CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3NPZ_1 3MTF_1 6LTB_1 Letter Amino acid
7 16 101 G Glycine
13 18 31 I Isoleucine
17 22 43 S Serine
11 15 150 A Alanine
9 12 28 Q Glutamine
18 15 82 E Glutamic acid
10 17 12 K Lycine
2 8 20 W Tryptophan
7 10 21 Y Tyrosine
9 8 26 H Histidine
5 9 11 M Methionine
5 9 36 F Phenylalanine
10 24 100 V Valine
12 20 110 R Arginine
10 13 15 N Asparagine
8 19 78 D Aspartic acid
6 7 6 C Cysteine
24 29 132 L Leucine
8 11 94 P Proline
8 19 57 T Threonine 

3NPZ_1|Chain A|Prolactin|Homo sapiens (9606)
>3MTF_1|Chains A, B|Activin receptor type-1|Homo sapiens (9606)
>6LTB_1|Chain A|Nonribosomal peptide synthetase|Streptomyces sp. Sp080513GE-23 (630397)
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 \(w=f(c)\)
3NPZ , Knot 96 199 0.85 40 152 194 
LPICPGGAARCQVTLRDLFDRAVVLSHYIHNLSSEMFSEFDKRYTHGRGFITKAINSCHTSSLATPEDKEQAQQMNQKDFLSLIVSILRSWNEPLYHLVTEVRGMQEAPEAILSKAVEIEEQTKRLLEGMELIVSQVHPETKENEIYPVWSGLPSLQMADEESRLSAYYNLLHCLRRDSHKIDNYLKLLKCRIIHNNNC
3MTF , Knot 134 301 0.84 40 199 293 
SMQRTVARDITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSRHSSTQLWLITHYHEMGSLYDYLQLTTLDTVSCLRIVLSIASGLAHLHIEIFGTQGKPAIAHRDLKSKNILVKKNGQCCIADLGLAVMHSQSTNQLDVGNNPRVGTKRYMAPEVLDETIQVDCFDSYKRVDIWAFGLVLWEVARRMVSNGIVEDYKPPFYDVVPNDPSFEDMRKVVCVDQQRPNIPNRWFSDPTLTSLAKLMKECWYQNPSARLTALRIKKTLTKID
6LTB , Knot 390 1153 0.79 40 279 898 
MNHKVHHHHHHIEGRHMTISVPGHGTLGAPDGAAAPGGEAAELPPLVPEPGDAGQPFPLTPTQQALWVGRADAVDLGDIGCYGYFEWERPELDLARYRRAWERLVAHHPGLRTVVRPDGTQHVLERPGPVPITVEDLRQDPDAVRRLEESRAERGHRALDPGTWPMFDLRVVLLSGRVRVQLGIDLQLMDASSLFLNLFSDLVTLYDDPDAALASQKLAFRDFARWLEEDVRGGARWRADWAYWQERLDGLPPAPDLPAARYGAQGPGKFERCMVRCPAEEFALLRERALAHGLTETELLVGAFAEVLRGWSSDPAFTLNVPVFQRFDVPGIEDVIGDYTNPILLEARPEGRTVAERIVALAARLRADTRHASVNGVEVLRELARRRGLAAAAMPVVVTSLLGLPSAARSITEFGTEVHSITQTPQVSLDFQIRPEDGELRLVWDHRSGAFAPGVVEGAFEAFLDLVGRMLADEPGHGVWEAPFADMRSRRDRAVWNETNDTAEPVPAVLLQERFFAQARRTPDAEAVVASGLRLTYDELARHAYRIGNTLRERGVRPGDLVGVVMEKGWEQYAAVYGILAAGGAYLPIDAASPRGRVARLLESAGAGIVLTQSRLRDELDLPAGTTVLRADTDFETASTAPLTPVQGPDDPAYVIYTSGSTGEPKGVVVAHRGVANLVRDVRRRFAVTPADRLLALSGLHFDASVYDVFGPLACGATVVVPPPFRRAEPDVWAELVRDERVTFWNSVPVLLELLVGEAESRDDRPLATLRLAVVSGDWIPLDLPGRARAQAPGLRVVGSGGPTETICWSLFHPIDAVDPQWTSIPYGKPIANQRYYIVDRDLRPRPTWARGEMAVASPLGLALGYLNDPERTAAKFVTLPGTGERAYLTGDFGRLLPDGGIEILGREDFQVKVAGQRIELGEIEALLHRADGVRAAVVTAPRSSADVVRLQAFVVPETGARLSADALREHLSAELPAAMVPAAIRLLPELPLTANGKVDRLALARLAAAPEEAPEPEARTDYAPRTDVGLLAELVAACVAELLGLDEVPTTGNFFRLGGDALSGTRLASRLQDLLGAPVPIRTVFGNPVLGDLASAIAGDPAAGPQAIRVARLLHTLEEPDEKPGEKPDAEPAGEPDAGSRTSAWSHPQFEK

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 \(c\).

\(|P_{f(3NPZ_1)}(2) \setminus P_{f(3MTF_1)}(2)|=71\), \(|P_{f(3MTF_1)}(2) \setminus P_{f(3NPZ_1)}(2)|=118\). 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 1:1110111110001010011001111000100100011001000000101110011000000011010000010010000110111011001001100110010110011011100110100000011011011100101000000101110111010110000010100011001000000100010110001100000
Pair \(Z_2\) Length of longest common subsequence
3NPZ_1,3MTF_1 189 3
3NPZ_1,6LTB_1 205 4
3MTF_1,6LTB_1 190 4

Newick tree

 
[
	6LTB_1:10.22,
	[
		3NPZ_1:94.5,3MTF_1:94.5
	]:5.72
]

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 \((0.85)(0.8)(\frac{500 }{\log_{20} 500}-\frac{199}{\log_{20}199})=87.3\)
Status Protein1 Protein2 d d1/2
Query variables 3NPZ_1 3MTF_1 113 93
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]