CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5ZGU_1 4TQS_1 3WMF_1 Letter Amino acid
17 21 29 D Aspartic acid
1 1 3 C Cysteine
13 38 38 I Isoleucine
17 28 65 L Leucine
16 11 29 T Threonine
4 15 19 Y Tyrosine
36 25 66 A Alanine
24 18 61 G Glycine
9 8 11 H Histidine
12 11 18 P Proline
15 30 55 V Valine
9 24 37 R Arginine
9 14 33 F Phenylalanine
12 19 45 S Serine
10 13 15 N Asparagine
12 4 26 Q Glutamine
6 33 32 E Glutamic acid
8 39 18 K Lycine
8 6 15 M Methionine
4 0 6 W Tryptophan 

5ZGU_1|Chains A, B|Metallo-beta-lactamase type 2|Klebsiella pneumoniae (573)
>4TQS_1|Chains A, B|DNA polymerase IV|Sulfolobus solfataricus (273057)
>3WMF_1|Chain A|ATP-binding cassette, sub-family B, member 1|Cyanidioschyzon merolae (45157)
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 \(w=f(c)\)
5ZGU , Knot 111 242 0.84 40 165 234 
GEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR
4TQS , Knot 150 358 0.82 38 183 335 
HHHHHHMIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFIEAIGLDKFFDT
3WMF , Knot 242 621 0.83 40 249 569 
ASGPESAYTTGVTARRIFALAWSSSATMIVIGFIASILEGATLPAFAIVFGRMFQVFTKSKSQIEGETWKYSVGFVGIGVFEFIVAGSRTALFGIASERLARDLRVAAFSNLVEQDVTYFDRRKAGELGGKLNNDVQVIQYSFSKLGAVLFNLAQCVVGIIVAFIFAPALTGVLIALSPLVVLAVVVQMIEMSGNTKRSSEAYASAGSVAAEVFSNIRTTKAFEAERYETQRYGSKLDPLYRLGRRRYISDGLFFGLSMLVIFCVYALALWWGGQLIARGSLNLGNLLTAFFSAILGFMGVGQAAQVWPDVTRGLGAGGELFAMIDRVPQYRRPDPGAEVVTQPLVLKQGIVFENVHFRYPTRMNVEVLRGISLTIPNGKTVAIVGGSGAGKSTIIQLLMRFYDIEPQGGGLLLFDGTPAWNYDFHALRSQIGLVSQEPVLFSGTIRDNILYGKRDATDEEVIQALREANAYSFVMALPDGLDTEVGERGLALSGGQKQRIAIARAILKHPTLLCLDESTSALDAESEALVQEALDRMMASDGVTSVVIAHRLSTVARADLILVMQDGVVVEQGNHSELMALGPSGFYYQLVEKQLASGDMSAASGRDYKDDDDKHHHHHH

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 \(c\).

\(|P_{f(5ZGU_1)}(2) \setminus P_{f(4TQS_1)}(2)|=74\), \(|P_{f(4TQS_1)}(2) \setminus P_{f(5ZGU_1)}(2)|=92\). 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 1:10101011001001000110111001110110000010111111110011110011011110011000001011011000101111111100100001111011011111001011000111001111100010111011101101101111011011110000010111010011111011000010011011010000011010111111101011110001100011100010110010
Pair \(Z_2\) Length of longest common subsequence
5ZGU_1,4TQS_1 166 4
5ZGU_1,3WMF_1 168 4
4TQS_1,3WMF_1 154 6

Newick tree

 
[
	5ZGU_1:85.55,
	[
		4TQS_1:77,3WMF_1:77
	]:8.55
]

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 \((0.85)(0.8)(\frac{600 }{\log_{20} 600}-\frac{242}{\log_{20}242})=101.\)
Status Protein1 Protein2 d d1/2
Query variables 5ZGU_1 4TQS_1 127 108
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]