CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4YFO_1 4GIM_1 5KPD_1 Letter Amino acid
3 27 102 I Isoleucine
1 1 11 W Tryptophan
9 27 93 V Valine
47 40 117 A Alanine
13 10 53 R Arginine
25 30 100 G Glycine
15 12 23 H Histidine
25 13 50 N Asparagine
20 10 52 D Aspartic acid
9 14 61 Q Glutamine
3 7 33 M Methionine
2 14 30 P Proline
18 22 81 S Serine
8 20 66 T Threonine
2 4 36 Y Tyrosine
11 25 70 E Glutamic acid
41 29 114 L Leucine
3 16 81 K Lycine
2 2 8 C Cysteine
2 12 67 F Phenylalanine 

4YFO_1|Chain A|beta1_ex1|synthetic construct (32630)
>4GIM_1|Chains A, B, C|Pseudouridine-5'-phosphate glycosidase|Escherichia coli (562)
>5KPD_1|Chains A, B|Multidrug resistance protein 1A|Mus musculus (10090)
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 \(w=f(c)\)
4YFO , Knot 91 259 0.65 40 107 181 
MGSSHHHHHHSSGLVPRGSHMNVGEILRHYAAGKRNFQHINLQEIELTNASLTGADLSYANLHHANLSRANLRSADLRNANLSHANLSGANLEEANLEAANLRGADLHEANLSGADLQEANLTQANLKDANLSDANLEQADLAGADLQGAVLDGANLHGADLNGADLKQADLSGADLGGANLNNANLSEAMLTRANLEQADLSGARTTGARLDDADLRGATVDPVLWRTASLVGARVDVDQAVAFAAAHGLCLAGGSGC
4GIM , Knot 141 335 0.81 40 188 313 
MGSDKIHHHHHHSSGENLYFQGHMSELKISPELLQISPEVQDALKNKKPVVALESTIISHGMPFPQNAQTAIEVEETIRKQGAVPATIAIIGGVMKVGLSKEEIELLGREGHNVTKVSRRDLPFVVAAGKNGATTVASTMIIAALAGIKVFATGGIGGVHRGAEHTFDISADLQELANTNVTVVCAGAASILDLGLTTEYLETFGVPLIGYQTKALPAFFCRTSPFDVSIRLDSASEIARAMVVKWQSGLNGGLVVANPIPEQFAMPEHTINAAIDQAVAEAEAQGVIGKESTPFLLARVAELTGGDSLKSNIQLVFNNAILASEIAKEYQRLAG
5KPD , Knot 424 1248 0.80 40 315 1013 
MELEEDLKGRADKNFSKMGKKSKKEKKEKKPAVSVLTMFRYAGWLDRLYMLVGTLAAIIHGVALPLMMLIFGDMTDSFASVGNVSKNSTNMSEADKRAMFAKLEEEMTTYAYYYTGIGAGVLIVAYIQVSFWCLAAGRQIHKIRQKFFHAIMNQEIGWFDVHDVGELNTRLTDDVSKINEGIGDKIGMFFQAMATFFGGFIIGFTRGWKLTLVILAISPVLGLSAGIWAKILSSFTDKELHAYAKAGAVAEEVLAAIRTVIAFGGQKKELERYNNNLEEAKRLGIKKAITANISMGAAFLLIYASYALAFWYGTSLVISKEYSIGQVLTVFFSVLIGAFSVGQASPNIEAFANARGAAYEVFKIIDNKPSIDSFSKSGHKPDNIQGNLEFKNIHFSYPSRKEVQILKGLNLKVKSGQTVALVGNSGCGKSTTVQLMQRLYDPLDGMVSIDGQDIRTINVRYLREIIGVVSQEPVLFATTIAENIRYGREDVTMDEIEKAVKEANAYDFIMKLPHQFDTLVGERGAQLSGGQKQRIAIARALVRNPKILLLDQATSALDTESEAVVQAALDKAREGRTTIVIAHRLSTVRNADVIAGFDGGVIVEQGNHDELMREKGIYFKLVMTQTAGNEIELGNEACKSKDEIDNLDALDEDVPPASFWRILKLNSTEWPYFVVGIFCAIINGGLQPAFSVIFSKVVGVFTNGGPPETQRQNSNLFSLLFLILGIISFITFFLQGFTFGKAGEILTKRLRYMVFKSMLRQDVSWFDDPKNTTGALTTRLANDAAQVKGATGSRLAVIFQNIANLGTGIIISLIYGWQLTLLLLAIVPIIAIAGVVEMKMLSGQALKDKKELEGSGKIATEAIENFRTVVSLTREQKFETMYAQSLQIPYRNAMKKAHVFGITFSFTQAMMYFSYAACFRFGAYLVTQQLMTFENVLLVFSAIVFGAMAVGQVSSFAPDYAKATVSASHIIRIIEKTPEIDSYSTQGLKPNMLEGNVQFSGVVFNYPTRPSIPVLQGLSLEVKKGQTLALVGSSGCGKSTVVQLLERFYDPMAGSVFLDGKEIKQLNVQWLRAQLGIVSQEPILFDCSIAENIAYGDNSRVVSYEEIVRAAKEANIHQFIDSLPDKYNTRVGDKGTQLSGGQKQRIAIARALVRQPHILLLDQATSALDTESEKVVQEALDKAREGRTCIVIAHRLSTIQNADLIVVIQNGKVKEHGTHQQLLAQKGIYFSMVSVQAGAKRSHHHHHH

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 \(c\).

\(|P_{f(4YFO_1)}(2) \setminus P_{f(4GIM_1)}(2)|=31\), \(|P_{f(4GIM_1)}(2) \setminus P_{f(4YFO_1)}(2)|=112\). 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 1:1100000000001111010010110110001110001001010010100101011010010100101001010010100101001010110100101011010110100101011010010100101001010010100101111010111101101011010110100101011011110100101001110010100101011000110100101011010111100101111010100111111101101111010
Pair \(Z_2\) Length of longest common subsequence
4YFO_1,4GIM_1 143 9
4YFO_1,5KPD_1 230 7
4GIM_1,5KPD_1 161 6

Newick tree

 
[
	5KPD_1:10.92,
	[
		4YFO_1:71.5,4GIM_1:71.5
	]:35.42
]

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 \((0.85)(0.8)(\frac{594 }{\log_{20} 594}-\frac{259}{\log_{20}259})=94.5\)
Status Protein1 Protein2 d d1/2
Query variables 4YFO_1 4GIM_1 117 94
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]