CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6BRM_1 3ZMS_1 8ALK_1 Letter Amino acid
25 88 27 A Alanine
21 35 31 D Aspartic acid
2 9 3 C Cysteine
17 70 35 E Glutamic acid
12 15 19 H Histidine
12 66 13 P Proline
17 60 20 V Valine
10 46 20 Q Glutamine
17 32 47 I Isoleucine
8 15 8 M Methionine
9 56 37 S Serine
18 44 37 T Threonine
8 22 12 Y Tyrosine
9 43 20 R Arginine
8 31 19 N Asparagine
16 51 31 K Lycine
4 9 2 W Tryptophan
16 73 27 G Glycine
30 80 40 L Leucine
10 27 21 F Phenylalanine 

6BRM_1|Chains A, B, C, D, E, F, G, H|Putative metal-dependent isothiocyanate hydrolase SaxA|Pectobacterium carotovorum (554)
>3ZMS_1|Chain A|LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A|HOMO SAPIENS (9606)
>8ALK_1|Chain A|Phosphocholine hydrolase Lem3|Legionella pneumophila (446)
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 \(w=f(c)\)
6BRM , Knot 120 269 0.83 40 174 262 
MKLTQIRNATLVLQYAGKKFLIDPMLAEKEAWDGFAGSARPHLRNPMVALPVPVEDLLAVDAVILTHTHTDHWDEAAQQAVPKDMLIYTQDEKDAALIRSQGFFNIRVLKDENHFVDGLTIYKTDGQHGSNELYADAQLGDLLGDACGLVFTHHDEKTIYIAGDTVWVKPYVKSLQRFKPEIVVLNTGYAVNDLYGPIIMGKEDTLRTLKMLPTATIVASHMESINHCLLTRAELREFSLEHGIEDKILIPADGETMAFSAWSHPQFEK
3ZMS , Knot 321 872 0.83 40 294 772 
MLSGKKAAAAAAAAAAAATGTEAGPGTAGGSENGSEVAAQPAGLSGPAEVGPGAVGERTPRKKEPPRASPPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGRRTSRRKRAKVEYREMDESLANLSEDEYYSEEERNAKAEKEKKLPPPPPQAPPEEENESEPEEPSGQAGGLQDDSSGGYGDGQPSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAMYTLPRQATPGVPAQQSPSM
8ALK , Knot 192 469 0.84 40 228 438 
GHMDKIITGKKIIFSQSVAKDQTKNLSSFLSERFYSVNQSHNHSIIIGSSLSHQENDIEHDTILDTSGVLVTTDTNGIVNGARVAITDGLGGGNGDQEEDDEIYRVSHSSCENFLNSDQNIDTTLSLITQPKASDKKQTAPKTLQHTEASMAAFIYQNHPGKGYIGEFANIGDGLIIILDKRFKIKHMVSASHIYRGFGTWTPPSLQALATTANKDALLVRQTLKLAEGDIIISMTDGVWGELKTSLIAQTNDRRDIGVDKEYFKTLFDELTDAPYPSSFDIARIITQRAMSRSLERRKTLIKLINEIEQQHFHEKSVKTINEVLEYFIKTGHVETAQTLKAILFEDGLSDGITYFENIEIPLEMVMHDLKSRCVGDCSTINVTRIPYHLDELIRGFINYPEKHQILAPLFKARVKSEADLEEAFHRLSLEMVQPEIESPISETHFERAFKKETLDKTQAVLTHYFRIS

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 \(c\).

\(|P_{f(6BRM_1)}(2) \setminus P_{f(3ZMS_1)}(2)|=29\), \(|P_{f(3ZMS_1)}(2) \setminus P_{f(6BRM_1)}(2)|=149\). 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 1:10100100101110011001110111100011011110101010011111111100111101111000000010011001110011100000001111000111010110000011011010000100100010101011011101011110000000101110011101010010010101111001011001011111100001001011101011100100100011001010010100110001111101001110110010100
Pair \(Z_2\) Length of longest common subsequence
6BRM_1,3ZMS_1 178 5
6BRM_1,8ALK_1 178 3
3ZMS_1,8ALK_1 140 5

Newick tree

 
[
	6BRM_1:94.48,
	[
		3ZMS_1:70,8ALK_1:70
	]:24.48
]

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 \((0.85)(0.8)(\frac{1141 }{\log_{20} 1141}-\frac{269}{\log_{20}269})=232.\)
Status Protein1 Protein2 d d1/2
Query variables 6BRM_1 3ZMS_1 290 187.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]