CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7KRK_1 4BEB_1 1VQQ_1 Letter Amino acid
5 15 9 H Histidine
28 85 44 L Leucine
10 87 86 K Lycine
15 64 41 S Serine
10 65 55 N Asparagine
7 81 42 E Glutamic acid
1 3 0 C Cysteine
7 15 17 M Methionine
4 69 13 F Phenylalanine
16 52 33 V Valine
34 70 27 A Alanine
15 75 53 D Aspartic acid
5 22 16 P Proline
15 55 27 Q Glutamine
21 65 55 I Isoleucine
10 71 31 T Threonine
0 7 7 W Tryptophan
4 40 35 Y Tyrosine
11 56 12 R Arginine
32 41 43 G Glycine 

7KRK_1|Chains A, B, C, D|3-oxoacyl-[acyl-carrier-protein] reductase|Acinetobacter baumannii (470)
>4BEB_1|Chains A, B, C, D|TYPE I RESTRICTION ENZYME HSDR|ESCHERICHIA COLI (562)
>1VQQ_1|Chains A, B|penicillin-binding protein mecA, low-affinity|Staphylococcus aureus (1280)
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 \(w=f(c)\)
7KRK , Knot 106 250 0.78 38 143 234 
SMLLQGKVALITGAASERGIGRATAEIFAQQGAKVIIVDLDLAQSQNAAKALGEGHMGLAANVANEEQVKAAVEQALQHYGKIDILINNAGITQPIKTLDIQRSDYDRVLDVSLRGTLIMSQAVIPSMKANGGGSIVCLSSVSAQRGGGIFGGPHYSAAKAGVLGLAKAMAREFGGDQIRVNSLTPGLIQTDITGGLMNDDRRHDILAGIPLGRLGKAQDVANAALFLASDLSAYLTGVTLDVNGGMLIH
4BEB , Knot 381 1038 0.85 40 296 911 
MTHQTHTIAESNNFIVLDKYIKAEPTGDSYQSESDLERELIQDLRNQGYEFISVKSQSAMLANVREQLQNLNGVVFNDSEWRRFTEQYLDNPSDGILDKTRKIHIDYICDFIFDDERLENIYLIDKKNLMRNKVQIIQQFEQAGSHANRYDVTILVNGLPLVQIELKKRGVAIREAFNQIHRYSKESFNSENSLFKYLQLFVISNGTDTRYFANTTKRDENSFDFTMNWAKSDNTLIKDLKDFTATCFQKHTLLNVLVNYSVFDSSQTLLVMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTSFKAARLATELDFIDKVFFVVDRKDLDYQTMKEYQRFSPDSVNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQFGEAQKNLKKKFKRYYQFGFTGTPIFPENALGSETTASVFGRELHSYVITDAIRDEKVLKFKVDYNDVRPQFKSLETETDEKKLSAAENQQAFLHPMRIQEITQYILNNFRQKTHRTFPGSKGFNAMLAVSSVDAAKAYYATFKRLQEEAANKSATYKPLRIATIFSFAANEEQNAIGEISDETFDTSAMDSSAKEFLDAAIREYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQDIDLLIVVGMFLTGFDAPTLNTLFVDKNLRYHGLMQAFSRTNRIYDATKTFGNIVTFRDLERSTIDAITLFGDKNTKNVVLEKSYTEYMEGFTDAATGEAKRGFMTVVSELEQRFPDPTSIESEKEKKDFVKLFGEYLRAENILQNYDEFATLKALQQIDLSDPVAVEKFKAEHYVDDEKFAELQTIRLPADRKIQDYRSAYNDIRDWQRREKEAEKKEKSTTDWDDVVFEVDLLKSQEINLDYILGLIFEHNRQNKGKGEMIEEVKRLIRSSLGNRAKEGLVVDFIQQTNLDDLPDKASIIDAFFTFAQREQQREAEALIKEENLNEDAAKRYIRTSLKREYATENGTELNETLPKLSPLNPQYKTKKQAVFQKIVSFIEKFKGVGGKI
1VQQ , Knot 248 646 0.82 38 246 582 
MASKDKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLEKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQGETGRQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE

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 \(c\).

\(|P_{f(7KRK_1)}(2) \setminus P_{f(4BEB_1)}(2)|=19\), \(|P_{f(4BEB_1)}(2) \setminus P_{f(7KRK_1)}(2)|=172\). 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 1:0111010111101110001110101011100110111101011000011011101011111011000010111001100010101110011100110010100000001101010101110011110101011101101001010011111111000110111111101110011100101001011110001011110000000111111110110100110111111001010101101010111110
Pair \(Z_2\) Length of longest common subsequence
7KRK_1,4BEB_1 191 5
7KRK_1,1VQQ_1 169 4
4BEB_1,1VQQ_1 116 5

Newick tree

 
[
	7KRK_1:98.58,
	[
		1VQQ_1:58,4BEB_1:58
	]:40.58
]

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 \((0.85)(0.8)(\frac{1288 }{\log_{20} 1288}-\frac{250}{\log_{20}250})=274.\)
Status Protein1 Protein2 d d1/2
Query variables 7KRK_1 4BEB_1 343 211.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]