OPENSEQ.org - 1411592075 - GREMLIN Submission

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ID:	1411592075	Query Sequence GKITFYEDRGFQGHCYECSSDCPNLQPYFSRCNSIRVDSGCWMLYERPNYQGHQYFLRRGDYPDYQQWMGFNDSIRSCRLIPQHTGTFRMRIYERDDFRGQMSEITDDCPSLQDRFHLTEVHSLNVLEGSWVLYEMPSYRGRQYLLRPGEYRRYLDWGAMNAKVGSLRRVMDFY	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	174 (173)
Sequences:	595 (331.1)
Seq/Len:	3.439
Nf(neff/√len):	25.2

HHblits Results: (2013_03)
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: 3.439).

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
130_S	145_L	1.954	1.00
5_F	18_C	1.791	0.99
81_I	134_Y	1.784	0.99
132_V	143_Q	1.774	0.99
135_E	142_R	1.753	0.99
144_Y	157_W	1.738	0.99
94_E	104_E	1.639	0.98
151_Y	158_G	1.533	0.97
7_E	11_F	1.508	0.97
154_Y	157_W	1.504	0.97
42_W	131_W	1.502	0.97
89_R	104_E	1.471	0.96
161_N	167_L	1.448	0.96
91_R	102_M	1.422	0.95
43_M	56_F	1.409	0.95
41_C	112_L	1.405	0.95
132_V	144_Y	1.393	0.94
132_V	159_A	1.368	0.94
55_Y	62_Y	1.359	0.93
122_H	134_Y	1.353	0.93
3_I	50_Y	1.320	0.92
55_Y	61_D	1.315	0.92
57_L	146_L	1.312	0.92
4_T	17_E	1.308	0.92
85_T	88_F	1.297	0.91
121_V	125_N	1.271	0.90
139_Y	169_R	1.261	0.89
133_L	167_L	1.260	0.89
4_T	38_D	1.259	0.89
135_E	163_K	1.253	0.89
90_M	107_D	1.247	0.89
35_I	44_L	1.239	0.88
153_R	157_W	1.236	0.88
54_Q	60_G	1.227	0.88
159_A	162_A	1.225	0.88
24_N	124_L	1.210	0.87
24_N	112_L	1.208	0.87
144_Y	159_A	1.205	0.86
118_L	121_V	1.203	0.86
126_V	129_G	1.192	0.86
46_E	55_Y	1.184	0.85
85_T	172_D	1.183	0.85
112_L	167_L	1.178	0.85
8_D	30_S	1.174	0.84
36_R	126_V	1.150	0.83
141_G	166_S	1.140	0.82
130_S	148_P	1.140	0.82
54_Q	70_G	1.138	0.82
110_P	139_Y	1.137	0.82
90_M	93_Y	1.127	0.81
8_D	35_I	1.117	0.80
7_E	19_S	1.108	0.79
157_W	165_G	1.103	0.79
35_I	68_W	1.103	0.79
96_D	111_S	1.101	0.79
2_K	17_E	1.101	0.79
25_L	76_R	1.099	0.79
3_I	93_Y	1.098	0.78
109_C	116_F	1.094	0.78
55_Y	70_G	1.092	0.78
121_V	143_Q	1.090	0.78
85_T	96_D	1.082	0.77
73_D	126_V	1.079	0.77
90_M	164_V	1.078	0.77
29_F	71_F	1.071	0.76
61_D	98_F	1.070	0.76
82_P	148_P	1.068	0.76
90_M	126_V	1.061	0.75
56_F	82_P	1.059	0.75
11_F	14_H	1.059	0.75
18_C	37_V	1.059	0.75
71_F	74_S	1.048	0.74
57_L	143_Q	1.044	0.73
18_C	32_C	1.042	0.73
157_W	164_V	1.042	0.73
5_F	35_I	1.041	0.73
99_R	106_T	1.040	0.73
112_L	121_V	1.038	0.73
111_S	114_D	1.036	0.73
16_Y	61_D	1.033	0.72
51_Q	138_S	1.031	0.72
93_Y	123_S	1.027	0.72
110_P	144_Y	1.025	0.71
45_Y	123_S	1.024	0.71
121_V	132_V	1.023	0.71
124_L	133_L	1.022	0.71
53_H	56_F	1.020	0.71
132_V	147_R	1.020	0.71
44_L	112_L	1.018	0.71
46_E	143_Q	1.018	0.71
150_E	163_K	1.013	0.70
65_Y	68_W	1.010	0.70
50_Y	77_S	1.008	0.70
113_Q	133_L	1.007	0.70
64_D	76_R	1.007	0.70
133_L	164_V	1.001	0.69
85_T	128_E	1.000	0.69

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: (17Jul14)
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
2m3cA	1	0.9943	100	0.048	Contact Map
2jdgA	1	0.9828	100	0.054	Contact Map
1h4aX	1	0.9943	100	0.056	Contact Map
1ytqA	1	1	100	0.066	Contact Map
1okiA	2	0.9943	100	0.07	Contact Map
3qk3A	3	0.9885	100	0.07	Contact Map
1zwmA	1	0.9885	100	0.074	Contact Map
3lwkA	1	0.9713	100	0.083	Contact Map
1bd7A	2	0.977	100	0.109	Contact Map
4iauA	1	0.8736	100	0.192	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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