CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4DUR_1 6PKZ_1 5ZJK_1 Letter Amino acid
37 19 13 A Alanine
54 27 8 E Glutamic acid
60 22 15 G Glycine
20 14 10 F Phenylalanine
46 18 14 V Valine
36 21 8 D Aspartic acid
22 23 10 I Isoleucine
42 26 9 L Leucine
47 36 8 K Lycine
30 12 16 Y Tyrosine
42 19 5 R Arginine
40 11 15 N Asparagine
23 9 12 H Histidine
69 14 8 P Proline
61 19 22 T Threonine
48 3 0 C Cysteine
30 13 10 Q Glutamine
10 7 3 M Methionine
55 21 22 S Serine
19 1 5 W Tryptophan 

4DUR_1|Chains A, B|Plasminogen|Homo sapiens (9606)
>6PKZ_1|Chain A|DNA polymerase beta|Homo sapiens (9606)
>5ZJK_1|Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R|Myroilysin|Myroides sp. CSLB8 (1736763)
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 \(w=f(c)\)
4DUR , Knot 288 791 0.81 40 288 666 
EPLDDYVNTQGASLFSVTKKQLGAGSIEECAAKCEEDEEFTCRAFQYHSKEQQCVIMAENRKSSIIIRMRDVVLFEKKVYLSECKTGNGKNYRGTMSKTKNGITCQKWSSTSPHRPRFSPATHPSEGLEENYCRNPDNDPQGPWCYTTDPEKRYDYCDILECEEECMHCSGENYDGKISKTMSGLECQAWDSQSPHAHGYIPSKFPNKNLKKNYCRNPDRELRPWCFTTDPNKRWELCDIPRCTTPPPSSGPTYQCLKGTGENYRGNVAVTVSGHTCQHWSAQTPHTHNRTPENFPCKNLDENYCRNPDGKRAPWCHTTNSQVRWEYCKIPSCDSSPVSTEQLAPTAPPELTPVVQDCYHGDGQSYRGTSSTTTTGKKCQSWSSMTPHRHQKTPENYPNAGLTMNYCRNPDADKGPWCFTTDPSVRWEYCNLKKCSGTEASVVAPPPVVLLPDVETPSEEDCMFGNGKGYRGKRATTVTGTPCQDWAAQEPHRHSIFTPETNPRAGLEKNYCRNPDGDVGGPWCYTTNPRKLYDYCDVPQCAAPSFDCGKPQVEPKKCPGRVVGGCVAHPHSWPWQVSLRTRFGMHFCGGTLISPEWVLTAAHCLEKSPRPSSYKVILGAHQEVNLEPHVQEIEVSRLFLEPTRKDIALLKLSSPAVITDKVIPACLPSPNYVVADRTECFITGWGETQGTFGAGLLKEAQLPVIENKVCNRYEFLNGRVQSTELCAGHLAGGTDSCQGDSGGPLVCFEKDKYILQGVTSWGLGCARPNKPGVYVRVSRFVTWIEGVMRNN
6PKZ , Knot 146 335 0.84 40 198 321 
MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFAKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
5ZJK , Knot 98 213 0.82 38 141 205 
GAVVRSTKWPNGSVITVGLYGGTPYVRSKVKQYAQEWSNYANITFNFVESGTPQIRVTFTQGAGSYSYLGTQALSIPSNEETMNFGWFDDSTSDTEFSRTVIHEFGHALGMIHEHQHPLTNIPWDKNKVYAYYAGYPNYWSKKDVDNNLFATYSTTQTQYSAYDTQSIMHYSISSALTTNGFSVGNNSVLSATDKQFIATVYPRNLEHHHHHH

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 \(c\).

\(|P_{f(4DUR_1)}(2) \setminus P_{f(6PKZ_1)}(2)|=139\), \(|P_{f(6PKZ_1)}(2) \setminus P_{f(4DUR_1)}(2)|=49\). 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 1:01100010001101101000011110100011000000010001100000000011110000001110100111100010100000101000010100000110000100001001010110010011000000010001011100000100000000110000001000100001010001011000110000101010110011000100000001000101101000100010100110000111001100001010100001011101010000010100100000010011000100000001010011100000001010000110000011000011101110101110000010100001000000010000010010100000010001011101000001010011101000101010000100001001011111111111010010000011101010010010010101000111001000011010001011100000001010111110000010010000011001110100101010100011011110110100111010100011101011011010111011001000101000011111000101010100101001110100001111010011110001111011010011100000110111000101111110010111100010000011010100001011011110000010011111010000011011001111010100111010100110110111000
Pair \(Z_2\) Length of longest common subsequence
4DUR_1,6PKZ_1 188 4
4DUR_1,5ZJK_1 205 4
6PKZ_1,5ZJK_1 179 4

Newick tree

 
[
	4DUR_1:10.11,
	[
		6PKZ_1:89.5,5ZJK_1:89.5
	]:11.61
]

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 \((0.85)(0.8)(\frac{1126 }{\log_{20} 1126}-\frac{335}{\log_{20}335})=209.\)
Status Protein1 Protein2 d d1/2
Query variables 4DUR_1 6PKZ_1 253 182
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]