OPENSEQ.org - 1447332327 - GREMLIN Submission

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ID:	1447332327	Query Sequence MMDLIISTILLSLFIHFFDKFAKKRTIDGAYRIYVSVSNNKDLKKNKEILEQLLTVKKELNATSSQDQFAKWARLNRKYEQLSQEWEKQSANVKIFQDTFKRVLSLFLWILTRGFRFYIQFKESKTPVFFLPAFLLPSWALWVLSLPRSIYGSVSLTVWNFAVQKTISGIF	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	171 (169)
Sequences:	185 (138.5)
Seq/Len:	1.095
Nf(neff/√len):	10.7

HHblits Results: (2015_06)
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: 1.095).

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
56_V	82_L	2.398	0.99
13_L	17_F	2.174	0.98
69_F	73_A	2.004	0.96
13_L	167_I	1.870	0.94
76_N	80_E	1.740	0.90
9_I	123_E	1.616	0.85
73_A	76_N	1.601	0.85
124_S	148_R	1.585	0.84
17_F	21_F	1.577	0.84
107_F	118_Y	1.545	0.82
33_I	52_Q	1.511	0.80
116_R	120_Q	1.504	0.79
147_P	152_G	1.480	0.78
65_S	68_Q	1.445	0.75
96_F	170_I	1.383	0.71
110_I	153_S	1.374	0.70
69_F	76_N	1.354	0.68
6_I	125_K	1.350	0.68
9_I	13_L	1.350	0.68
60_L	86_W	1.348	0.68
42_D	93_V	1.348	0.68
54_L	60_L	1.341	0.67
134_F	166_T	1.339	0.67
63_T	145_S	1.325	0.66
162_A	166_T	1.317	0.65
109_W	114_G	1.302	0.64
71_K	131_L	1.256	0.60
3_D	156_L	1.232	0.58
31_Y	141_L	1.231	0.58
7_S	24_K	1.229	0.57
11_L	109_W	1.228	0.57
125_K	167_I	1.223	0.57
44_K	47_K	1.220	0.57
142_W	147_P	1.212	0.56
65_S	166_T	1.205	0.55
45_K	154_V	1.201	0.55
145_S	151_Y	1.177	0.53
63_T	73_A	1.172	0.52
15_I	113_R	1.172	0.52
66_Q	72_W	1.156	0.51
63_T	149_S	1.155	0.50
35_V	50_L	1.153	0.50
9_I	18_F	1.147	0.50
47_K	63_T	1.133	0.48
20_K	25_R	1.128	0.48
43_L	146_L	1.125	0.48
11_L	104_L	1.116	0.47
122_K	132_P	1.112	0.46
161_F	165_K	1.111	0.46
46_N	86_W	1.104	0.46
31_Y	108_L	1.102	0.45
129_F	147_P	1.099	0.45
69_F	135_L	1.094	0.45
57_K	128_V	1.089	0.44
72_W	77_R	1.088	0.44
123_E	160_N	1.082	0.44
58_K	62_A	1.081	0.43
85_E	136_L	1.080	0.43
31_Y	148_R	1.075	0.43
60_L	69_F	1.066	0.42
120_Q	160_N	1.061	0.42
48_E	52_Q	1.055	0.41
48_E	85_E	1.045	0.40
8_T	14_F	1.045	0.40
7_S	124_S	1.042	0.40
7_S	130_F	1.039	0.40
80_E	147_P	1.037	0.39
88_K	91_A	1.033	0.39
50_L	86_W	1.027	0.38
50_L	57_K	1.027	0.38
152_G	159_W	1.026	0.38
56_V	68_Q	1.025	0.38
87_E	155_S	1.024	0.38
91_A	127_P	1.018	0.38
40_N	43_L	1.017	0.38
18_F	169_G	1.013	0.37
114_G	155_S	1.009	0.37
54_L	86_W	1.006	0.37
19_D	30_A	1.005	0.37
20_K	30_A	1.004	0.36
72_W	80_E	1.002	0.36
21_F	143_V	1.001	0.36

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
3vlcE	1	0.3801	99.9	0.641	Contact Map
3b2eE	4	0.4211	99.9	0.649	Contact Map
3sjbC	2	0.4211	99.9	0.663	Contact Map
3sjaC	5	0.3567	99.8	0.705	Contact Map
4bgnA	2	0.2456	36.5	0.948	Contact Map
3rvyA	2	0.1696	31.8	0.95	Contact Map
1uixA	2	0.386	26.3	0.952	Contact Map
3effK	4	0.4152	23	0.953	Contact Map
3kqgA	6	0.4094	18.5	0.955	Contact Map
4ltoA	4	0.4269	14.6	0.957	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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