CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2FTE_1 5JTT_1 4DQN_1 Letter Amino acid
29 63 29 A Alanine
18 50 18 I Isoleucine
15 63 11 R Arginine
4 22 11 H Histidine
25 79 29 L Leucine
10 48 20 K Lycine
9 22 4 M Methionine
15 65 21 E Glutamic acid
22 48 34 G Glycine
9 38 18 F Phenylalanine
10 36 21 P Proline
4 12 3 W Tryptophan
20 36 20 T Threonine
7 36 19 Y Tyrosine
17 62 25 V Valine
16 46 9 N Asparagine
19 49 27 D Aspartic acid
1 9 2 C Cysteine
12 30 9 Q Glutamine
20 29 15 S Serine 

2FTE_1|Chains A, B, C, D, E, F, G|major capsid protein|Enterobacteria phage HK97 (37554)
>5JTT_1|Chain A|Glycogen phosphorylase, muscle form|Oryctolagus cuniculus (9986)
>4DQN_1|Chain A|Putative branched-chain amino acid aminotransferase IlvE|Streptococcus mutans (1309)
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 \(w=f(c)\)
2FTE , Knot 127 282 0.84 40 179 273 
SLGSDADSAGSLIQPMQIPGIIMPGLRRLTIRDLLAQGRTSSNALEYVREEVFTNNADVVAEKALKPESDITFSKQTANVKTIAHWVQASRQVMDDAPMLQSYINNRLMYGLALKEEGQLLNGDGTGDNLEGLNKVATAYDTSLNATGDTRADIIAHAIYQVTESEFSASGIVLNPRDWHNIALLKDNEGRYIFGGPQAFTSNIMWGLPVVPTKAQAAGTFTVGGFDMASQVWDRMDATVEVSREDRDNFVKNMLTILCEERLALAHYRPTAIIKGTFSSGS
5JTT , Knot 322 843 0.85 40 316 774 
MSRPLSDQEKRKQISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRDHLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEATYQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEFGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQGAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLKDFNVGGYIQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSKFGCRDPVRTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEPSRQRLPAPDEKIP
4DQN , Knot 145 345 0.81 40 203 325 
GPLGSTVDLDWKNLGFEYHKLPFRYISYYKDGKWDDGKLTEDATLHISESSPALHYGQEAFEGLKAYRTKDGSVQLFRPNMNAERLQRTADRLLMPQVPTDKFIDAAKQVVRANEEYVPPYGTGATLYLRPLLIGVGDVIGVHPADEYIFTIFAMPVGNYFKGGLAPTNFLIQDDYDRAAPHGTGAAKVGGNYAASLLPGKVAHERQFSDVIYLDPATHTKIEEVGSANFFGITKDNEFITPLSPSILPSVTKYSLLYLAEHRFGMKAIEGDVCVDELDKFVEAGACGTAAVISPIGGVQHGDDFHVFYSETEVGPVTHKLYDELTGIQFGDVKAPEGWIYKVDD

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 \(c\).

\(|P_{f(2FTE_1)}(2) \setminus P_{f(5JTT_1)}(2)|=24\), \(|P_{f(5JTT_1)}(2) \setminus P_{f(2FTE_1)}(2)|=161\). 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 1:011001001101101101111111110010100111010000011001000110001011100110100010100001010011011010001100111100010001101111000101101010100101100110100001010100010111011001000010101111010010011110000100111110110001111111110010111010111101100110010101010000000110011011000011110001011101010010
Pair \(Z_2\) Length of longest common subsequence
2FTE_1,5JTT_1 185 4
2FTE_1,4DQN_1 158 4
5JTT_1,4DQN_1 165 4

Newick tree

 
[
	5JTT_1:90.34,
	[
		2FTE_1:79,4DQN_1:79
	]:11.34
]

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 \((0.85)(0.8)(\frac{1125 }{\log_{20} 1125}-\frac{282}{\log_{20}282})=224.\)
Status Protein1 Protein2 d d1/2
Query variables 2FTE_1 5JTT_1 283 186.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]