IGDRPT (Indian Genetic Disease Risk Prediction Tool)

Disease Name: Cystinosis nephropathic

1 .Inheritance

Autosomal Recessive

2. Gene Name

CTNS

3. Protein Name

Cystinosin

4. Chromosomal Location

17p13

5. Protein Sequence

>sp|O60931|CTNS_HUMAN Cystinosin OS=Homo sapiens OX=9606 GN=CTNS PE=1 SV=2

MIRNWLTIFILFPLKLVEKCESSVSLTVPPVVKLENGSSTNVSLTLRPPLNATLVITFEI

TFRSKNITILELPDEVVVPPGVTNSSFQVTSQNVGQLTVYLHGNHSNQTGPRIRFLVIRS

SAISIINQVIGWIYFVAWSISFYPQVIMNWRRKSVIGLSFDFVALNLTGFVAYSVFNIGL

LWVPYIKEQFLLKYPNGVNPVNSNDVFFSLHAVVLTLIIIVQCCLYERGGQRVSWPAIGF

LVLAWLFAFVTMIVAAVGVTTWLQFLFCFSYIKLAVTLVKYFPQAYMNFYYKSTEGWSIG

NVLLDFTGGSFSLLQMFLQSYNNDQWTLIFGDPTKFGLGVFSIVFDVVFFIQHFCLYRKR

PGYDQLN

6. Gene Sequence

>NM_001031681.2 Homo sapiens cystinosin, lysosomal cystine transporter (CTNS), transcript variant 1, mRNA

GATTTCCGCCCAATGGAGGGCGGTCTGAGCTTCGCTCACGAAAGGAGCCGGGAGGCGCTGGCGGCTCCAA

GAGTCTCTGTGTCCCTGGCAGCGGACCTCATCTTCCCTCACGCCGGAGCCCCGATCTCTGCGCCCCGGCC

CGACCCAGCTGCGCTCTGTCCGTCTAAGACGCGCGGAAACTACAACTCCCAGAGCTCATCTCGCCGAGAT

CCGGCCCCACGAGTCAGGTGGCGGAGGTCAGATTGCTTTGGAGACGCTGAGAGAACCTTTGCGAGAGCGC

CGGTTGACGTGCGGAGTGCGGGGCTCCGGGGGACTGAGCAGCACGAGACCCCATCCTCCCCTCCGGGTTT

TCACACTGGGCGAAGGGAGGACTCCTGAGCTCTGCCTCTTCCAGTAACATTGAGGATTACTGTGTTTTGT

GAGAGCTCGCTAGGCGCCCTAAGCAACAGAGTTCTGAGAAATCGAGAAACATGATAAGGAATTGGCTGAC

TATTTTTATCCTTTTTCCCCTGAAGCTCGTAGAGAAATGTGAGTCAAGCGTCAGCCTCACTGTTCCTCCT

GTCGTAAAGCTGGAGAACGGCAGCTCGACCAACGTCAGCCTCACCCTGCGGCCACCATTAAATGCAACCC

TGGTGATCACTTTTGAAATCACATTTCGTTCCAAAAATATTACTATCCTTGAGCTCCCCGATGAAGTTGT

GGTGCCTCCTGGAGTGACAAACTCCTCTTTTCAAGTGACATCTCAAAATGTTGGACAACTTACTGTTTAT

CTACATGGAAATCACTCCAATCAGACCGGCCCGAGGATACGCTTTCTTGTGATCCGCAGCAGCGCCATTA

GCATCATAAACCAGGTGATTGGCTGGATCTACTTTGTGGCCTGGTCCATCTCCTTCTACCCTCAGGTGAT

CATGAATTGGAGGCGGAAAAGTGTCATTGGTCTGAGCTTCGACTTCGTGGCTCTGAACCTGACGGGCTTC

GTGGCCTACAGTGTATTCAACATCGGCCTCCTCTGGGTGCCCTACATCAAGGAGCAGTTTCTCCTCAAAT

ACCCCAACGGAGTGAACCCCGTGAACAGCAACGACGTCTTCTTCAGCCTGCACGCGGTTGTCCTCACGCT

GATCATCATCGTGCAGTGCTGCCTGTATGAGCGCGGTGGCCAGCGCGTGTCCTGGCCTGCCATCGGCTTC

CTGGTGCTCGCGTGGCTCTTCGCATTTGTCACCATGATCGTGGCTGCAGTGGGAGTGACCACGTGGCTGC

AGTTTCTCTTCTGCTTCTCCTACATCAAGCTCGCAGTCACGCTGGTCAAGTATTTTCCACAGGCCTACAT

GAACTTTTACTACAAAAGCACTGAGGGCTGGAGCATTGGCAACGTGCTCCTGGACTTCACCGGGGGCAGC

TTCAGCCTCCTGCAGATGTTCCTCCAGTCCTACAACAACGACCAGTGGACGCTGATCTTCGGAGACCCAA

CCAAGTTTGGACTCGGGGTCTTCTCCATCGTCTTCGACGTCGTCTTCTTCATCCAGCACTTCTGTTTGTA

CAGAAAGAGACCGGGGCTTCAGGCAGCGCGCACAGGCTCTGGCAGCCGTCTCAGGCAGGACTGGGCACCA

AGCTTGCAGCCGAAGGCCTTGCCCCAAACTACCAGCGTTTCTGCAAGCAGCTTGAAGGGCTGACCTTGCA

GCCGGGTGAGCCAAGGGCACTTTGCTGCCACCGCTGCATTCCCAGAGATCAAGCAGCCCGGTGCCGTGGC

CAGTGAACTCAGAGGTGCTGGTGGACGGGCTAGGACTTTGGGGTTAGGCCATGGGGCTCTTTCTCTGAAG

GCCACTTTCCTGACGTACTCTCTGTACATAACTCAGCGTCCGTGACTGCAGTAACAGCCAGCCCTACCCA

GAGTATTTCTGAGCCATGAGGGGCCCACCAGATTGGTTCTGAATTGGATTCATGCCCAGCGCATTAGCAT

AGTAACTCCTTTCAGATTTTTTGGAGGGACGTTTGGAAGTGGCTTACTCTCTTCTGCCCTCTCTCCTACC

TCCACCTTCTCAGATTAGCCCCATCTGAGCACATCCAGCTGCTCCTTACCCAGCATCTGGAGTACAGGAC

ATAGCTCTCTCCTGCTACCAGTCTGTGCCTTAGAGGTCTGTTAGGCCTGCCAAACGGCGACCAGCTCCCC

TGGAGCGAGGGCAGGCCCCTTCCCTCTCTTTCCCCAGACACCTACTTGAGACTCACCAATTTCTGGCCTG

TTCAGGAGCCTCAGATAAGTATTTGTACTTGAGACCACCTCACACAATCTGTATGGGCCCAACCCTGATC

TCAAACCTCCTTCCCTCTGCCCAAAGCTGTCCTTCCTATGGCAGGAGGGGTGGGGGTCCCAGGACGTGCC

TCATACATGACTTGAGCTTGTCAGTCCACTGAGTTTCCTTCTACGAGATCAACGCGAGGGGCCTGTATCT

TGAATTAAAACCTACTCGCTTCCTTTCTGCACTCTGTGTGCTCGATACAGAAGGCAGGTGTGCTGGCCTT

CAGAGCCAGGTGCCCTGCTCCCCTCGTGTAAGGAAGCGCATAAGGTTGTGAAGGTCACTGACCCGAGAGC

GCTGCGTGCTGACCCCACACTTCACTGGGGAGCCCTCTTGGGTAGCGCGAGACGCCTACCCGCCCAGGGC

CAGGTCAGTCTCCCAGGCTCCGTGTCTTCACGGTTACCAGGGCACGCCACTCAATCTGGATGTGAGCCGG

GGTGGATGAGGTTCTGAAGGGCACACCAGCACTGGGAGCGGGGGCAGTGGGGGTCTTATTCTCCAGACGC

TTCCTCTATCTAGTTGTAACAAACGTCAAAGAATGTCAGGTCTTGTTTCTGCAGAGCAGACTTTGGCCTG

ACGGGGTCCACAGACCTGTTTCACTTGCAACACCCAGTAAATGTGTTACTGGGTGCCCTACTTTAAAAAT

CAGAGATTTCAAATGATTGACTTTTCCGGCTGAGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGG

AGGCCAAGGCAGATGGATCACCTGACATCAGGAGTTCGAGACCAGCCTAGCCAACATTGCAAAACCCCAT

CTCTACTAAAGATACAAAAATTAGCTGGGCATGGTGGCGGGCACCTGTAATCCCAGCTACTTGGTTGGCT

GAGGCAGGAGAATTACTTGAACCCAGGAGGCGGAGGTTGCAGTGAGCGAAGATCACGCCATTGCACTCCA

GCCTGGGCAACAAGAACGAAACTCCATCTCAAAAAAAAAAAAAAATTATTGACTTTTCTTTAAAATCTGA

TTTGGCAGTGCTAGGTAGGTCCAGGAGTGCTAACACCTTCCCAGAGGTGGTACGCAGGTAGTCAGGTGCT

CTCTGACTCACCCCCATCTGGCCAGATCACGGCCCCCAGCAACACGTGGGGTTGTGTCCCTCGCTGGGAT

ACACGGAGTGCCCTTATAGGCAGGGAGTCTTATAGGCAGGGGTCTCTCCCAGGCACCTCTGGGTGTCCCT

ACGGCCCCTCCCAGGTGGGAGCTGAGGCTAGGTTGCAAAAAGGAGGTTGGGAGCAAGTAGGGGCTTCACA

GTAACACCCAAGAAAGCACACGCACCCCAGGGTCCCACCCCAGTGCTCCCAGACACTCCCACAGATGTGG

TTCTGGTCAGGCGCAGTGCAGCTGCTGCGGCTCCACCAGCCCCGGGCTTTCAGGCAGGTGGGCCTGGGAG

TAGTTGAGCTTTGTCCCAGAACAGTGGGGGATGGGGCCATCATTAAAACCACAGCTCTGGCCCCAATATC

CCACCGCCACCCCCACCCCGATATCCCAGCCCATGCCTCAGCAAAGCCCCCTGTGAATTCCAGCATTTTT

ATTGAGCGCACCACATCGGGGAGGGGCGGCAGTGGTTTCCACGGTAACCAAAGTAAGGCTTGTGCACTTG

CTGAGCTTCCAGATGCGAATTAGTAAAAGCTAAATTCAAAAGTAGAATGGGCATCTCCAAAGAGTACGAT

AAAAACATTTTGTATCAAACTTGTGATTAAAAAAATACAAAAGTTAAACCCA

7. Motif

Pfam (1 motif)

Pfam

Position(Independent E-value)

Description

PQ-loop

126..182(1.5e-19)

267..324(8.9e-18)

PF04193, PQ loop repeat

8. Evolutionary Relationship

Evolutionary analysis by Maximum Likelihood method

The evolutionary history was inferred by using the Maximum Likelihood method and JTT matrix-based model [1]. The tree with the highest log likelihood (-9127.70) is shown. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. The proportion of sites where at least 1 unambiguous base is present in at least 1 sequence for each descendent clade is shown next to each internal node in the tree. This analysis involved 100 amino acid sequences. There were a total of 556 positions in the final dataset.

9. SNP

SNP	COORDINATE	AMINO ACID CHANGE	GENE ID	TRANSCRIPT ID	PROTEIN ID	SIFT SCORE	SIFT MEDIAN	SIFT PREDICTION
rs35086888	3550800	V42I	ENSG00000040531	ENST00000399306	ENSP00000382245	0.134	3.48	TOLERATED
rs35086888	3550800	V42I	ENSG00000040531	ENST00000452111	ENSP00000408652	0.199	3.54	TOLERATED
rs35086888	3550800	V42I	ENSG00000040531	ENST00000381870	ENSP00000371294	0.497	2.74	TOLERATED
rs35086888	3550800	V42I	ENSG00000040531	ENST00000046640	ENSP00000046640	0.688	2.81	TOLERATED
rs113994205	3558599	W138*	ENSG00000040531	ENST00000046640	ENSP00000046640
rs113994205	3558599	W138*	ENSG00000040531	ENST00000381870	ENSP00000371294
rs113994205	3558599	W30*	ENSG00000040531	ENST00000441220	ENSP00000411465
rs113994205	3558599		ENSG00000040531	ENST00000414524	ENSP00000395471
rs113994205	3558599		ENSG00000040531	ENST00000574218	ENSP00000458912
rs113994205	3558599		ENSG00000040531	ENST00000574776	ENSP00000461118
rs113994206	3559792	L158P	ENSG00000040531	ENST00000046640	ENSP00000046640	0	2.69	DELETERIOUS
rs113994206	3559792	L158P	ENSG00000040531	ENST00000381870	ENSP00000371294	0	2.68	DELETERIOUS
rs113994206	3559792	L50P	ENSG00000040531	ENST00000441220	ENSP00000411465	0	2.55	DELETERIOUS
rs113994206	3559792	L11P	ENSG00000040531	ENST00000574776	ENSP00000461118
rs113994206	3559792	L11P	ENSG00000040531	ENST00000414524	ENSP00000395471	0.001	2.63	DELETERIOUS
rs113994207	3559997	G197R	ENSG00000040531	ENST00000381870	ENSP00000371294	0.003	2.68	DELETERIOUS
rs113994207	3559997	G197R	ENSG00000040531	ENST00000046640	ENSP00000046640	0.004	2.69	DELETERIOUS
rs113994207	3559997	G50R	ENSG00000040531	ENST00000414524	ENSP00000395471	0.029	2.64	DELETERIOUS
rs113994207	3559997	G89R	ENSG00000040531	ENST00000441220	ENSP00000411465	0.04	2.54	DELETERIOUS
rs113994208	3560021	D58N	ENSG00000040531	ENST00000414524	ENSP00000395471	0.004	2.64	DELETERIOUS
rs113994208	3560021	D97N	ENSG00000040531	ENST00000441220	ENSP00000411465	0.004	2.54	DELETERIOUS
rs113994208	3560021	D205N	ENSG00000040531	ENST00000381870	ENSP00000371294	0.009	2.68	DELETERIOUS
rs113994208	3560021	D205N	ENSG00000040531	ENST00000046640	ENSP00000046640	0.011	2.69	DELETERIOUS
rs121908124	3558349	G95*	ENSG00000040531	ENST00000046640	ENSP00000046640
rs121908124	3558349	G95*	ENSG00000040531	ENST00000381870	ENSP00000371294
rs121908124	3558349		ENSG00000040531	ENST00000414524	ENSP00000395471
rs121908124	3558349		ENSG00000040531	ENST00000574218	ENSP00000458912
rs121908126	3559825	G169D	ENSG00000040531	ENST00000046640	ENSP00000046640	0	2.69	DELETERIOUS
rs121908126	3559825	G169D	ENSG00000040531	ENST00000381870	ENSP00000371294	0	2.68	DELETERIOUS
rs121908126	3559825	G22D	ENSG00000040531	ENST00000414524	ENSP00000395471	0.003	2.64	DELETERIOUS
rs121908126	3559825	G61D	ENSG00000040531	ENST00000441220	ENSP00000411465	0.003	2.54	DELETERIOUS
rs121908127	3563574	G339R	ENSG00000040531	ENST00000046640	ENSP00000046640	0	2.69	DELETERIOUS
rs121908127	3563574	G339R	ENSG00000040531	ENST00000381870	ENSP00000371294	0.001	2.69	DELETERIOUS
rs121908127	3563574	G192R	ENSG00000040531	ENST00000414524	ENSP00000395471	0.001	2.62	DELETERIOUS
rs121908127	3563574	G231R	ENSG00000040531	ENST00000441220	ENSP00000411465	0.001	2.55	DELETERIOUS
rs121908128	3563268	N323K	ENSG00000040531	ENST00000381870	ENSP00000371294	0.245	2.68	TOLERATED
rs121908128	3563268	N215K	ENSG00000040531	ENST00000441220	ENSP00000411465	0.251	2.64	TOLERATED
rs121908128	3563268	N176K	ENSG00000040531	ENST00000414524	ENSP00000395471	0.256	2.61	TOLERATED
rs121908128	3563268	N323K	ENSG00000040531	ENST00000046640	ENSP00000046640	0.258	2.69	TOLERATED
rs121908128	3563268	N176N	ENSG00000040531	ENST00000414524	ENSP00000395471	0.422	2.61	TOLERATED
rs121908128	3563268	N215N	ENSG00000040531	ENST00000441220	ENSP00000411465	0.503	2.64	TOLERATED
rs121908128	3563268	N323N	ENSG00000040531	ENST00000381870	ENSP00000371294	0.536	2.68	TOLERATED
rs121908128	3563268	N323N	ENSG00000040531	ENST00000046640	ENSP00000046640	0.622	2.69	TOLERATED
rs121908129	3558395	G110V	ENSG00000040531	ENST00000046640	ENSP00000046640	0.525	2.7	TOLERATED
rs121908129	3558395	G110V	ENSG00000040531	ENST00000381870	ENSP00000371294	0.636	2.71	TOLERATED
rs121908129	3558395		ENSG00000040531	ENST00000414524	ENSP00000395471
rs121908129	3558395		ENSG00000040531	ENST00000574218	ENSP00000458912
rs267606754	3558601	S31F	ENSG00000040531	ENST00000441220	ENSP00000411465	0	2.54	DELETERIOUS
rs267606754	3558601	S139F	ENSG00000040531	ENST00000046640	ENSP00000046640	0.001	2.69	DELETERIOUS
rs267606754	3558601	S139F	ENSG00000040531	ENST00000381870	ENSP00000371294	0.001	2.68	DELETERIOUS
rs267606754	3558601		ENSG00000040531	ENST00000414524	ENSP00000395471
rs267606754	3558601		ENSG00000040531	ENST00000574218	ENSP00000458912
rs267606754	3558601		ENSG00000040531	ENST00000574776	ENSP00000461118

Evolutionary analysis of coding SNPs

SNP	Substitution	Probability of deleterious effect	Prediction Score
rs35086888	V42I	possibly damaging	0.5
rs35086888	V42I	possibly damaging	0.5
rs35086888	V42I	possibly damaging	0.5
rs35086888	V42I	possibly damaging	0.5
rs113994206	L158P	probably damaging	0.89
rs113994206	L158P	probably damaging	0.89
rs113994206	L50P	probably damaging	0.85
rs113994206	L11P	possibly damaging	0.5
rs113994206	L11P	possibly damaging	0.5
rs113994207	G197R	probably damaging	0.85
rs113994207	G197R	probably damaging	0.85
rs113994208	D205N	probably damaging	0.89
rs113994208	D205N	probably damaging	0.89
rs121908126	G169D	probably damaging	0.89
rs121908126	G169D	probably damaging	0.89
rs121908127	G339R	probably damaging	0.89
rs121908127	G339R	probably damaging	0.89
rs121908128	N323K	probably damaging	0.85
rs121908128	N323K	probably damaging	0.85
rs121908128	N323N	probably damaging	0.85
rs121908128	N323N	probably damaging	0.85
rs121908129	G110V	probably benign	0.13
rs121908129	G110V	probably benign	0.13
rs267606754	S139F	probably damaging	0.85
rs267606754	S139F	probably damaging	0.85

Provean

SNP Id’s	Amino Acid Change	Probability	Prediction	Score
rs5036	K56E	Neutral	Tolerated	2.13
rs2285644	P854L	Deleterious	Damaging	-2.86
rs13306787	E68K	Neutral	Tolerated	-0.99
rs28929480	E90K	Deleterious	Damaging	-2.71
rs28931583	P327R	Neutral	Damaging	-2.27
rs28931584	V488M	Neutral	Damaging	-2.17
rs28931585	R870W	Deleterious	Damaging	-6.38
rs121912741	G771D	Deleterious	Damaging	-6.02
rs121912744	R589H	Deleterious	Damaging	-4.71
rs121912745	R589C	Deleterious	Damaging	-7.51
rs121912745	R589S	Deleterious	Damaging	-5.64
rs121912746	S613F	Deleterious	Damaging	-3.95
rs121912748	G701D	Deleterious	Damaging	-6.14
rs121912751	A858D	Deleterious	Damaging	-4.96
rs121912753	S773P	Deleterious	Damaging	-4.3
rs121912754	R602P	Deleterious	Damaging	-6.3
rs121912755	R760Q	Deleterious	Damaging	-3.44
rs121912757	R646Q	Deleterious	Damaging	-3.59
rs121912758	R646W	Deleterious	Damaging	-7.18
rs121912759	P868L	Deleterious	Damaging	-8.42
rs373916826	R760W	Deleterious	Damaging	-6.88

SNAP2

Wildetype Amino Acid	Position	Variant Amino Acid	Predicted Effect	Score	Expected Accurancy
T	56	K	Effect	26	90%
T	854	K	Effect	98	80%
T	68	K	Effect	67	75%
T	90	K	Effect	34	26%
T	327	K	Effect	26	98%
E	488	V	Effect	59	78%
E	870	V	Effect	96	85%
N	771	V	Effect	36	55%
N	589	D	Effect	78	55%
N	589	D	Neutral	26	45%
N	589	D	Neutral	68	65%
N	613	D	Effect	26	98%
N	701	D	Neutral	-29	65%
L	858	V	Neutral	57	32%
L	773	V	Neutral	56	65%
L	602	V	Effect	78	65%
L	760	V	Effect	69	23%
L	646	V	Effect	98	36%
M	646	T	Neutral	56	36%
M	868	T	Neutral	56	56%
M	760	T	Neutral	65	78%

Polyphen 2

Rs_Id	Mutation Probability	Score
rs5036	Probably damaging	0.999
rs2285644	Possibly damaging	0.999
rs13306787	Probably damaging	1.00
rs28929480	Probably damaging	0.98
rs28931583	Possibly damaging	1.00
rs28931584	Probably damaging	0.999
rs28931585	Possibly damaging	0.999
rs121912741	Probably damaging	1.00
rs121912744	Probably damaging	0.98

Hope Prediction

Rs_Ids	Mutation	Mapping Issues	AA Variant	Function Impact	Score
rs5036	CTNS _K56E		K56E	High	6.68
rs2285644	CTNS _P854L	Uniprot Residue:A	P854L	Medium	3.96
rs13306787	CTNS _E68K		E68K	Low	0.12
rs28929480	CTNS _E90K		E90K	High	5.02
rs28931583	CTNS _P327R	Uniprot Residue:G	P327R	High	5.73
rs28931584	CTNS _V488M		V488M	High	6.09
rs28931585	CTNS _R870W		R870W	High	10.32
rs121912741	CTNS _G771D		G771D	High	8.02
rs121912744	CTNS _R589H	Uniprot Residue:I	R589H	Medium	4.60
rs121912745	CTNS _R589C		R589C	Medium	3.96
rs121912745	CTNS _R589S	Uniprot Residue:M	R589S	Low	0.42
rs121912746	CTNS _S613F		S613F	High	7.58
rs121912748	CTNS _G701D		G701D	Low	0.92
rs121912751	CTNS _A858D		A858D	Medium	2.96
rs121912753	CTNS _S773P		S773P	High	6.94
rs121912754	CTNS _R602P	Uniprot Residue:L	R602P	Low	0.82
rs121912755	CTNS _R760Q		R760Q	High	7.88
rs121912757	CTNS _R646Q		R646Q	Low	0.22

10. Active Site

Rank	C-Score	Cluster Size	PDB Hit	Lig Name	Consensus Building Residues
1	0.06	3	4k7qA	ZLD	316,317
2	0.06	4	1e3dB	F3S	280,284
3	0.05	3	3tijA	DMU	282,289
4	0.04	2	1xvgC	BRJ	267,270,274
5	0.03	2	3c7kA	MG	159,294
6	0.03	2	3a0hK	CLA	142,145
7	0.03	1	N/A	N/A	138,141,142,144,145, 149,158,159,162,166, 170,280,281,284,296, 298,301,302,305,342, 345,346,349
8	0.03	2	3fg4C	ACD	302,306,345,346,349
9	0.03	2	3arcD	CLA	133,307,310,313,314,343
10	0.03	2	1tidA	MG	138,308

11. Primary Sequence Analysis

Number of amino acids

367

Molecular weight

41737.92

Theoretical pI

9.12

Amino acid composition

Ala (A) 13 3.5%

Arg (R) 12 3.3%

Asn (N) 22 6.0%

Asp (D) 8 2.2%

Cys (C) 5 1.4%

Gln (Q) 16 4.4%

Glu (E) 9 2.5%

Gly (G) 22 6.0%

His (H) 4 1.1%

Ile (I) 29 7.9%

Leu (L) 42 11.4%

Lys (K) 12 3.3%

Met (M) 5 1.4%

Phe (F) 33 9.0%

Pro (P) 17 4.6%

Ser (S) 29 7.9%

Thr (T) 22 6.0%

Trp (W) 10 2.7%

Tyr (Y) 15 4.1%

Val (V) 42 11.4%

Pyl (O) 0 0.0%

Sec (U) 0 0.0%

Total number of negatively charged residues (Asp + Glu)

Total number of positively charged residues (Arg + Lys)

Formula

C₁₉₇₄H₂₉₉₁N₄₇₁O₅₀₆S₁₀

Total number of atoms

5952

Instability index(II)

32.77

Stability

stable

Aliphatic index(AI)

112.18

GRAVY

0.532

12. Secondary structure analysis

Alpha helix (Hh) : 148 is 40.33%

310 helix (Gg) : 0 is 0.00%

Pi helix (Ii) : 0 is 0.00%

Beta bridge (Bb) : 0 is 0.00%

Extended strand (Ee) : 85 is 23.16%

Beta turn (Tt) : 0 is 0.00%

Bend region (Ss) : 0 is 0.00%

Random coil (Cc) : 134 is 36.51%

Ambiguous states (?) : 0 is 0.00%

Other states : 0 is 0.00%

Secondary Structure Prediction

Amino Acid Type

13. Enzymes

Name of enzyme	No. of cleavages
Arg-C proteinase	12
Asp-N endopeptidase	8
Asp-N endopeptidase + N-terminal Glu	17
BNPS-Skatole	10
CNBr	5
Chymotrypsin-high specificity (C-term to [FYW], not before P)	53
Chymotrypsin-low specificity (C-term to [FYWML], not before P)	103
Clostripain	12
Formic acid	8
Glutamyl endopeptidase	9
Iodosobenzoic acid	10
Hydroxylamine	2
LysC	12
LysN	12
NTCB (2-nitro-5-thiocyanobenzoic acid)	5
Pepsin (pH1.3)	121
Pepsin (pH>2)	154
Proline-endopeptidase	1
Proteinase K	215
Staphylococcal peptidase I	9
Thermolysin	151
Thrombin	1
Trypsin	22

14. Epitope

Rank	Start position	Sequence	Score	Prediction
1	185	YIKEQFLLKYPNGVNP	0.91	Epitope
2	327	TLIFGDPTKFGLGVFS	0.87	Epitope
3	348	VFFIQHFCLYRKRPGY	0.85	Epitope
4	53	TLVITFEITFRSKNIT	0.84	Epitope
4	278	LVKYFPQAYMNFYYKS	0.84	Epitope
5	135	FVAWSISFYPQVIMNW	0.83	Epitope
6	64	SKNITILELPDEVVVP	0.82	Epitope
6	153	KSVIGLSFDFVALNLT	0.82	Epitope
7	144	PQVIMNWRRKSVIGLS	0.78	Epitope
8	27	TVPPVVKLENGSSTNV	0.77	Epitope
9	93	NVGQLTVYLHGNHSNQ	0.76	Epitope
9	258	GVTTWLQFLFCFSYIK	0.76	Epitope
10	291	YKSTEGWSIGNVLLDF	0.75	Epitope

15. Protein-Protein Interaction

No of Nodes	11
No of Edges	18
Avg node degree	3.27
avg. local clustering coefficient	0.898
expected number of e, dges	10
p-value	0.021
Protein – Protein Interaction network

16. MRNA

RNA Base Pairing Probability Plot