OPENSEQ.org - 1488207595 - GREMLIN Submission

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ID:	1488207595	Query Sequence TPAAESLNARWRTAVVDGWNNAFSGRYPFKNVSSDASLPLLAKYLNTDTGRIARFLQNNLSGVLHREGSRWVPDTINTAGLTFNPAFLKAINTLSEIADVAFTTGNAGLHFELRPGTAAGVMQTTLITDNQKLIYVNQMPVWKRFTWPADTEAPGASLSWVSTQAGTRQYADLPGSWGLIRLLEMARRKAAPGVASGWSLSWQAQDGRMLNYTLRTEAGEGPLVLLKLRNFVLPETVFE	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	239 (237)
Sequences:	906 (580.6)
Seq/Len:	3.823
Nf(neff/√len):	37.7

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: 3.823).

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
19_W	233_L	2.941	1.00
123_Q	134_I	2.840	1.00
156_A	182_L	2.555	1.00
133_L	145_F	2.314	1.00
29_F	36_A	2.310	1.00
126_L	158_L	2.286	1.00
113_L	126_L	2.221	1.00
124_T	212_Y	2.191	1.00
111_F	214_L	1.972	1.00
135_Y	139_M	1.956	1.00
56_L	91_I	1.926	1.00
130_N	149_A	1.921	1.00
11_W	16_V	1.916	1.00
111_F	145_F	1.874	1.00
41_L	101_A	1.831	1.00
162_S	165_A	1.798	0.99
27_Y	184_E	1.728	0.99
114_R	213_T	1.707	0.99
135_Y	138_Q	1.688	0.99
93_T	230_N	1.688	0.99
70_R	92_N	1.660	0.99
183_L	214_L	1.634	0.99
127_I	130_N	1.589	0.98
115_P	212_Y	1.577	0.98
16_V	19_W	1.564	0.98
36_A	101_A	1.560	0.98
48_D	53_A	1.556	0.98
186_A	202_W	1.544	0.98
18_G	22_A	1.531	0.98
37_S	40_L	1.530	0.98
102_F	148_P	1.489	0.97
126_L	133_L	1.476	0.97
35_D	104_T	1.451	0.97
56_L	64_L	1.418	0.96
110_H	146_T	1.416	0.96
45_L	97_I	1.414	0.96
127_I	157_S	1.402	0.96
35_D	181_R	1.393	0.95
36_A	41_L	1.375	0.95
53_A	98_A	1.371	0.95
200_L	214_L	1.364	0.95
180_I	184_E	1.364	0.95
174_P	178_G	1.343	0.94
42_A	107_A	1.342	0.94
127_I	150_D	1.308	0.93
112_E	215_R	1.296	0.92
25_G	71_W	1.296	0.92
23_F	44_Y	1.284	0.92
65_H	71_W	1.281	0.92
7_L	25_G	1.268	0.91
19_W	44_Y	1.264	0.91
52_I	200_L	1.253	0.91
38_L	111_F	1.225	0.89
64_L	83_F	1.223	0.89
11_W	111_F	1.213	0.89
129_D	149_A	1.199	0.88
58_N	236_T	1.197	0.88
19_W	23_F	1.194	0.88
41_L	45_L	1.187	0.87
8_N	11_W	1.187	0.87
47_T	128_T	1.186	0.87
156_A	178_G	1.175	0.87
198_W	214_L	1.160	0.86
113_L	133_L	1.160	0.86
97_I	102_F	1.151	0.85
147_W	179_L	1.148	0.85
160_W	210_L	1.142	0.84
77_N	125_T	1.141	0.84
178_G	228_L	1.138	0.84
41_L	102_F	1.130	0.84
157_S	186_A	1.127	0.83
57_Q	61_S	1.121	0.83
187_R	203_Q	1.117	0.83
27_Y	222_P	1.109	0.82
109_L	180_I	1.108	0.82
216_T	221_G	1.104	0.82
40_L	56_L	1.098	0.81
11_W	83_F	1.091	0.81
16_V	233_L	1.091	0.81
199_S	213_T	1.090	0.80
197_G	213_T	1.085	0.80
18_G	51_R	1.075	0.79
70_R	181_R	1.073	0.79
44_Y	52_I	1.071	0.79
113_L	214_L	1.070	0.79
54_R	58_N	1.067	0.78
66_R	71_W	1.067	0.78
97_I	101_A	1.066	0.78
203_Q	209_M	1.059	0.78
187_R	201_S	1.056	0.77
38_L	180_I	1.054	0.77
3_A	63_V	1.050	0.77
161_V	167_T	1.049	0.77
32_V	190_A	1.048	0.77
118_A	137_N	1.048	0.77
39_P	74_D	1.047	0.77
103_T	107_A	1.041	0.76
29_F	147_W	1.039	0.76
92_N	130_N	1.034	0.75
194_V	230_N	1.031	0.75
7_L	55_F	1.028	0.75
90_A	231_F	1.027	0.75
43_K	51_R	1.021	0.74
149_A	213_T	1.013	0.73
10_R	14_A	1.012	0.73
52_I	55_F	1.007	0.73
177_W	180_I	1.007	0.73
181_R	222_P	1.000	0.72

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
4y7lA	2	0	100	0.071	Contact Map
4y7mC	2	0	100	0.077	Contact Map
3mhsB	1	0.2427	7.2	0.959	Contact Map
4mvcA	2	0.1172	6.6	0.96	Contact Map
4rgiA	1	0.1297	5.5	0.961	Contact Map
4kbmB	1	0.2594	4.9	0.962	Contact Map
4dhxB	4	0.2636	4.8	0.962	Contact Map
2lwjA	1	0.2636	3.4	0.965	Contact Map
3exmA	1	0.2343	3.4	0.965	Contact Map
4l68A	2	0.4603	3	0.966	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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