CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8GUB_1 2BWI_1 6LJH_1 Letter Amino acid
45 13 16 F Phenylalanine
60 6 27 S Serine
60 20 16 D Aspartic acid
49 7 9 Q Glutamine
77 21 22 E Glutamic acid
51 34 39 G Glycine
41 9 6 M Methionine
72 17 29 K Lycine
42 28 22 T Threonine
19 4 3 W Tryptophan
60 12 8 R Arginine
35 15 16 H Histidine
56 34 32 V Valine
52 23 20 P Proline
43 13 7 Y Tyrosine
46 33 25 A Alanine
57 14 11 N Asparagine
32 1 15 C Cysteine
72 12 30 I Isoleucine
127 24 33 L Leucine 

8GUB_1|Chain A|Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform|Homo sapiens (9606)
>2BWI_1|Chain A|COPPER-CONTAINING NITRITE REDUCTASE|ACHROMOBACTER CYCLOCLASTES (223)
>6LJH_1|Chain A|Alcohol dehydrogenase 1|Artemisia annua (35608)
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 \(w=f(c)\)
8GUB , Knot 404 1096 0.86 40 345 985 
MSYYHHHHHHDYDIPTTENLYFQGAMGSMPPRPSSGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTATPYMNGETSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDARHGGWTTKMDWIFHTIKQHALN
2BWI , Knot 140 340 0.80 40 195 317 
AAGAAPVDISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVVKPASM
6LJH , Knot 164 386 0.84 40 215 359 
MAQKAPGVITCKAAVVWESSGPVVLEEIRVDPPKASEVRIKMLCASLCHTDVLCTKGFPIPLFPRIPGHEGVGVIESIGKDAKGLKPGDIVMPLYLGECGQCLNCKTGKTNLCHVYPPSFSGLMNDGTSRMSIARTGESIYHFASCSTWTEYAVADCNYVLKINPKISYPHASFLSCGFTTGFGATWRETQVSKGSSVAVFGIGTVGLGVIKGAQLQGASKIIGVDVNQYKAAKGKVFGMTDFINPKDHPDKSVSELVKELTHGLGVDHCFECTGVPSLLNEALEASKIGIGTVVPIGAGGEASVAINSLILFSGRTLKFTAFGGVRTQSDLPVIIDKCLNKEIQLDELLTHEIHLDNIQEAFEILKKPDCVKILIKFLEHHHHHH

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 \(c\).

\(|P_{f(8GUB_1)}(2) \setminus P_{f(2BWI_1)}(2)|=169\), \(|P_{f(2BWI_1)}(2) \setminus P_{f(8GUB_1)}(2)|=19\). 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 1:1000000000000110000101011110111010010111101111011100111011110100100101101000110010001100110000001110100010000110000010010110111011011100000110001111111110010110010100100011010001101001001000110101101000101100100010010111111111010000000010100001100111011000000111000010101100010011010100001100011000001000111101101111100010001110010110000010010101010000001111001101011010010101001001010011001101100010000110001010011000101101101101010100101001100000111110101100000110101110111110110011011110100100001010101011001101101011000101010001110000111000110000100000001011000011001000000111000000101101110111010100000110100110011110100110110000101110111100100010000100011011011000001001110111001100001101111010001000010001111100000101101001000101100110100110000000000101011100100101101101110110110011010100001100100111101001011001110000111001001000110101101100110001101011101010110011110110000011010001110111010000100110000010100111011000011001101111110000001110001011010110110000001100000111110001111100110000000010010010001011100010111011011110111010010011010001110000001100110010010011100010111001000110
Pair \(Z_2\) Length of longest common subsequence
8GUB_1,2BWI_1 188 4
8GUB_1,6LJH_1 178 6
2BWI_1,6LJH_1 162 4

Newick tree

 
[
	8GUB_1:94.78,
	[
		6LJH_1:81,2BWI_1:81
	]:13.78
]

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 \((0.85)(0.8)(\frac{1436 }{\log_{20} 1436}-\frac{340}{\log_{20}340})=283.\)
Status Protein1 Protein2 d d1/2
Query variables 8GUB_1 2BWI_1 368 237
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]