CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5CNK_1 8IGG_1 4TVF_1 Letter Amino acid
31 36 42 R Arginine
30 39 35 D Aspartic acid
20 59 14 Q Glutamine
29 19 6 K Lycine
7 7 3 W Tryptophan
31 31 20 I Isoleucine
11 14 13 M Methionine
22 14 7 Y Tyrosine
30 37 26 V Valine
28 44 5 N Asparagine
30 24 23 E Glutamic acid
49 50 49 L Leucine
26 28 14 F Phenylalanine
15 31 28 P Proline
41 32 14 S Serine
22 47 26 T Threonine
41 64 47 A Alanine
7 2 5 C Cysteine
31 48 35 G Glycine
16 14 19 H Histidine 

5CNK_1|Chains A, B, C|Metabotropic glutamate receptor 3|Homo sapiens (9606)
>8IGG_1|Chains A, B, C, D[auth E]|Chimallin|Pseudomonas phage 201phi2-1 (198110)
>4TVF_1|Chain A|OxyB|Actinoplanes teichomyceticus (1867)
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 \(w=f(c)\)
5CNK , Knot 208 517 0.83 40 259 492 
MALKMLTRLQVLTLALFSKGFLLSLGDHNFLRREIKIEGDLVLGGLFPINEKGTGTEECGRINEDRGIQRLEAMLFAIDEINKDDYLLPGVKLGVHILDTCSRDTYALEQSLEFVRASLTKVDEAEYMCPDGSYAIQENIPLLIAGVIGGSYSSVSIQVANLLRLFQIPQISYASTSAKLSDKSRYDYFARTVPPDFYQAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFEQEARLRNISIATAEKVGRSNIRKSYDSVIRELLQKPNARVVVLFMRSDDSRELIAAASRANASFTWVASDGWGAQESIIKGSEHVAYGAITLELASQPVRQFDRYFQSLNPYNNHRNPWFRDFWEQKFQCSLQNKRNHRRVCDKHLAIDSSNYEQESKIMFVVNAVYAMAHALHKMQRTLCPNTTKLCDAMKILDGKKLYKDYLLKINFTAPFNPNKDADSIVKFDTFGDGMGRYNVFNFQNVGGKYSYLKVGHWAETLSLDVNSIHWSRNSVPTSEGHHHHHH
8IGG , Knot 248 640 0.83 40 268 597 
MIRDTATNTTQTQAAPQQAPAQQFTQAPQEKPMQSTQSQPTPSYAGTGGINSQFTRSGNVQGGDARASEALTVFTRLKEQAVAQQDLADDFSILRFDRDQHQVGWSSLVIAKQISLNGQPVIAVRPLILPNNSIELPKRKTNIVNGMQTDVIESDIDVGTVFSAQYFNRLSTYVQNTLGKPGAKVVLAGPFPIPADLVLKDSELQLRNLLIKSVNACDDILALHSGERPFTIAGLKGQQGETLAAKVDIRTQPLHDTVGNPIRADIVVTTQRVRRNGQQENEFYETDVKLNQVAMFTNLERTPQAQAQTLFPNQQQVATPAPWVASVVITDVRNADGIQANTPEMYWFALSNAFRSTHGHAWARPFLPMTGVAKDMKDIGALGWMSALRNRIDTKAANFDDAQFGQLMLSQVQPNPVFQIDLNRMGETAQMDSLQLDAAGGPNAQKAAATIIRQINNLGGGGFERFFDHTTQPILERTGQVIDLGNWFDGDEKRDRRDLDNLAALNAAEGNENEFWGFYGAQLNPNLHPDLRNRQSRNYDRQYLGSTVTYTGKAERCTYNAKFIEALDRYLAEAGLQITMDNTSVLNSGQRFMGNSVIGNNMVSGQAQVHSAYAGTQGFNTQYQTGPSSFYALEHHHHHH
4TVF , Knot 173 431 0.81 40 211 394 
MHHHHHHGKPIPNPLLGLDSTENLYFQGIDPFTMSGDGSPPIHTRRQGFDPADELRAAGTLTKISIGSGADAETTWLAAGHAVVRQVLGDHKRFSTRRRFDRRDEIGGTGVFRPRELVGNLMDYDPPEHTRLRHLLTPGFTQRRMRRLAPRIEEIVTDRLDAMEQAGPPADLIELFADEVPGAVLCELIGVPRDDQAMFLQLCHRHLDASLSARKRAAAGEAFARYLVAMMARERKDPGDGFIGSIVAEHGDTITDEELRGVCVQLMLAGDDNVSGMIGLGVLALLRHPEQIAALRGDDQSADRAVDELIRYLTVPYAPTPRTAVEDVMVADQVIKEGETVLCSLPMANRDRALLPDADRLDVTRTPVPHVAFGHGIHHCLGAALTRLQLRIAYTALWRRFPALQLADPAQEIMFRTSTPAYGLTSLLVAW

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 \(c\).

\(|P_{f(5CNK_1)}(2) \setminus P_{f(8IGG_1)}(2)|=53\), \(|P_{f(8IGG_1)}(2) \setminus P_{f(5CNK_1)}(2)|=62\). 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 1:1110110010110111100111101100011000101010111111111000101000010100001100101111110010000011111011101100000000110001011010100100100101010011000111111111110000101011011011011010010001010000000011001110100101110110110100100110010010011011000101001011010011000100000011001100101011111100000001111100101010111001111000110100011011101011001100100010010100000011100110001000100000000100001110000000000111110110111011001000101000010011011010010000110101011101000100110100110111000110100111000010110110010101001010000110001000000
Pair \(Z_2\) Length of longest common subsequence
5CNK_1,8IGG_1 115 6
5CNK_1,4TVF_1 152 6
8IGG_1,4TVF_1 143 6

Newick tree

 
[
	4TVF_1:78.46,
	[
		5CNK_1:57.5,8IGG_1:57.5
	]:20.96
]

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 \((0.85)(0.8)(\frac{1157 }{\log_{20} 1157}-\frac{517}{\log_{20}517})=165.\)
Status Protein1 Protein2 d d1/2
Query variables 5CNK_1 8IGG_1 205 188
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]