CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6MAV_1 2WLH_1 5IBQ_1 Letter Amino acid
14 15 24 D Aspartic acid
8 20 9 H Histidine
8 20 17 S Serine
6 8 17 N Asparagine
3 5 16 Q Glutamine
8 20 22 I Isoleucine
6 6 23 K Lycine
13 22 15 T Threonine
3 4 1 W Tryptophan
7 19 5 R Arginine
13 13 7 P Proline
8 18 21 V Valine
0 3 1 C Cysteine
9 14 18 E Glutamic acid
13 22 25 G Glycine
16 35 18 L Leucine
2 9 10 M Methionine
10 18 7 F Phenylalanine
8 7 9 Y Tyrosine
13 23 45 A Alanine 

6MAV_1|Chain A|Stromelysin-1|Homo sapiens (9606)
>2WLH_1|Chain A|POTASSIUM CHANNEL|MAGNETOSPIRILLUM MAGNETOTACTICUM (188)
>5IBQ_1|Chain A|Probable ribose ABC transporter, substrate-binding protein|Rhizobium etli (347834)
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 \(w=f(c)\)
6MAV , Knot 81 168 0.82 38 125 162 
FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYGPPP
2WLH , Knot 129 301 0.81 40 178 289 
MTGGMKPPARKPRILNSDGSSNITRLGLEKRGWLDDHYHDLLTVSWPVFITLITGLYLVTNALFALAYLACGDVIENARPGSFTDAFFFSVQTMATIGYGKLIPIGPLANTLVTLEALCGMLGLAVAASLIYARFTRPTAGVLFSSRMVISDFEGKPTLMMRLANLRIEQIIEADVHLVLVRSEISQEGMVFRRFHDLTLTRSRSPIFSLSWTVMHPIDHHSPIYGETDETLRNSHSEFLVLFTGHHEAFAQNVHARHAYSCDEIIWGGHFVDVFTTLPDGRRALDLGKFHEIAQHHHHHH
5IBQ , Knot 129 310 0.79 40 174 289 
MHHHHHHSSGVDLGTENLYFQSMADLIAIITPAHDNPFFKAEAVGAEAKAKELGYETLVMTHDDDANKQSEMIDTAIGRGAKAIILDNAGADASVAAVKKAKDAGIPSFLIDREINATGVAVAQIVSNNYQGAQLGAQEFVKLMGEKGNYVELVGKESDTNAGIRSQGYHDVIDDYPEMKSVAKQSANWSQTEAYSKMETILQANPDIKGVISGNDTMAMGAIAALQAAGRKDVIVVGFDGSNDVRDSIKSGGIKATVLQPAYAQAQLAVEQADAYIKNKTTPKEEKQLMDCVLINADNAGKLETFALTN

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 \(c\).

\(|P_{f(6MAV_1)}(2) \setminus P_{f(2WLH_1)}(2)|=52\), \(|P_{f(2WLH_1)}(2) \setminus P_{f(6MAV_1)}(2)|=105\). 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 1:100111110100001000110001011001100110011011001011010010010101110111000101011011101110101111110101010000010000010011111100110011110010001110110001001001010000101100101111
Pair \(Z_2\) Length of longest common subsequence
6MAV_1,2WLH_1 157 3
6MAV_1,5IBQ_1 161 3
2WLH_1,5IBQ_1 166 6

Newick tree

 
[
	5IBQ_1:82.81,
	[
		6MAV_1:78.5,2WLH_1:78.5
	]:4.31
]

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 \((0.85)(0.8)(\frac{469 }{\log_{20} 469}-\frac{168}{\log_{20}168})=88.5\)
Status Protein1 Protein2 d d1/2
Query variables 6MAV_1 2WLH_1 110 87.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]