OPENSEQ.org - 1411608479 - GREMLIN Submission

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1DG6A

ID:	1411608479	Query Sequence QRVAAHITGTRGRSNTLSSPNSKNEKALGRKINSWESSRSGHSFLSNLHLRNGELVIHEKGFYYIYSQTYFRFQEEIKENTKNDKQMVQYIYKYTSYPAPILLMKSARNSCWSKDAEYGLYSIYQGGIFELKENDRIFVSVTNEHLIDMDHEASFFGAFLVG	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	162 (154)
Sequences:	261 (151.1)
Seq/Len:	1.695
Nf(neff/√len):	12.2

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: 1.695).

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
64_Y	139_V	2.338	1.00
54_E	136_R	2.320	1.00
65_I	137_I	2.178	0.99
4_A	9_G	1.922	0.98
48_L	142_T	1.761	0.96
111_C	129_F	1.703	0.95
124_Y	129_F	1.610	0.92
106_S	123_I	1.598	0.92
116_A	127_G	1.598	0.92
127_G	137_I	1.575	0.91
6_H	126_G	1.522	0.89
57_I	65_I	1.468	0.87
67_S	111_C	1.462	0.87
36_E	41_G	1.451	0.86
45_L	55_L	1.384	0.82
41_G	151_H	1.365	0.81
95_T	103_L	1.361	0.81
104_M	128_I	1.358	0.81
89_Q	125_Q	1.356	0.81
44_F	155_F	1.350	0.80
127_G	155_F	1.345	0.80
6_H	9_G	1.302	0.77
33_N	55_L	1.301	0.77
95_T	99_A	1.273	0.74
67_S	129_F	1.265	0.74
141_V	156_F	1.263	0.74
71_F	124_Y	1.261	0.73
5_A	8_T	1.260	0.73
67_S	97_Y	1.246	0.72
106_S	147_I	1.224	0.70
68_Q	160_L	1.219	0.70
62_F	128_I	1.217	0.70
47_N	89_Q	1.209	0.69
1_Q	67_S	1.207	0.69
92_Y	142_T	1.204	0.68
50_L	139_V	1.202	0.68
95_T	159_F	1.200	0.68
105_K	112_W	1.194	0.67
66_Y	156_F	1.154	0.64
33_N	140_S	1.153	0.63
4_A	25_E	1.152	0.63
10_T	13_R	1.131	0.61
32_I	64_Y	1.125	0.61
111_C	150_D	1.122	0.60
126_G	157_G	1.118	0.60
48_L	158_A	1.117	0.60
141_V	147_I	1.116	0.60
97_Y	124_Y	1.114	0.60
37_S	48_L	1.109	0.59
9_G	92_Y	1.106	0.59
5_A	55_L	1.103	0.58
54_E	155_F	1.103	0.58
33_N	154_S	1.095	0.58
57_I	71_F	1.095	0.58
86_Q	112_W	1.083	0.56
68_Q	124_Y	1.082	0.56
72_R	142_T	1.072	0.55
50_L	55_L	1.070	0.55
5_A	9_G	1.070	0.55
68_Q	96_S	1.070	0.55
43_S	126_G	1.064	0.54
127_G	150_D	1.062	0.54
8_T	98_P	1.062	0.54
106_S	109_N	1.058	0.54
64_Y	110_S	1.053	0.53
97_Y	158_A	1.051	0.53
64_Y	127_G	1.050	0.53
106_S	110_S	1.049	0.53
25_E	28_L	1.046	0.52
67_S	124_Y	1.031	0.51
105_K	120_L	1.028	0.50
62_F	161_V	1.027	0.50
44_F	146_L	1.026	0.50
106_S	137_I	1.026	0.50
9_G	26_K	1.018	0.49
71_F	141_V	1.017	0.49
36_E	154_S	1.015	0.49
29_G	38_S	1.014	0.49
137_I	153_A	1.012	0.49
68_Q	126_G	1.011	0.49
57_I	135_D	1.010	0.49
44_F	98_P	1.008	0.48
7_I	12_G	1.004	0.48
60_K	130_E	1.001	0.48
57_I	153_A	1.001	0.48

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: (06Sep14)
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
1dg6A	1	0.9198	100	0.132	Contact Map
4mxwY	4	0.8086	100	0.209	Contact Map
1s55A	3	0.9383	100	0.214	Contact Map
2rjlA	1	0.8457	100	0.231	Contact Map
1tnrA	1	0.8765	100	0.237	Contact Map
4kg8A	3	0.8025	100	0.238	Contact Map
2tnfA	3	0.858	100	0.251	Contact Map
4msvA	1	0.8457	100	0.263	Contact Map
1alyA	1	0.858	100	0.263	Contact Map
2x29A	1	0.8148	100	0.288	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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