CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
9HNO_1 4BBJ_1 9OAO_1 Letter Amino acid
16 9 7 W Tryptophan
55 82 14 A Alanine
40 68 21 G Glycine
12 24 3 H Histidine
26 35 12 P Proline
22 19 7 F Phenylalanine
18 48 29 S Serine
28 76 23 V Valine
53 28 7 R Arginine
16 46 3 I Isoleucine
15 35 12 K Lycine
22 27 2 M Methionine
14 16 9 N Asparagine
49 77 15 L Leucine
13 7 9 Y Tyrosine
18 37 20 T Threonine
40 27 5 D Aspartic acid
7 6 5 C Cysteine
16 23 12 Q Glutamine
29 46 6 E Glutamic acid 

9HNO_1|Chain A|Cryptochrome/photolyase family protein|Caulobacter vibrioides (155892)
>4BBJ_1|Chain A|COPPER EFFLUX ATPASE|LEGIONELLA PNEUMOPHILA SUBSP. PNEUMOPHILA (91891)
>9OAO_1|Chain A[auth H]|G001-0087 Fab heavy chain|Homo sapiens (9606)
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 \(w=f(c)\)
9HNO , Knot 203 509 0.82 40 249 473 
MAGALRLVLGDQLSDNLSALVDADLSRDQVLMVESRVEATAWKHHKQKLVLVWSAMRQFAERLRARGFNVRYVTLEDPDNTGSIGGELRRALEARAFDRVIRTACGKWGLESHLLSLDLPVPMETREDDRFLCSRAQFAAWAEGRRELRMEFFYREMRRKTGLLMDGDQPAGGRWNFDAENRRKLPPGLRPPERLRIPPNPTTQTVLEQVSRGFDDHFGEVEGFGWPTNPDEATAILDHFIADMLPSFGDWQDAMSWRRPFLWHSLISPALNIGLLDPLDICRRAEAAWREGRAPLNAVEGFIRQIIGWREFVRGIYWLKMPEYAQRNALDAQGKLPGFYWTGQTDMACVADTVRAAHDHAYAHHIQRLMVTGNLAMLLGVHPDAVDDWYMVVFADAYEWVEMPNTRGMATFADGGIVGSKPYAASGAYIDRMSDYCKGCRYDVKKRLGDDACPFNALYWDFIDRHAQRLAGNGRMMMPLRTLEKMPDAEREAFRKQARALRVKMGVSG
4BBJ , Knot 279 736 0.83 40 268 648 
MKHDHHQGHTHSGKGHACHHEHNSPKTQQASSKMEGPIVYTCPMHPEIRQSAPGHCPLCGMALEPETVTVSEVVSPEYLDMRRRFWIALMLTIPVVILEMGGHGLKHFISGNGSSWIQLLLATPVVLWGGWPFFKRGWQSLKTGQLNMFTLIAMGIGVAWIYSMVAVLWPGVFPHAFRSQEGVVAVYFEAAAVITTLVLLGQVLELKAREQTGSAIRALLKLVPESAHRIKEDGSEEEVSLDNVAVGDLLRVRPGEKIPVDGEVQEGRSFVDESMVTGEPIPVAKEASAKVIGATINQTGSFVMKALHVGSDTMLARIVQMVSDAQRSRAPIQRLADTVSGWFVPAVILVAVLSFIVWALLGPQPALSYGLIAAVSVLIIACPCALGLATPMSIMVGVGKGAQSGVLIKNAEALERMEKVNTLVVDKTGTLTEGHPKLTRIVTDDFVEDNALALAAALEHQSEHPLANAIVHAAKEKGLSLGSVEAFEAPTGKGVVGQVDGHHVAIGNARLMQEHGGDNAPLFEKADELRGKGASVMFMAVDGKTVALLVVEDPIKSSTPETILELQQSGIEIVMLTGDSKRTAEAVAGTLGIKKVVAEIMPEDKSRIVSELKDKGLIVAMAGDGVNDAPALAKADIGIAMGTGTDVAIESAGVTLLHGDLRGIAKARRLSESTMSNIRQNLFFAFIYNVLGVPLAAGVLYPLTGLLLSPMIAAAAMALSSVSVIINALRLKRVTL
9OAO , Knot 99 221 0.80 40 148 209 
QVQLVQSGAEVKKPGASVKVSCKASGYTFTGNYIHWVRQAPGQGLEWVGWLNPNSGGTNYAQQFQGRVTMTRDTSISTAYMELNRLRSDDTAVFYCARGLWQWEFRYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

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 \(c\).

\(|P_{f(9HNO_1)}(2) \setminus P_{f(4BBJ_1)}(2)|=71\), \(|P_{f(4BBJ_1)}(2) \setminus P_{f(9HNO_1)}(2)|=90\). 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 1:11111011110010001011101010000111100010101100000011111011001100101011010010100100010111010011010110011001010111000110101111100000001100010111110100010101100010000111101001111010101000001111101100101110100001100100110001101011111001001011100111011101101001101001111001101110111101101000101110010111011011100111100110110110110010001101010111101010001101100101100010100100111010111111101011001011111010011011000111011011111001011011010010000010000100011001011011010110001001110101111100100110100011000101101011101
Pair \(Z_2\) Length of longest common subsequence
9HNO_1,4BBJ_1 161 4
9HNO_1,9OAO_1 189 3
4BBJ_1,9OAO_1 206 4

Newick tree

 
[
	9OAO_1:10.24,
	[
		9HNO_1:80.5,4BBJ_1:80.5
	]:23.74
]

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 \((0.85)(0.8)(\frac{1245 }{\log_{20} 1245}-\frac{509}{\log_{20}509})=189.\)
Status Protein1 Protein2 d d1/2
Query variables 9HNO_1 4BBJ_1 237 202.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]