OPENSEQ.org - 1481925924 - GREMLIN Submission

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ID:	1481925924	Query Sequence MSTMFADTLLIVFISVCTALLAEGITWVLVYRTDKYKRLKAEVEKQSKKLEKKKETITESAGRQQKKKIERQEEKLKNNNRDLSMVRMKSMFAIGFCFTALMGMFNSIFDGRVVAKLPFTPLSYIQGLSHRNLLGDDTTDCSFIFLYILCTMSIRQNIQKILGLAPSRAATKQAGGFLGPPPPSGKFS	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	188 (182)
Sequences:	302 (198.5)
Seq/Len:	1.659
Nf(neff/√len):	14.7

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: 1.659).

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
16_V	158_I	1.752	0.96
70_E	73_E	1.679	0.94
26_T	30_V	1.614	0.92
96_F	158_I	1.468	0.87
62_G	65_Q	1.462	0.86
177_F	180_P	1.447	0.85
26_T	159_Q	1.440	0.85
5_F	181_P	1.434	0.85
23_E	36_Y	1.432	0.85
171_T	174_A	1.428	0.84
16_V	38_R	1.386	0.82
179_G	182_P	1.359	0.80
5_F	179_G	1.345	0.79
174_A	177_F	1.335	0.79
180_P	183_P	1.328	0.78
99_T	144_I	1.318	0.77
51_E	55_E	1.310	0.77
147_Y	151_T	1.309	0.77
176_G	186_K	1.306	0.76
179_G	186_K	1.306	0.76
182_P	185_G	1.300	0.76
76_L	119_F	1.292	0.75
35_K	158_I	1.286	0.75
70_E	101_L	1.282	0.75
175_G	180_P	1.276	0.74
104_M	143_F	1.262	0.73
171_T	180_P	1.262	0.73
182_P	186_K	1.259	0.73
180_P	184_S	1.241	0.71
54_K	57_I	1.240	0.71
73_E	145_F	1.237	0.71
98_F	143_F	1.231	0.70
180_P	185_G	1.227	0.70
33_T	51_E	1.220	0.69
179_G	185_G	1.217	0.69
50_L	54_K	1.206	0.68
101_L	105_F	1.190	0.66
177_F	185_G	1.187	0.66
183_P	186_K	1.187	0.66
29_L	33_T	1.178	0.65
172_K	179_G	1.178	0.65
111_G	158_I	1.175	0.65
176_G	180_P	1.172	0.65
118_P	130_H	1.171	0.65
176_G	183_P	1.165	0.64
34_D	37_K	1.164	0.64
5_F	8_T	1.162	0.64
60_S	176_G	1.157	0.63
15_S	177_F	1.157	0.63
83_L	153_S	1.157	0.63
39_L	152_M	1.156	0.63
68_K	178_L	1.149	0.62
129_S	137_D	1.137	0.61
28_V	154_I	1.136	0.61
180_P	186_K	1.132	0.61
61_A	182_P	1.131	0.61
144_I	167_S	1.127	0.60
174_A	182_P	1.123	0.60
36_Y	43_V	1.115	0.59
174_A	179_G	1.109	0.58
174_A	181_P	1.105	0.58
179_G	184_S	1.097	0.57
174_A	180_P	1.093	0.57
178_L	183_P	1.091	0.56
61_A	177_F	1.091	0.56
25_I	97_C	1.090	0.56
174_A	178_L	1.088	0.56
60_S	175_G	1.081	0.55
5_F	185_G	1.081	0.55
5_F	180_P	1.080	0.55
5_F	182_P	1.079	0.55
176_G	179_G	1.071	0.54
61_A	183_P	1.067	0.54
123_S	155_R	1.065	0.54
181_P	184_S	1.061	0.53
118_P	129_S	1.060	0.53
175_G	185_G	1.060	0.53
68_K	165_A	1.058	0.53
5_F	183_P	1.057	0.53
174_A	185_G	1.056	0.53
57_I	67_K	1.052	0.52
172_K	180_P	1.052	0.52
130_H	134_L	1.051	0.52
171_T	185_G	1.049	0.52
27_W	118_P	1.049	0.52
144_I	156_Q	1.047	0.52
27_W	160_K	1.046	0.52
98_F	119_F	1.046	0.52
9_L	133_L	1.041	0.51
174_A	184_S	1.039	0.51
95_G	157_N	1.032	0.50
5_F	174_A	1.031	0.50
91_M	100_A	1.027	0.50
27_W	146_L	1.026	0.50
119_F	129_S	1.026	0.50
14_I	101_L	1.026	0.50
117_L	155_R	1.026	0.50
123_S	133_L	1.024	0.49
175_G	182_P	1.024	0.49
133_L	145_F	1.021	0.49
48_K	111_G	1.009	0.48
11_I	17_C	1.009	0.48
18_T	49_K	1.008	0.48
174_A	183_P	1.007	0.48
25_I	100_A	1.007	0.48
34_D	52_K	1.007	0.48
67_K	73_E	1.003	0.47
52_K	55_E	1.001	0.47
19_A	126_Q	1.001	0.47
40_K	104_M	1.000	0.47

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
3wo6A	1	0.8298	90.2	0.896	Contact Map
3wvfA	2	0.7819	87	0.902	Contact Map
3pjsK	4	0.3777	52.3	0.926	Contact Map
3rvyA	2	0.133	50.2	0.927	Contact Map
4bgnA	2	0.2021	49	0.927	Contact Map
3effK	4	0.3777	45.8	0.929	Contact Map
2bnxA	2	0.1915	33.6	0.934	Contact Map
3hd7A	2	0.4362	27.5	0.937	Contact Map
4ltoA	4	0.367	22.6	0.939	Contact Map
4h33A	1	0.1649	22.4	0.939	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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