CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5HOP_1 7JRV_1 4GTM_1 Letter Amino acid
29 46 37 L Leucine
16 23 15 K Lycine
19 42 22 S Serine
6 28 25 R Arginine
8 13 18 Y Tyrosine
9 13 26 Q Glutamine
10 44 12 G Glycine
4 11 9 H Histidine
16 18 21 I Isoleucine
14 33 8 T Threonine
18 63 27 A Alanine
14 19 19 N Asparagine
15 46 27 D Aspartic acid
4 10 10 W Tryptophan
15 32 22 V Valine
12 5 9 F Phenylalanine
10 34 26 P Proline
1 8 2 C Cysteine
19 16 36 E Glutamic acid
9 5 6 M Methionine 

5HOP_1|Chains A, B|Lmo0182 protein|Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (169963)
>7JRV_1|Chain A|Phospholipase D|Streptomyces antibioticus (1890)
>4GTM_1|Chain A|Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha|Rattus norvegicus (10116)
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 \(w=f(c)\)
5HOP , Knot 116 248 0.86 40 176 241 
SNAMSKFTKLMQGYLHLIEGKNEKIKPILLETKPNFTTDSVLETASWLWLSSKINHYDREEVEPVIAFLVENWNRPEKSIWGSAENDIYLATISSVYSALLDVKNTFPKPELQQTITIIRDYCFDNLLKGDSILTGFNTRKVSTDQLLSVLPFGLFSPEDLVMVAAVGKMEQQLVQDDGVLPYSGAPRVNSFATALMALYFLEKSDQDKALHYLNMAMKMEDNDELGAIFIEINQAFRAMESEVTAHI
7JRV , Knot 206 509 0.84 40 235 470 
ADTPPTPHLDAIERSLRDTSPGLEGSVWQRTDGNRLDAPDGDPAGWLLQTPGCWGDAGCKDRAGTRRLLDKMTRNIADARHTVDISSLAPFPNGGFEDAVVDGLKASVAAGHSPRVRILVGAAPIYHLNVVPSRYRDELIGKLGAAAGKVTLNVASMTTSKTSLSWNHSKLLVVDGKTAITGGINTNKDDYLDTAHPVSDVDMALSGPAARSAGKYLDTLWDWTCRNASDPAKVWLATSNGASCMPSMEQDEAGSAPAEPTGDVPVIAVGGLGVGIKESDPSSGYHPDLPTAPDTKCTVGLHDNTNADRDYDTVNPEENALRSLIASARSHVEISQQDLNATCPPLPRYDIRTYDTLAGKLAAGVKVRIVVSDPANRGAVGSGGRSQIKSLDEISDTLRTRLVALTGDNEKASRALCGNLQLASFRSSDAAKWADGKPYALHHKLVSVDDSAFYIGSKNLYPAWLQDFGYIVESPAAAQQLKTELLDPEWKYSQQAAATPAGCPARQAG
4GTM , Knot 156 377 0.81 40 213 348 
MAATEGVGESAPGGEPGQPEQPPPPPPPPPAQQPQEEEMAAEAGEAAASPMDDGFLSLDSPTYVLYRDRAEWADIDPVPQNDGPSPVVQIIYSEKFRDVYDYFRAVLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLRSLQKDLQEEMNYIIAIIEEQPKNYQVWHHRRVLVEWLKDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFRLWDNELQYVDQLLKEDVRNNSVWNQRHFVISNTTGYSDRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQDRGLSRYPNLLNQLLDLQPSHSSPYLIAFLVDIYEDMLENQCDNKEDILNKALELCEILAKEKDTIRKEYWRYIGRSLQSKHSRESDIPASV

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 \(c\).

\(|P_{f(5HOP_1)}(2) \setminus P_{f(7JRV_1)}(2)|=48\), \(|P_{f(7JRV_1)}(2) \setminus P_{f(5HOP_1)}(2)|=107\). 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 1:00110010011010101101000010111100010100001100101111000100000001011111110010010001110100010110100100111010001101010001011000010011010011011000010000110111111101001111111101000110001111001110100110111110110000000110010111010000011111101001101100010101
Pair \(Z_2\) Length of longest common subsequence
5HOP_1,7JRV_1 155 4
5HOP_1,4GTM_1 171 5
7JRV_1,4GTM_1 146 4

Newick tree

 
[
	5HOP_1:84.26,
	[
		7JRV_1:73,4GTM_1:73
	]:11.26
]

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 \((0.85)(0.8)(\frac{757 }{\log_{20} 757}-\frac{248}{\log_{20}248})=140.\)
Status Protein1 Protein2 d d1/2
Query variables 5HOP_1 7JRV_1 178 131
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]