OPENSEQ.org - 1482111130 - GREMLIN Submission

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ID:	1482111130	Query Sequence VQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQ	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	254 (245)
Sequences:	251 (234.3)
Seq/Len:	1.024
Nf(neff/√len):	15.0

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: 1.024).

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
240_Q	247_E	3.315	1.00
157_D	184_Y	3.311	1.00
8_K	37_S	2.846	1.00
236_T	249_R	2.705	1.00
104_L	240_Q	2.442	0.99
152_H	195_Q	2.197	0.98
47_V	92_K	2.122	0.97
104_L	124_G	2.023	0.96
156_L	202_L	2.018	0.96
64_L	99_L	1.957	0.95
42_Y	98_K	1.895	0.94
41_A	98_K	1.875	0.93
180_V	202_L	1.871	0.93
45_L	99_L	1.780	0.91
45_L	252_L	1.776	0.91
164_S	181_L	1.740	0.89
68_T	71_E	1.701	0.88
174_D	177_L	1.667	0.86
45_L	64_L	1.621	0.84
13_P	18_D	1.587	0.83
68_T	124_G	1.564	0.81
237_L	253_S	1.558	0.81
136_F	152_H	1.526	0.79
198_N	216_Y	1.501	0.77
47_V	60_S	1.477	0.76
7_S	35_F	1.475	0.76
191_P	194_E	1.463	0.75
20_L	34_G	1.453	0.74
187_H	246_Y	1.451	0.74
12_L	36_D	1.430	0.72
106_E	238_I	1.410	0.71
103_S	237_L	1.364	0.67
241_S	244_G	1.356	0.67
106_E	112_K	1.349	0.66
8_K	12_L	1.318	0.63
2_Q	101_K	1.318	0.63
130_P	133_Y	1.308	0.63
133_Y	158_E	1.305	0.62
239_H	250_I	1.302	0.62
23_R	126_E	1.290	0.61
199_I	225_R	1.290	0.61
239_H	248_T	1.276	0.60
40_V	66_G	1.257	0.58
23_R	27_W	1.247	0.57
63_E	91_V	1.246	0.57
96_I	128_A	1.246	0.57
133_Y	155_Y	1.214	0.54
40_V	118_A	1.210	0.54
218_D	224_K	1.202	0.53
39_T	69_I	1.201	0.53
122_Q	156_L	1.174	0.50
55_S	126_E	1.173	0.50
201_H	204_T	1.165	0.49
44_V	83_L	1.161	0.49
67_I	72_R	1.152	0.48
120_E	225_R	1.151	0.48
31_K	98_K	1.148	0.48
114_M	124_G	1.146	0.48
5_G	98_K	1.145	0.48
13_P	128_A	1.144	0.47
67_I	166_F	1.143	0.47
236_T	247_E	1.140	0.47
44_V	245_L	1.133	0.46
36_D	124_G	1.133	0.46
96_I	230_K	1.125	0.46
117_S	120_E	1.125	0.46
101_K	118_A	1.123	0.46
44_V	97_I	1.120	0.45
130_P	158_E	1.118	0.45
19_K	99_L	1.118	0.45
47_V	156_L	1.115	0.45
15_R	213_A	1.112	0.45
102_Y	238_I	1.108	0.44
160_I	180_V	1.106	0.44
149_V	195_Q	1.103	0.44
105_F	137_L	1.099	0.43
214_F	224_K	1.099	0.43
38_P	70_M	1.097	0.43
56_K	252_L	1.086	0.42
5_G	99_L	1.086	0.42
11_I	92_K	1.085	0.42
64_L	242_I	1.085	0.42
150_E	189_D	1.085	0.42
115_L	236_T	1.084	0.42
163_I	180_V	1.084	0.42
45_L	95_L	1.081	0.42
105_F	125_N	1.079	0.41
69_I	73_S	1.073	0.41
209_G	224_K	1.062	0.40
94_D	137_L	1.060	0.40
99_L	223_R	1.059	0.40
3_T	126_E	1.058	0.40
214_F	217_F	1.056	0.39
150_E	153_K	1.050	0.39
150_E	220_T	1.043	0.38
219_T	245_L	1.037	0.38
89_K	180_V	1.037	0.38
188_R	237_L	1.035	0.38
103_S	123_K	1.034	0.37
242_I	246_Y	1.033	0.37
43_S	62_K	1.026	0.37
103_S	125_N	1.026	0.37
38_P	113_R	1.023	0.37
28_D	95_L	1.021	0.36
41_A	177_L	1.020	0.36
44_V	67_I	1.019	0.36
24_K	248_T	1.019	0.36
29_P	44_V	1.018	0.36
129_L	159_I	1.018	0.36
42_Y	180_V	1.015	0.36
9_E	248_T	1.013	0.36
18_D	132_K	1.007	0.35
117_S	128_A	1.005	0.35
103_S	126_E	1.005	0.35
212_A	222_D	1.004	0.35
115_L	129_L	1.001	0.35
187_H	190_K	1.000	0.35

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
4un4B	1	0.9685	100	0.202	Contact Map
4bwqB	4	0.1024	2.8	0.968	Contact Map
4xb4A	2	0	2.2	0.97	Contact Map
2mlpA	1	0.1024	1.7	0.972	Contact Map
1q14A	1	0.1969	1.5	0.973	Contact Map
2mgvA	1	0.2165	1.3	0.973	Contact Map
3mg1A	2	0.5157	1.2	0.974	Contact Map
4gxbB	1	0.0591	1.1	0.975	Contact Map
2ffgA	2	0.2087	1	0.975	Contact Map
4n78F	1	0.4291	1	0.975	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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