OPENSEQ.org - 1398961466 - GREMLIN Submission

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T0760

ID:	1398961466	Query Sequence MYMKKLKFITLTLAIIITLPMLQSCLDDNDHQSRSLVISTINQISEDSKEFYFTLDNGKTMFPSNSQAWGGEKFENGQRAFVIFNELEQPVNGYDYNIQVRDITKVLTKEIVTMDDEENTEEKIGDDKINATYMWISKDKKYLTIEFQYYSTHSEDKKHFLNLVINNKEADSAAENEDNTDDEYINLEFRHNSERDSPDHLGEGYVSFKLDKIEEQIEGKKGLNIRVRTLYDGIKNYKVQFP	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	242 (232)
Sequences:	313 (271.2)
Seq/Len:	1.349
Nf(neff/√len):	17.8

Jackhmmer Results: (2014_04_16)
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: 1.349).

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
161_L	189_F	3.136	1.00
107_L	206_V	2.425	1.00
147_F	204_G	2.310	0.99
41_I	80_A	2.013	0.98
53_F	82_V	1.756	0.94
56_D	79_R	1.661	0.91
222_G	240_Q	1.637	0.90
56_D	127_D	1.618	0.89
129_I	239_V	1.592	0.88
79_R	144_T	1.552	0.87
83_I	101_R	1.537	0.86
42_N	141_K	1.511	0.85
159_H	196_D	1.507	0.84
38_I	44_I	1.507	0.84
162_N	208_F	1.475	0.83
125_G	190_R	1.470	0.82
109_K	125_G	1.469	0.82
143_L	210_L	1.451	0.81
159_H	191_H	1.448	0.81
61_M	82_V	1.436	0.80
115_D	120_T	1.426	0.80
189_F	206_V	1.405	0.78
17_I	22_L	1.381	0.76
111_I	187_L	1.362	0.75
134_M	225_I	1.362	0.75
31_H	89_Q	1.353	0.74
109_K	162_N	1.347	0.74
229_T	233_G	1.334	0.73
39_S	144_T	1.331	0.73
87_L	99_Q	1.311	0.71
205_Y	229_T	1.308	0.71
69_W	72_E	1.304	0.70
56_D	144_T	1.301	0.70
114_M	164_V	1.273	0.68
144_T	207_S	1.268	0.67
222_G	238_K	1.254	0.66
111_I	189_F	1.250	0.66
130_N	146_E	1.247	0.65
39_S	55_L	1.245	0.65
16_I	133_Y	1.234	0.64
15_I	234_I	1.232	0.64
114_M	120_T	1.231	0.64
227_V	237_Y	1.231	0.64
145_I	189_F	1.222	0.63
58_G	187_L	1.213	0.62
193_S	199_D	1.210	0.62
124_I	164_V	1.197	0.61
15_I	21_M	1.197	0.61
78_Q	105_K	1.196	0.61
11_L	18_T	1.190	0.60
45_S	51_F	1.175	0.59
129_I	220_K	1.171	0.58
11_L	19_L	1.170	0.58
5_K	8_F	1.162	0.57
125_G	163_L	1.161	0.57
127_D	193_S	1.156	0.57
112_V	162_N	1.147	0.56
27_D	31_H	1.142	0.55
100_V	147_F	1.136	0.55
51_F	65_N	1.135	0.55
147_F	208_F	1.131	0.54
159_H	210_L	1.125	0.54
125_G	162_N	1.124	0.54
72_E	78_Q	1.124	0.54
160_F	189_F	1.121	0.53
49_K	129_I	1.121	0.53
20_P	156_D	1.119	0.53
22_L	110_E	1.118	0.53
79_R	127_D	1.117	0.53
80_A	103_I	1.111	0.52
112_V	115_D	1.110	0.52
19_L	88_E	1.105	0.52
110_E	187_L	1.105	0.52
85_N	101_R	1.099	0.51
148_Q	203_E	1.095	0.51
224_N	238_K	1.093	0.50
53_F	97_N	1.092	0.50
80_A	208_F	1.090	0.50
10_T	16_I	1.090	0.50
184_Y	222_G	1.089	0.50
166_N	188_E	1.087	0.50
50_E	234_I	1.082	0.49
84_F	96_Y	1.076	0.49
109_K	147_F	1.075	0.49
132_T	146_E	1.073	0.48
60_T	225_I	1.071	0.48
43_Q	53_F	1.069	0.48
29_N	53_F	1.068	0.48
97_N	164_V	1.066	0.48
77_G	222_G	1.066	0.48
7_K	33_S	1.065	0.48
106_V	178_D	1.065	0.48
206_V	220_K	1.064	0.48
45_S	189_F	1.061	0.47
42_N	137_S	1.055	0.47
62_F	89_Q	1.054	0.47
78_Q	221_K	1.053	0.46
226_R	234_I	1.050	0.46
24_S	105_K	1.049	0.46
5_K	9_I	1.043	0.45
16_I	24_S	1.042	0.45
52_Y	60_T	1.042	0.45
183_E	222_G	1.042	0.45
55_L	59_K	1.041	0.45
39_S	42_N	1.040	0.45
125_G	192_N	1.038	0.45
27_D	32_Q	1.037	0.45
150_Y	201_L	1.036	0.45
215_E	218_E	1.036	0.45
132_T	231_Y	1.035	0.45
199_D	225_I	1.033	0.44
49_K	61_M	1.032	0.44
40_T	168_K	1.030	0.44
32_Q	89_Q	1.027	0.44
74_F	202_G	1.017	0.43
190_R	222_G	1.008	0.42
18_T	22_L	1.004	0.42
44_I	77_G	1.003	0.42
99_Q	162_N	1.002	0.41

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: (17Apr14)
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
4j8qA	1	0.7893	100	0.241	Contact Map
3k6oA	2	0.7851	100	0.264	Contact Map
3k0yA	1	0.7562	100	0.279	Contact Map
3qwnA	12	0.8099	100	0.32	Contact Map
3nqiA	4	0.7851	99.6	0.726	Contact Map
4k3bA	1	0.8388	21.4	0.95	Contact Map
4lmhA	4	0.6612	18.8	0.951	Contact Map
4bbwA	1	0.7893	16.1	0.953	Contact Map
3zbiC	14	0.1157	11	0.956	Contact Map
3p24A	4	0.5785	9.4	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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