CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4NJH_1 3BPX_1 6UUW_1 Letter Amino acid
22 6 90 A Alanine
10 6 72 K Lycine
10 7 44 F Phenylalanine
13 4 58 P Proline
11 23 48 R Arginine
16 9 59 D Aspartic acid
11 5 25 H Histidine
9 12 77 I Isoleucine
5 2 11 W Tryptophan
5 1 40 Y Tyrosine
16 6 80 V Valine
8 2 35 N Asparagine
7 2 16 C Cysteine
9 3 34 Q Glutamine
11 19 62 E Glutamic acid
10 6 63 T Threonine
21 9 102 G Glycine
20 19 90 L Leucine
5 3 34 M Methionine
11 4 61 S Serine 

4NJH_1|Chains A, B|7-carboxy-7-deazaguanine synthase|Burkholderia multivorans (395019)
>3BPX_1|Chains A, B|Transcriptional regulator|Methanobacterium thermoautotrophicum
>6UUW_1|Chains A, B, C, D|ATP-citrate synthase|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 \(w=f(c)\)
4NJH , Knot 110 230 0.86 40 167 220 
MGSSHHHHHHSSGLVPRGSHMTYAVKEIFYTLQGEGANAGRPAVFCRFAGCNLWSGREEDRAQAVCRFCDTDFVGTDGENGGKFKDADALVATIAGLWPAGEAHRFVVCTGGEPMLQLDQPLVDALHAAGFGIAIETNGSLPVLESIDWICVSPKADAPLVVTKGNELKVVIPQDNQRLADYAKLDFEYFLVQPMDGPSRDLNTKLAIDWCKRHPQWRLSMQTHKYLNIP
3BPX , Knot 71 148 0.80 40 109 142 
GSHMDRDIPLKGLLSIILRSHRVFIGRELGHLNLTDAQVACLLRIHREPGIKQDELATFFHVDKGTIARTLRRLEESGFIEREQDPENRRRYILEVTRRGEEIIPLILKVEERWEDLLFRDFTEDERKLFRKMCRRLAEEAVRMRGEW
6UUW , Knot 400 1101 0.84 40 330 973 
MSAKAISEQTGKELLYKFICTTSAIQNRFKYARVTPDTDWARLLQDHPWLLSQNLVVKPDQLIKRRGKLGLVGVNLTLDGVKSWLKPRLGQEATVGKATGFLKNFLIEPFVPHSQAEEFYVCIYATREGDYVLFHHEGGVDVGDVDAKAQKLLVGVDEKLNPEDIKKHLLVHAPEDKKEILASFISGLFNFYEDLYFTYLEINPLVVTKDGVYVLDLAAKVDATADYICKVKWGDIEFPPPFGREAYPEEAYIADLDAKSGASLKLTLLNPKGRIWTMVAGGGASVVYSDTICDLGGVNELANYGEYSGAPSEQQTYDYAKTILSLMTREKHPDGKILIIGGSIANFTNVAATFKGIVRAIRDYQGPLKEHEVTIFVRRGGPNYQEGLRVMGEVGKTTGIPIHVFGTETHMTAIVGMALGHRPIPNQPPTAAHTANFLLNASGSTSTPAPSRTASFSESRADEVAPAKKAKPAMPQDSVPSPRSLQGKSTTLFSRHTKAIVWGMQTRAVQGMLDFDYVCSRDEPSVAAMVYPFTGDHKQKFYWGHKEILIPVFKNMADAMRKHPEVDVLINFASLRSAYDSTMETMNYAQIRTIAIIAQGIPEALTRKLIKKADQKGVTIIGPATVGGIKPGCFKIGNTGGMLDNILASKLYRPGSVAYVSRSGGMSNELNNIISRTTDGVYEGVAIGGDRYPGSTFMDHVLRYQDTPGVKMIVVLGEIGGTEEYKICRGIKEGRLTKPIVCWCIGTCATMFSSEVQFGHAGACANQASETAVAKNQALKEAGVFVPRSFDELGEIIQSVYEDLVANGVIVPAQEVPPPTVPMDYSWARELGLIRKPASFMTSICDERGQELIYAGMPITEVFKEEMGIGGVLGLLWFQKRLPKYSCQFIEMCLMVTADHGPAVSGAHNTIICARAGKDLVSSLTSGLLTIGDRFGGALDAAAKMFSKAFDSGIIPMEFVNKMKKEGKLIMGIGHRVKSINNPDMRVQILKDYVRQHFPATPLLDYALEVEKITTSKKPNLILNVDGLIGVAFVDMLRNCGSFTREEADEYIDIGALNGIFVLGRSMGFIGHYLDQKRLKQGLYRHPWDDISYVLPEHMSM

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 \(c\).

\(|P_{f(4NJH_1)}(2) \setminus P_{f(3BPX_1)}(2)|=113\), \(|P_{f(3BPX_1)}(2) \setminus P_{f(4NJH_1)}(2)|=55\). 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 1:11000000000011110100100110011001010110110111100111001101000001011001000011100100110100101111011111111010011100110111010011101101111111100010111100101101010101111100100101111000001100101010011101101100010001110100001010101000001011
Pair \(Z_2\) Length of longest common subsequence
4NJH_1,3BPX_1 168 4
4NJH_1,6UUW_1 191 6
3BPX_1,6UUW_1 241 4

Newick tree

 
[
	6UUW_1:11.79,
	[
		4NJH_1:84,3BPX_1:84
	]:31.79
]

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 \((0.85)(0.8)(\frac{378 }{\log_{20} 378}-\frac{148}{\log_{20}148})=69.4\)
Status Protein1 Protein2 d d1/2
Query variables 4NJH_1 3BPX_1 92 72
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]