CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4UHN_1 5VUE_1 2RDQ_1 Letter Amino acid
5 4 2 C Cysteine
14 5 10 M Methionine
28 13 18 V Valine
19 25 18 R Arginine
20 9 15 H Histidine
20 19 21 T Threonine
22 23 20 E Glutamic acid
28 9 11 I Isoleucine
23 7 10 K Lycine
25 13 20 S Serine
20 6 17 F Phenylalanine
21 16 19 P Proline
56 27 18 A Alanine
19 5 8 N Asparagine
25 18 21 D Aspartic acid
17 16 6 Q Glutamine
51 19 20 G Glycine
38 19 22 L Leucine
5 9 3 W Tryptophan
12 14 9 Y Tyrosine 

4UHN_1|Chain A|OMEGA AMINO ACID-PYRUVATE AMINOTRANSFERASE|PSEUDOMONAS SP. (306)
>5VUE_1|Chain A|HLA class I histocompatibility antigen, B-57 alpha chain|Homo sapiens (9606)
>2RDQ_1|Chain A|1-deoxypentalenic acid 11-beta hydroxylase; Fe(II)/alpha-ketoglutarate dependent hydroxylase|Streptomyces avermitilis (33903)
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 \(w=f(c)\)
4UHN , Knot 191 468 0.83 40 237 441 
MGSSHHHHHHSSGLVPRGSHMNQQVNVAPSAAADLNLKAHWMPFSANRNFHKDPRIIVAAEGSWLVDDKGRRIYDSLSGLWTCGAGHSRKEIADAVAKQIGTLDYSPGFQYGHPLSFQLAEKIAQMTPGTLDHVFFTGSGSECADTSIKMARAYWRIKGQAQKTKLIGRARGYHGVNVAGTSLGGIGGNRKMFGPLMDVDHLPHTLQPGMAFTKGAAETGGVELANELLKLIELHDASNIAAVIVEPMSGSAGVIVPPKGYLQRLREICDANDILLIFDEVITAFGRMGKATGAEYFGVTPDIMNVAKQVTNGAVPMGAVIASSEIYDTFMNQNLPEYAVEFGHGYTYSAHPVACAAGIAALDLLQKENLIQQSAELAPHFEKALHGLKGTKNVIDIRNCGLAGAIQIAARDGDAIVRPFEASMKLWKEGFYVRFGGDTLQFGPTFNAKPEDLDRLFDAVGEALNGVA
5VUE , Knot 123 276 0.83 40 185 266 
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRMAPRAPWIEQEGPEYWDGETRNMKASAQTYRENLRIALRYYNQSEAGSHIIQVMYGCDVGPDGRLLRGHDQSAYDGKDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGLCVEWLRRYLENGKETLQRADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP
2RDQ , Knot 132 288 0.86 40 190 282 
GSHMTNVTGDYTDCTPLLGDRAALDSFYEEHGYLFLRNVLDRDLVKTVAEQMREGLVALGAADPHATLEELTIDSFESVDEVAMHDYVKYDAFWNNPSTIKVFEQVFGEPVFVFLSTTIRYYPSQAGSEEPSFHYLTPFHQDGFYIGPNQDFRTFWIPLIRTTRESGGVALADGSHRRGKRDHVLNESFRRFGHPVRGIPPTEVSEDEHLLHSPMEPGDILLFHAHMCHKSIPNLSKDPRLMRMSMDTRVQPAKSHRGFNAMTPWTESAKDASKGIMAKITGTPTDVE

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 \(c\).

\(|P_{f(4UHN_1)}(2) \setminus P_{f(5VUE_1)}(2)|=104\), \(|P_{f(5VUE_1)}(2) \setminus P_{f(4UHN_1)}(2)|=52\). 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 1:110000000000111101001000101110111010101011110100010001011111010111000100100010111001110000011011100110100011100101101011001101011010011101010001000101101010101010000111010100110111001111110001111110100110010111110011100111011001101101001001111110110101111111010100100100100111110011011101101011001110101101100100111111111100010001100011001101101000010111011111110110000110001011101001101101000110100011111101110010111011010101100110101110010111010101001001101110110111
Pair \(Z_2\) Length of longest common subsequence
4UHN_1,5VUE_1 156 3
4UHN_1,2RDQ_1 161 4
5VUE_1,2RDQ_1 169 4

Newick tree

 
[
	2RDQ_1:83.97,
	[
		4UHN_1:78,5VUE_1:78
	]:5.97
]

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 \((0.85)(0.8)(\frac{744 }{\log_{20} 744}-\frac{276}{\log_{20}276})=129.\)
Status Protein1 Protein2 d d1/2
Query variables 4UHN_1 5VUE_1 163 129.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]