptophan
26 27 28 V Valine
45 35 27 A Alanine
33 41 39 L Leucine
18 5 18 K Lycine
6 7 21 N Asparagine
18 19 11 D Aspartic acid
16 17 26 E Glutamic acid
18 17 19 P Proline
32 13 22 S Serine
11 7 13 Y Tyrosine
14 26 22 R Arginine 

2PTG_1|Chains A, B|Enoyl-acyl carrier reductase|Eimeria tenella (413949)
>4BKM_1|Chains A, B, C, D|PYRIDOXAL PHOSPHATE PHOSPHATASE, PHOSPHOGLYCOLATE PHOSPHATASE, PYRIDOXAL PHOSPHATE PHOSPHATASE|MUS MUSCULUS (10090)
>5BRF_1|Chains A, B|Glucokinase 1, putative|Trypanosoma cruzi (strain CL Brener) (353153)
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 \(w=f(c)\)
2PTG , Knot 133 319 0.80 40 170 294 
GPLPVDLRGKTAFVAGVADSNGYGWAICKLLRAAGARVLVGTWPPVYSIFKKGLESSRFEQDSFYAQEPSSKVAAEAAEKPVDLVFDKIYPLDAVFDTPQDVPPEVSSNKRYAGVGGFTISEVAEAVRADVGQIDILVHSLANGPEVTKPLLQTSRKGYLAAVSSSSYSFVSLLQHFLPLMKEGGSALALSYIASEKVIPGYGGGMSSAKAALESDCRTLAFEAGRARAVRVNCISAGPLKSRAASAIGKAGDKTFIDLAIDYSEANAPLQKELESDDVGRAALFLLSPLARAVTGATLYVDNGLHAMGQALDSKSLTP
4BKM , Knot 129 309 0.79 40 166 294 
GAMGMARCERLRGAALRDVLGQAQGVLFDCDGVLWNGERIVPGAPELLQRLARAGKNTLFVSNNSRRARPELALRFARLGFAGLRAEQLFSSALCAARLLRQRLAGVPDPKAYVLGSPALAAELEAVGVTSVGVGPDVLHGDGPSDWLAVPLEPDVRAVVVGFDPHFSYMKLTKAVRYLQQPDCLLVGTNMDNRLPLENGRFIAGTGCLVRAVEMAAQRQADIIGKPSPYMFQCITEDFSVDPARTLMVGDRLETDILFGHRCGMTTVLTLTGVSSLEEAQAYLTAGQRDLVPHYYVESIADLMEGLED
5BRF , Knot 159 381 0.82 40 217 358 
MGRGSHHHHHHGMAMNIKELSLHELCEELKTPAWNVPLTFVGDVGGTSARMGFVREGKNDSVHACVTRYSMKRKDITELIEFFNEIIELMPASVIKRVKAGVINVPGPVTGGAVGGPFNNLKGIARLSDYPKALFPPGRSAILNDLEAGGFGVLAVSDAHVFSEYFGVMWEGTQWRTCEQEPAGSVIGRGRCLVLAPGTGLGSSLIYYNPMNQQHIVVPLELGSQTIPMRKDIDYIQTLHAELKLLPNYENMVSGAGLEFHYRQVVRGSRPPCSAGEIAKLASEGDANACKAMKKYHEYLMRVGSEASMALLPLTIVLVGDNIVNNAFFYRNPQNLKEMHREALNHEMERFGFQSRVTYLRQKKLLNLNLMGCYRCGLDLS

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 \(c\).

\(|P_{f(2PTG_1)}(2) \setminus P_{f(4BKM_1)}(2)|=79\), \(|P_{f(4BKM_1)}(2) \setminus P_{f(2PTG_1)}(2)|=75\). 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 1:1111101010011111110001011110011011110111101111001100110000100001010010001110110011011100101101110010011101000000111111010011011010110101110011011010011100000101111000000110110011111001101111001100011110111100101110000001110110101101001011110001101110110001101110000101110001000011011111101110110110101001101110110000101
Pair \(Z_2\) Length of longest common subsequence
2PTG_1,4BKM_1 154 4
2PTG_1,5BRF_1 167 4
4BKM_1,5BRF_1 175 4

Newick tree

 
[
	5BRF_1:88.18,
	[
		2PTG_1:77,4BKM_1:77
	]:11.18
]

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 \((0.85)(0.8)(\frac{628 }{\log_{20} 628}-\frac{309}{\log_{20}309})=88.7\)
Status Protein1 Protein2 d d1/2
Query variables 2PTG_1 4BKM_1 109 106.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]