CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6PCM_1 7ZDW_1 7BCA_1 Letter Amino acid
34 30 3 I Isoleucine
48 18 4 P Proline
7 7 2 W Tryptophan
58 35 11 V Valine
65 40 12 R Arginine
25 11 3 N Asparagine
68 26 10 E Glutamic acid
11 11 0 H Histidine
39 10 5 K Lycine
23 21 1 F Phenylalanine
57 34 7 S Serine
28 14 0 Y Tyrosine
79 60 11 A Alanine
0 2 0 C Cysteine
75 99 9 L Leucine
10 13 2 M Methionine
56 36 3 T Threonine
55 20 7 D Aspartic acid
33 39 5 Q Glutamine
71 47 3 G Glycine 

6PCM_1|Chains A, B|DNA topoisomerase 1|Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (246196)
>7ZDW_1|Chain A[auth C]|ATP-binding/permease protein CydC|Escherichia coli K-12 (83333)
>7BCA_1|Chains A, B|KORA domain-containing protein|Escherichia coli K-12 (83333)
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 \(w=f(c)\)
6PCM , Knot 313 842 0.83 38 275 745 
SNAMAGGDRGSGGTGNVRRLVIVESPTKARKIAGYLGSNYVVESSRGHIRDLPRNAADVPAKFKSEPWARLGVNVDQNFEPLYIVSPEKKSTVTELKGLLKDVDELYLATDGDREGEAIAWHLLETLKPRVPVKRMVFHEITEPAIRNAAENPRDLDIALVDAQETRRILDRLYGYEVSPVLWKKVAPKLSAGRVQSVATRIIVQRERERMAFHSASYWDVTAELDASVSDPSASPPKFTAKLNTVDGRRVATGRDFDSLGQLKRPDEVLVLDEASAGALASGLRGAQLAVTSVEQKPYTRRPYAPFMTSTLQQEAARKLRFSSERTMSIAQRLYENGYITYMRTDSTTLSESAINAARTQARQLYGEEYVHPSPRQYTRKVKNAQEAHEAIRPAGDVFQTPGQLHSALDTDEFRLYELIWQRTVASQMADARGTTLSLRIGGSASSGEQVVFNASGRTITFPGFLKAYVESIDELAGGESDDAESRLPNLTQGQRVDAADLSADGHQTSPPARYTEASLIKALEELGIGRPSTYSSIIKTIQDRGYVQKKGSALVPSWVAFAVVGLLEQHFGRLVDYDFTAAMEDELDEIANGQEQRTNWLNNFYFGGEHGVEGSIARAGGLKQLVGGNLEGIDAREVNSIKVFDDSEGRPVYVRVGRNGPYLERMVDDPDNPGEQKPQRANLKEDLTPDELTPELAEKLFATPQEGRSLGIDPETGHEIVAKDGRFGPYVTEVLPEPEDGGDDGTAGTPAKKGKKPTGPKPRTGSLFRSMDLETVTLEDALKLLSLPRVVGVDPTTNEEITAQNGRYGPYLKRGTDSRSLATEDQIFTITLDEALKIYAE
7ZDW , Knot 216 573 0.79 40 227 509 
MRALLPYLALYKRHKWMLSLGIVLAIVTLLASIGLLTLSGWFLSASAVAGVAGLYSFNYMLPAAGVRGAAITRTAGRYFERLVSHDATFRVLQHLRIYTFSKLLPLSPAGLARYRQGELLNRVVADVDTLDHLYLRVISPLVGAFVVIMVVTIGLSFLDFTLAFTLGGIMLLTLFLMPPLFYRAGKSTGQNLTHLRGQYRQQLTAWLQGQAELTIFGASDRYRTQLENTEIQWLEAQRRQSELTALSQAIMLLIGALAVILMLWMASGGVGGNAQPGALIALFVFCALAAFEALAPVTGAFQHLGQVIASAVRISDLTDQKPEVTFPDTQTRVADRVSLTLRDVQFTYPEQSQQALKGISLQVNAGEHIAILGRTGCGKSTLLQQLTRAWDPQQGEILLNDSPIASLNEAALRQTISVVPQRVHLFSATLRDNLLLASPGSSDEALSEILRRVGLEKLLEDAGLNSWLGEGGRQLSGGELRRLAIARALLHDAPLVLLDQPTEGLDATTESQILELLAEMMREKTVLMVTHRLRGLSRFQQIIVMDNGQIIEQGTHAELLARQGRYYQFKQGL
7BCA , Knot 50 98 0.78 34 78 92 
FDDLRPRLGRLTEETIDIAREVLVEGKSQSDVARERGLSRQRVSSMVKSVVSAANEIPREWQRVEVWLPPNLAEKVRQMEADAKADVARKNQLTDAAL

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 \(c\).

\(|P_{f(6PCM_1)}(2) \setminus P_{f(7ZDW_1)}(2)|=87\), \(|P_{f(7ZDW_1)}(2) \setminus P_{f(6PCM_1)}(2)|=39\). 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 1:00111110010110101001111001001001110110001100001010011001101110100011101110100010110110100000100101110010010110010001011110110010101110011100100111001100100101111010000011001010010111100111010110100110011100000011100100101010101010010101101010100101001101001001101001001111001011111011011011100100010000101111000100011001010000010110010001010010000001000110110001001010001010100000010010010011011101100110100110000101001110001100110101001010111010010011101010010111110101001001111000010001101001001011010101000011100001011011001111010000011001000101000101111011111111110001101100010111000100110100000011001011100110101101111001111010110100100101100001011010110011010011001001100010010100010100101011001110100100111010010011100101110100111010011001011011001001011010010110010100101001101101101111010000010100100110100100000110000110101001101010
Pair \(Z_2\) Length of longest common subsequence
6PCM_1,7ZDW_1 126 4
6PCM_1,7BCA_1 205 4
7ZDW_1,7BCA_1 199 5

Newick tree

 
[
	7BCA_1:11.82,
	[
		6PCM_1:63,7ZDW_1:63
	]:47.82
]

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 \((0.85)(0.8)(\frac{1415 }{\log_{20} 1415}-\frac{573}{\log_{20}573})=213.\)
Status Protein1 Protein2 d d1/2
Query variables 6PCM_1 7ZDW_1 271 223.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]