OPENSEQ.org - 1484241308 - GREMLIN Submission

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ID:	1484241308	Query Sequence MRNLVKYVGIGLLVMGLAACDDKDTNATAQGSVAESNATGNPVNLLDGKLSFSLPADMTDQSGKLGTQANNMHVWSDATGQKAVIVIMGDDPKEDLAVLAKRLEDQQRSRDPQLQVVTNKAIELKGHKMQQLDSIISAKGQTAYSSVILGNVGNQLLTMQITLPADDQQKAQTTAENIINTLVIQ	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	185 (185)
Sequences:	152 (73.4)
Seq/Len:	0.822
Nf(neff/√len):	5.4

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: 0.822).

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
129_M	150_G	2.029	0.94
54_L	120_K	1.779	0.87
140_G	182_L	1.735	0.85
113_Q	137_S	1.695	0.83
23_K	148_I	1.661	0.81
77_D	179_I	1.636	0.80
4_L	15_M	1.635	0.80
167_D	170_K	1.619	0.79
2_R	16_G	1.606	0.78
70_N	103_L	1.555	0.75
45_L	50_L	1.535	0.74
107_Q	134_S	1.515	0.72
77_D	146_S	1.488	0.70
66_G	149_L	1.482	0.70
8_V	15_M	1.456	0.68
66_G	160_Q	1.456	0.68
106_Q	161_I	1.452	0.68
54_L	178_I	1.419	0.65
113_Q	142_T	1.412	0.65
83_A	162_T	1.381	0.62
148_I	159_M	1.363	0.60
39_T	125_K	1.350	0.59
10_I	50_L	1.341	0.59
51_S	125_K	1.315	0.56
106_Q	149_L	1.313	0.56
119_N	163_L	1.312	0.56
84_V	139_K	1.305	0.56
60_D	164_P	1.286	0.54
50_L	62_S	1.271	0.53
62_S	162_T	1.265	0.52
44_N	117_V	1.249	0.51
147_V	162_T	1.236	0.49
134_S	154_N	1.236	0.49
103_L	122_I	1.230	0.49
44_N	51_S	1.209	0.47
70_N	181_T	1.193	0.46
88_M	127_H	1.187	0.45
58_M	89_G	1.186	0.45
85_I	148_I	1.181	0.45
8_V	56_A	1.180	0.45
89_G	178_I	1.176	0.44
8_V	26_N	1.163	0.43
47_D	84_V	1.163	0.43
58_M	82_K	1.160	0.43
4_L	7_Y	1.160	0.43
34_A	40_G	1.157	0.43
120_K	131_Q	1.152	0.42
46_L	183_V	1.152	0.42
20_C	99_L	1.149	0.42
119_N	162_T	1.148	0.42
7_Y	10_I	1.146	0.42
123_E	139_K	1.139	0.41
135_I	182_L	1.129	0.40
32_S	132_L	1.128	0.40
82_K	130_Q	1.128	0.40
79_T	150_G	1.121	0.39
5_V	25_T	1.117	0.39
171_A	182_L	1.115	0.39
141_Q	159_M	1.104	0.38
5_V	184_I	1.104	0.38
22_D	146_S	1.104	0.38
49_K	77_D	1.103	0.38
60_D	73_H	1.103	0.38
4_L	78_A	1.096	0.37
10_I	77_D	1.094	0.37
5_V	142_T	1.092	0.37
58_M	74_V	1.089	0.37
74_V	94_E	1.089	0.37
72_M	181_T	1.087	0.37
70_N	160_Q	1.086	0.37
8_V	183_V	1.082	0.36
11_G	124_L	1.078	0.36
8_V	57_D	1.076	0.36
49_K	85_I	1.068	0.35
99_L	158_T	1.065	0.35
58_M	174_T	1.063	0.35
67_T	149_L	1.059	0.34
42_P	53_S	1.051	0.34
174_T	177_N	1.050	0.34
41_N	185_Q	1.049	0.34
62_S	179_I	1.041	0.33
103_L	111_D	1.040	0.33
59_T	117_V	1.040	0.33
118_T	176_E	1.039	0.33
121_A	128_K	1.038	0.33
90_D	154_N	1.037	0.33
63_G	72_M	1.034	0.32
83_A	147_V	1.033	0.32
15_M	127_H	1.031	0.32
99_L	124_L	1.025	0.32
5_V	8_V	1.021	0.31
79_T	84_V	1.020	0.31
47_D	90_D	1.019	0.31
113_Q	144_Y	1.015	0.31
118_T	169_Q	1.005	0.30
111_D	160_Q	1.002	0.30
138_A	183_V	1.000	0.30

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
1tu1A	2	0.7459	99.2	0.806	Contact Map
3lydA	2	0.7946	98.3	0.861	Contact Map
2lnjA	1	0.8378	96.8	0.896	Contact Map
2xb3A	1	0.7622	96.1	0.904	Contact Map
1v2bA	2	0.7459	94.5	0.913	Contact Map
4pwsA	1	0.8108	66.2	0.941	Contact Map
4wzzA	1	0.4757	22.2	0.956	Contact Map
4r9fA	1	0.5459	19.6	0.957	Contact Map
4kysA	2	0.4919	18.6	0.957	Contact Map
4yv7A	1	0.4703	17.2	0.958	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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