OPENSEQ.org - 1687874188 - GREMLIN Submission

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cx26-gremlin

ID:	1687874188	Query Sequence MDWGTLQTILGGVNKHSTSIGKIWLTVLFIFRIMILVVAAKEVWGDEQADFVCNTLQPGCKNVCYDHYFPISHIRLWALQLIFVSTPALLVAMHVAYRRHEKKRKFIKGEIKSEFKDIEEIKTQKVRIEGSLWWTYTSSIFFRVIFEAAFMYVFYVMYDGFSMQRLVKCNAWPCPNTVDCFVSRPTEKTVFTVFMIAVSGICILLNVTELSYLLIRYSSGKSKKPV	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	226 (224)
Sequences:	652 (298.8)
Seq/Len:	2.911
Nf(neff/√len):	20.0

HHblits Results: (2016_02)
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
54_N	179_D	2.419	1.00
148_A	152_Y	2.359	1.00
168_K	176_N	2.268	1.00
197_A	201_I	2.100	1.00
199_S	202_C	2.024	1.00
48_Q	62_N	1.735	0.99
40_A	44_W	1.708	0.98
55_T	59_G	1.689	0.98
94_H	135_T	1.688	0.98
72_S	75_R	1.649	0.98
51_F	57_Q	1.624	0.97
170_N	177_T	1.595	0.97
60_C	64_C	1.576	0.97
162_S	189_T	1.530	0.96
68_Y	164_Q	1.519	0.96
36_L	44_W	1.492	0.95
189_T	206_N	1.477	0.95
4_G	7_Q	1.465	0.95
60_C	77_W	1.432	0.94
4_G	19_S	1.427	0.94
47_E	51_F	1.401	0.93
103_K	106_F	1.395	0.93
54_N	72_S	1.392	0.92
192_T	202_C	1.378	0.92
148_A	163_M	1.374	0.92
54_N	181_F	1.372	0.92
13_V	17_S	1.363	0.91
154_F	159_D	1.351	0.91
65_Y	73_H	1.334	0.90
58_P	66_D	1.329	0.90
209_E	213_L	1.319	0.89
1_M	14_N	1.318	0.89
169_C	174_C	1.308	0.89
144_V	181_F	1.294	0.88
207_V	220_G	1.277	0.87
58_P	63_V	1.271	0.87
44_W	76_L	1.270	0.87
126_V	207_V	1.268	0.87
149_A	153_V	1.261	0.86
108_K	204_L	1.256	0.86
51_F	65_Y	1.251	0.86
154_F	196_I	1.247	0.86
76_L	79_L	1.247	0.86
53_C	60_C	1.246	0.86
175_P	179_D	1.244	0.85
60_C	70_P	1.242	0.85
195_M	209_E	1.216	0.84
190_V	193_V	1.212	0.83
178_V	185_P	1.211	0.83
116_K	119_E	1.197	0.82
45_G	65_Y	1.193	0.82
1_M	7_Q	1.190	0.82
59_G	64_C	1.189	0.82
58_P	72_S	1.186	0.81
147_E	160_G	1.183	0.81
48_Q	51_F	1.182	0.81
44_W	69_F	1.182	0.81
66_D	72_S	1.182	0.81
90_L	210_L	1.178	0.81
29_F	94_H	1.168	0.80
70_P	77_W	1.167	0.80
22_K	28_L	1.147	0.78
1_M	38_V	1.145	0.78
54_N	57_Q	1.143	0.78
117_D	120_E	1.138	0.78
46_D	75_R	1.113	0.75
144_V	197_A	1.108	0.75
129_E	152_Y	1.105	0.75
144_V	211_S	1.102	0.74
207_V	211_S	1.101	0.74
204_L	207_V	1.098	0.74
22_K	62_N	1.097	0.74
31_F	191_F	1.096	0.74
176_N	179_D	1.096	0.74
35_I	43_V	1.092	0.73
46_D	72_S	1.092	0.73
90_L	149_A	1.082	0.72
201_I	211_S	1.078	0.72
143_R	163_M	1.069	0.71
4_G	8_T	1.064	0.71
36_L	158_Y	1.061	0.70
32_R	53_C	1.060	0.70
45_G	149_A	1.059	0.70
173_P	178_V	1.059	0.70
195_M	213_L	1.058	0.70
65_Y	191_F	1.053	0.70
12_G	15_K	1.053	0.70
6_L	65_Y	1.051	0.69
39_A	186_T	1.049	0.69
68_Y	76_L	1.048	0.69
47_E	72_S	1.048	0.69
211_S	215_I	1.045	0.69
199_S	210_L	1.040	0.68
33_I	164_Q	1.039	0.68
103_K	200_G	1.039	0.68
91_V	133_W	1.037	0.68
10_L	17_S	1.033	0.67
70_P	75_R	1.032	0.67
11_G	14_N	1.030	0.67
2_D	11_G	1.028	0.67
37_V	140_I	1.026	0.67
101_E	110_E	1.021	0.66
139_S	179_D	1.018	0.66
166_L	179_D	1.016	0.66
40_A	82_I	1.013	0.65
117_D	208_T	1.011	0.65
54_N	175_P	1.008	0.65
175_P	181_F	1.008	0.65
29_F	44_W	1.008	0.65
2_D	14_N	1.006	0.64
88_A	189_T	1.006	0.64
103_K	109_G	1.005	0.64
69_F	158_Y	1.005	0.64
82_I	90_L	1.003	0.64
56_L	142_F	1.002	0.64
42_E	155_Y	1.001	0.64
26_T	153_V	1.000	0.64

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
2zw3A	6	0.8894	100	-0.044	Contact Map
2nx7A	1	0.1239	7.7	0.969	Contact Map
3c5nA	2	0.2345	7.6	0.969	Contact Map
2a65A	1	0.3938	5.6	0.971	Contact Map
4qinA	1	0.3274	5	0.972	Contact Map
2mfrA	1	0.208	3.5	0.974	Contact Map
1wlfA	1	0.292	3	0.975	Contact Map
4bw5A	4	0.4071	2.5	0.976	Contact Map
4xesA	1	0	2.4	0.976	Contact Map
2z73A	2	0.2389	2.4	0.976	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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