CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4QIG_1 5KMP_1 6IQQ_1 Letter Amino acid
4 7 5 M Methionine
3 18 8 P Proline
3 10 18 Q Glutamine
11 42 15 G Glycine
6 32 21 E Glutamic acid
8 17 12 H Histidine
6 37 7 I Isoleucine
0 2 4 W Tryptophan
14 35 12 V Valine
3 21 14 R Arginine
2 17 14 N Asparagine
5 31 45 L Leucine
2 12 21 S Serine
6 19 10 T Threonine
17 33 28 A Alanine
4 18 24 D Aspartic acid
0 13 11 F Phenylalanine
1 15 16 Y Tyrosine
1 3 0 C Cysteine
6 23 11 K Lycine 

4QIG_1|Chains A, B, C, D, E, F, G|Propanediol utilization protein PduA|Salmonella enterica subsp. enterica serovar Typhimurium (99287)
>5KMP_1|Chains A, B|FAD-dependent pyridine nucleotide-disulfide oxidoreductase|Caldalkalibacillus thermarum TA2.A1 (986075)
>6IQQ_1|Chains A, B|Lipoprotein NlpI|Escherichia coli (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 \(w=f(c)\)
4QIG , Knot 50 102 0.75 36 73 94 
MHHHHHHGTQQEALGMVETKGLTAAIEAADAMVASANVMLVGYEKIGCGLVTVIVRGDVGAVKAATDAGAAAARNVGEVKAVHVIPRPHTDVEKILPKGISQ
5KMP , Knot 165 405 0.81 40 211 374 
MSKPSIVILGAGYGGIVAALGLQKRLNYNEADITLVNKNDYHYITTELHQPAAGTMHHDQARVGIKELIDEKKIKFVKDTVVAIDREQQKVTLQNGELHYDYLVVGLGSEPETFGIEGLREHAFSINSINSVRIIRQHIEYQFAKFAAEPERTDYLTIVVGGAEFTGIEFVGELADRMPELCAEYDVDPKLVRIINVEAAPTVLPGFDPALVNYAMDVLGGKGVEFKIGTPIKRCTPEGVVIEVDGEEEEIKAATVVWTGGVRGNSIVEKSGFETMRGRIKVDPYLRAPGHENIFIVGDCALIINEENNRPYPPTAQIAIQHGENVAANLAALIRGGSMTPFKPHIRGTVASLGRNDAIGIVGGRKVYGHAASWLKKLIDMRYLYLIGGLSLVLKKGRFHHHHHH
6IQQ , Knot 124 296 0.79 38 169 272 
MGSSHHHHHHSSGLVPRGSHMSNTSWRKSEVLAVPLQPTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDKEQWGWNIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANNVHNFVEHRYALLELSLLGQDQDDLAESDQQ

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 \(c\).

\(|P_{f(4QIG_1)}(2) \setminus P_{f(5KMP_1)}(2)|=19\), \(|P_{f(5KMP_1)}(2) \setminus P_{f(4QIG_1)}(2)|=157\). 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 1:100000010000111110001101110110111101011111000110111011101011110110011111100110101101110100010011101100
Pair \(Z_2\) Length of longest common subsequence
4QIG_1,5KMP_1 176 6
4QIG_1,6IQQ_1 156 6
5KMP_1,6IQQ_1 172 6

Newick tree

 
[
	5KMP_1:89.80,
	[
		4QIG_1:78,6IQQ_1:78
	]:11.80
]

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 \((0.85)(0.8)(\frac{507 }{\log_{20} 507}-\frac{102}{\log_{20}102})=120.\)
Status Protein1 Protein2 d d1/2
Query variables 4QIG_1 5KMP_1 147 90
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]

Graphviz Engine:
Graphviz Engine: