OPENSEQ.org - 1400509302 - GREMLIN Submission

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ID:	1400509302	Query Sequence KWNNRVVSFVHAIVSSIWGLYILLNDPELWSDWPDDPWYYSSWLVKFYYAFSLGYFLYDLIVMLLYYRKRGDFWEMLLHHVVTLVLFYFSYFYNFGRFGIVVFLLHEISTPFLNLRWFLKYLGGYSKKSSLYRFNGVLFAVTFFVFRIVLFPYLIYWVYWDVWPLPLWKVPWPVPWIFLVLLLVLFVLNIYWFYLILR	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	198 (197)
Sequences:	685 (500.8)
Seq/Len:	3.477
Nf(neff/√len):	35.7

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: 3.477).

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
113_L	139_F	2.610	1.00
136_G	139_F	2.019	1.00
107_E	110_T	1.886	1.00
12_A	110_T	1.836	0.99
135_N	193_F	1.805	0.99
109_S	143_F	1.801	0.99
130_S	134_F	1.668	0.99
143_F	151_F	1.646	0.98
159_Y	163_W	1.642	0.98
110_T	114_N	1.635	0.98
144_F	148_I	1.617	0.98
9_F	12_A	1.554	0.98
191_Y	195_L	1.543	0.97
140_A	196_I	1.520	0.97
139_F	196_I	1.486	0.97
103_F	186_F	1.471	0.96
144_F	193_F	1.469	0.96
103_F	151_F	1.421	0.95
5_R	12_A	1.418	0.95
143_F	148_I	1.412	0.95
113_L	136_G	1.388	0.94
172_W	176_W	1.380	0.94
112_F	135_N	1.378	0.94
19_G	22_I	1.359	0.93
49_Y	99_G	1.327	0.92
120_K	136_G	1.327	0.92
49_Y	90_S	1.319	0.92
8_S	11_H	1.314	0.92
83_T	91_Y	1.313	0.92
85_V	113_L	1.306	0.92
1_K	5_R	1.301	0.91
116_R	132_Y	1.295	0.91
106_H	110_T	1.294	0.91
56_F	107_E	1.289	0.91
145_V	149_V	1.288	0.91
143_F	146_F	1.271	0.90
152_P	189_N	1.243	0.89
8_S	12_A	1.241	0.89
115_L	137_V	1.228	0.88
159_Y	167_L	1.228	0.88
59_D	107_E	1.227	0.88
109_S	114_N	1.223	0.88
57_L	124_G	1.215	0.87
8_S	55_Y	1.213	0.87
105_L	181_L	1.207	0.87
144_F	149_V	1.189	0.86
109_S	192_W	1.180	0.85
5_R	9_F	1.166	0.84
117_W	196_I	1.163	0.84
56_F	59_D	1.161	0.84
148_I	184_V	1.153	0.83
107_E	116_R	1.151	0.83
5_R	11_H	1.147	0.83
117_W	121_Y	1.144	0.82
32_D	35_D	1.141	0.82
67_Y	71_G	1.138	0.82
48_Y	73_F	1.122	0.81
192_W	196_I	1.115	0.80
5_R	192_W	1.115	0.80
4_N	8_S	1.114	0.80
179_L	183_L	1.113	0.80
27_P	159_Y	1.109	0.80
111_P	143_F	1.105	0.79
152_P	155_I	1.105	0.79
22_I	36_D	1.100	0.79
117_W	136_G	1.096	0.79
139_F	192_W	1.094	0.78
52_S	104_L	1.093	0.78
5_R	106_H	1.091	0.78
52_S	56_F	1.091	0.78
140_A	193_F	1.090	0.78
29_L	36_D	1.087	0.78
132_Y	136_G	1.087	0.78
60_L	80_H	1.085	0.78
13_I	17_I	1.082	0.77
114_N	118_F	1.079	0.77
180_V	190_I	1.076	0.77
106_H	155_I	1.068	0.76
13_I	138_L	1.062	0.75
19_G	48_Y	1.057	0.75
5_R	196_I	1.054	0.75
59_D	114_N	1.051	0.74
13_I	73_F	1.049	0.74
135_N	139_F	1.047	0.74
19_G	99_G	1.038	0.73
14_V	24_L	1.037	0.73
50_A	82_V	1.035	0.73
4_N	80_H	1.034	0.73
10_V	35_D	1.033	0.73
12_A	16_S	1.031	0.72
103_F	139_F	1.021	0.71
39_Y	78_L	1.020	0.71
51_F	82_V	1.019	0.71
73_F	148_I	1.015	0.71
59_D	116_R	1.011	0.70
107_E	136_G	1.011	0.70
53_L	57_L	1.010	0.70
15_S	20_L	1.008	0.70
58_Y	80_H	1.006	0.70
99_G	107_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: (10May14)
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
3wguG	2	0.1364	0.9	0.967	Contact Map
3omdA	2	0.2475	0.8	0.967	Contact Map
1scfA	4	0	0.8	0.968	Contact Map
2k2wA	1	0.202	0.7	0.969	Contact Map
4gh4D	1	0.101	0.6	0.97	Contact Map
4h44H	1	0.0707	0.6	0.97	Contact Map
2o3aA	2	0.2525	0.6	0.97	Contact Map
2rnzA	1	0.1616	0.6	0.971	Contact Map
4izzA	2	0.298	0.6	0.971	Contact Map
2rspA	2	0.2121	0.6	0.971	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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