OPENSEQ.org - 1516175609 - GREMLIN Submission

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ID:	1516175609	Query Sequence IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPKK	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	244 (237)
Sequences:	13941 (10070.8)
Seq/Len:	58.823
Nf(neff/√len):	654.2

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: 58.823).

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
125_C	200_C	4.511	1.00
29_C	45_C	3.697	1.00
38_W	96_E	3.030	1.00
75_S	96_E	2.988	1.00
38_W	94_L	2.886	1.00
11_K	147_Q	2.858	1.00
31_G	39_V	2.832	1.00
6_E	146_K	2.741	1.00
46_V	93_A	2.601	1.00
73_P	98_E	2.525	1.00
15_Q	128_T	2.482	1.00
17_S	27_H	2.482	1.00
32_S	208_Q	2.460	1.00
12_W	147_Q	2.441	1.00
90_A	233_Y	2.338	1.00
33_L	101_V	2.310	1.00
60_L	101_V	2.296	1.00
190_C	218_C	2.241	1.00
40_L	208_Q	2.232	1.00
37_Q	100_P	2.201	1.00
76_R	96_E	2.199	1.00
148_V	187_R	2.181	1.00
37_Q	96_E	2.155	1.00
44_H	194_S	2.127	1.00
16_V	31_G	2.111	1.00
214_W	226_I	2.100	1.00
12_W	128_T	2.090	1.00
158_C	181_C	2.085	1.00
97_L	101_V	2.077	1.00
6_E	144_P	2.046	1.00
36_P	100_P	2.004	1.00
35_H	38_W	1.995	1.00
127_V	189_S	1.993	1.00
81_P	240_Y	1.963	1.00
78_I	240_Y	1.923	1.00
92_I	233_Y	1.911	1.00
59_Q	71_L	1.904	1.00
16_V	60_L	1.898	1.00
1_I	4_G	1.887	1.00
178_D	232_Y	1.822	1.00
75_S	98_E	1.810	1.00
234_L	238_H	1.804	1.00
128_T	199_V	1.792	1.00
74_V	95_L	1.766	1.00
103_V	109_T	1.747	1.00
72_L	101_V	1.736	1.00
89_G	178_D	1.724	1.00
72_L	98_E	1.714	1.00
82_Q	90_A	1.697	1.00
125_C	152_I	1.683	1.00
16_V	39_V	1.595	1.00
14_W	199_V	1.554	1.00
127_V	148_V	1.550	1.00
19_R	27_H	1.508	1.00
228_T	233_Y	1.505	1.00
198_L	227_Y	1.504	1.00
7_A	12_W	1.495	1.00
110_V	208_Q	1.479	1.00
59_Q	62_E	1.446	1.00
80_H	90_A	1.414	1.00
41_T	46_V	1.405	0.99
10_S	63_Q	1.401	0.99
62_E	69_D	1.399	0.99
180_L	198_L	1.393	0.99
229_R	232_Y	1.391	0.99
189_S	212_V	1.382	0.99
64_H	143_F	1.354	0.99
126_W	149_K	1.348	0.99
188_D	225_G	1.332	0.99
200_C	209_A	1.331	0.99
79_V	93_A	1.328	0.99
9_R	63_Q	1.326	0.99
46_V	79_V	1.319	0.99
212_V	215_G	1.318	0.99
133_V	146_K	1.313	0.99
14_W	111_T	1.311	0.99
15_Q	145_L	1.310	0.99
8_P	11_K	1.309	0.99
57_R	71_L	1.305	0.99
78_I	96_E	1.304	0.99
32_S	110_V	1.288	0.99
92_I	228_T	1.288	0.99
124_P	149_K	1.287	0.99
42_A	211_V	1.275	0.99
66_Y	143_F	1.269	0.99
179_M	214_W	1.268	0.99
44_H	91_D	1.254	0.99
32_S	211_V	1.251	0.99
153_M	224_P	1.248	0.99
110_V	199_V	1.243	0.98
15_Q	130_W	1.238	0.98
15_Q	30_G	1.204	0.98
137_E	220_Q	1.196	0.98
77_I	95_L	1.193	0.98
33_L	60_L	1.188	0.98
18_L	58_V	1.173	0.98
72_L	99_E	1.173	0.98
127_V	150_V	1.165	0.97
90_A	178_D	1.164	0.97
14_W	206_W	1.156	0.97
32_S	40_L	1.143	0.97
38_W	240_Y	1.140	0.97
195_G	198_L	1.139	0.97
236_W	240_Y	1.129	0.97
216_E	223_R	1.121	0.97
5_Q	147_Q	1.109	0.96
64_H	144_P	1.106	0.96
154_E	157_I	1.105	0.96
80_H	83_F	1.081	0.95
39_V	58_V	1.078	0.95
84_Y	87_Q	1.078	0.95
125_C	198_L	1.063	0.95
6_E	63_Q	1.060	0.95
12_W	126_W	1.056	0.95
142_P	146_K	1.051	0.94
124_P	151_P	1.043	0.94
201_K	206_W	1.042	0.94
151_P	183_G	1.035	0.94
199_V	206_W	1.033	0.94
10_S	106_H	1.028	0.94
155_N	229_R	1.023	0.93
89_G	176_R	1.021	0.93
19_R	59_Q	1.013	0.93
33_L	39_V	1.013	0.93
7_A	147_Q	1.011	0.93
12_W	206_W	1.009	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
2f83A	1	0.8689	100	-0.017	Contact Map
2f9nA	4	0.9836	100	0.012	Contact Map
4nzqA	1	0.9467	100	0.012	Contact Map
2xxlA	2	0.9426	100	0.012	Contact Map
4kkdA	2	0.9631	100	0.019	Contact Map
3nxpA	1	0.9385	100	0.021	Contact Map
2b9lA	1	0.9713	100	0.026	Contact Map
4crgA	1	0.9385	100	0.027	Contact Map
2anyA	1	0.9549	100	0.03	Contact Map
3gylB	1	0.9713	100	0.031	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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