OPENSEQ.org - 1486792935 - GREMLIN Submission

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ToMV_Hel_672_1111 150-420

ID:	1486792935	Query Sequence PHVSSAKVVLVDGVPGCGKTKEILSRVNFEEDLILVPGRQAAEMIRRRANASGIIVATKDNVRTVDSFLMNYGKGARCQFKRLFIDEGLMLHTGCVNFLVEMSLCDIAYVYGDTQQIPYINRVTGFPYPAHFAKLEVDEVETRRTTLRCPADVTHFLNQRYEGHVMCTSSEKKSVSQEMVSGAASINPVSKPLKGKILTFTQSDKEALLSRGYADVHTVHEVQGETYADVSLVRLTPTPVSIIARDSPHVLVSLSRHTKSLKYYTVVMDPL	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	271 (264)
Sequences:	3184 (2208.2)
Seq/Len:	12.061
Nf(neff/√len):	135.9

HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied

Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 12.061).

Sequences per length for each position, AFTER the coverage/gap filter was applied

Legend: If visible, the positions blocked in grey are regions that have > 75% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

GREMLIN Results:
Residue pairs sorted by coevolution strength:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.

i	j	Scaled score	Prob
228_A	258_T	4.871	1.00
228_A	259_K	3.350	1.00
23_I	84_F	3.067	1.00
90_M	223_Q	2.880	1.00
220_H	249_H	2.770	1.00
229_D	260_S	2.686	1.00
31_E	81_K	2.683	1.00
196_K	227_Y	2.618	1.00
157_L	255_S	2.533	1.00
232_L	253_S	2.458	1.00
146_T	149_C	2.296	1.00
222_V	227_Y	2.153	1.00
194_K	228_A	2.115	1.00
200_F	246_D	2.074	1.00
219_V	253_S	2.030	1.00
151_A	155_H	1.934	1.00
198_L	222_V	1.921	1.00
14_V	17_C	1.887	1.00
34_I	45_I	1.866	1.00
44_M	48_R	1.848	1.00
61_N	80_F	1.833	1.00
25_S	28_N	1.764	1.00
96_V	99_L	1.757	1.00
36_V	42_A	1.710	1.00
89_L	223_Q	1.708	1.00
26_R	109_Y	1.676	1.00
198_L	219_V	1.648	1.00
217_H	221_E	1.618	1.00
27_V	34_I	1.605	1.00
177_Q	265_T	1.592	1.00
146_T	154_T	1.591	1.00
231_S	264_Y	1.578	1.00
9_V	141_E	1.577	1.00
13_G	18_G	1.577	1.00
32_D	81_K	1.567	1.00
13_G	17_C	1.556	1.00
231_S	262_K	1.554	1.00
37_P	223_Q	1.551	1.00
227_Y	230_V	1.537	1.00
217_H	222_V	1.531	1.00
254_L	261_L	1.527	1.00
222_V	230_V	1.526	1.00
113_D	116_Q	1.514	1.00
118_P	223_Q	1.513	1.00
25_S	29_F	1.488	1.00
12_D	140_V	1.471	1.00
196_K	230_V	1.470	1.00
43_E	46_R	1.466	1.00
40_Q	225_E	1.444	1.00
196_K	222_V	1.439	1.00
232_L	263_Y	1.436	1.00
230_V	257_H	1.430	1.00
21_K	48_R	1.429	1.00
143_R	226_T	1.418	1.00
223_Q	251_L	1.407	0.99
16_G	19_K	1.405	0.99
215_D	227_Y	1.402	0.99
149_C	154_T	1.385	0.99
88_G	110_V	1.382	0.99
81_K	106_D	1.381	0.99
88_G	112_G	1.378	0.99
92_H	95_C	1.373	0.99
223_Q	252_V	1.370	0.99
82_R	109_Y	1.370	0.99
37_P	90_M	1.369	0.99
250_V	254_L	1.360	0.99
40_Q	221_E	1.340	0.99
91_L	95_C	1.340	0.99
20_T	45_I	1.338	0.99
90_M	118_P	1.324	0.99
23_I	111_Y	1.319	0.99
201_T	204_D	1.315	0.99
186_I	195_G	1.307	0.99
208_L	216_V	1.301	0.99
253_S	256_R	1.294	0.99
229_D	262_K	1.288	0.99
200_F	219_V	1.274	0.99
232_L	261_L	1.272	0.99
189_V	229_D	1.259	0.99
119_Y	220_H	1.257	0.99
215_D	225_E	1.256	0.99
224_G	256_R	1.244	0.98
198_L	253_S	1.239	0.98
153_V	257_H	1.229	0.98
24_L	48_R	1.227	0.98
39_R	64_T	1.216	0.98
36_V	41_A	1.205	0.98
199_T	205_K	1.203	0.98
16_G	20_T	1.199	0.98
15_P	251_L	1.182	0.98
96_V	100_V	1.179	0.98
82_R	107_I	1.166	0.97
39_R	43_E	1.155	0.97
197_I	231_S	1.142	0.97
42_A	62_V	1.134	0.97
13_G	19_K	1.132	0.97
145_T	166_M	1.125	0.97
90_M	251_L	1.125	0.97
153_V	261_L	1.118	0.96
21_K	25_S	1.112	0.96
13_G	16_G	1.111	0.96
34_I	84_F	1.100	0.96
198_L	217_H	1.085	0.96
217_H	227_Y	1.085	0.96
117_I	223_Q	1.084	0.96
197_I	214_A	1.082	0.96
203_S	206_E	1.079	0.95
202_Q	205_K	1.073	0.95
63_R	71_N	1.073	0.95
197_I	216_V	1.072	0.95
229_D	259_K	1.071	0.95
252_V	256_R	1.069	0.95
83_L	103_S	1.065	0.95
39_R	42_A	1.035	0.94
15_P	252_V	1.029	0.94
23_I	34_I	1.023	0.93
8_V	108_A	1.018	0.93
83_L	106_D	1.017	0.93
131_H	134_K	1.015	0.93
40_Q	43_E	1.011	0.93
205_K	209_L	1.009	0.93
38_G	218_T	1.008	0.93
24_L	49_A	1.006	0.93
246_D	249_H	1.003	0.93

Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).

Text file of contact predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

NEW Features

Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.

HHsearch Results: (06Aug15)
GREMLIN results overlayed on top 10 PDB hits:

Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.

PDB	M	Cov	P(%)	HHΔ
3vkwA	1	1	100	0.209	Contact Map
2xzlA	1	0.9963	100	0.332	Contact Map
4pj3A	1	0.9963	100	0.348	Contact Map
2gk6A	2	0.9742	100	0.353	Contact Map
4b3fX	1	0.9779	100	0.354	Contact Map
2wjyA	1	0.9963	100	0.357	Contact Map
3upuA	3	0.9336	100	0.393	Contact Map
4c2tA	4	0.9889	100	0.394	Contact Map
1pjrA	1	0.9852	100	0.394	Contact Map
4n0nA	1	0.893	100	0.399	Contact Map

M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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