OPENSEQ.org - 1435613743 - GREMLIN Submission

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2L6X

ID:	1435613743	Query Sequence MGGGDLDASDYTGVSFWLVTAALLASTVFFFVERDRVSAKWKTSLTVSGLVTGIAFWHYMYMRGVWIETGDSPTVFRYIDWLLTVPLLICEFYLILAAATNVAGSLFKKLLVGSLVMLVFGYMGEAGIMAAWPAFIIGCLAWVYMIYELWAGEGKSACNTASPAVQSAYNTMMYIIIFGWAIYPVGYFTGYLMGDGGSALNLNLIYNLADFVNKILFGLIIWNVAVKESSNAPGGGSHHHHHH	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	243 (228)
Sequences:	364 (286.7)
Seq/Len:	1.596
Nf(neff/√len):	19.0

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: 1.596).

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_I	83_L	4.691	1.00
22_A	211_F	2.512	1.00
17_W	63_R	2.425	1.00
85_V	114_S	2.120	0.99
80_D	214_K	2.087	0.99
84_T	87_L	1.903	0.97
80_D	84_T	1.822	0.96
27_T	52_T	1.717	0.95
199_A	203_N	1.702	0.94
30_F	218_G	1.680	0.94
58_H	62_M	1.628	0.92
61_Y	134_A	1.585	0.91
56_F	106_L	1.534	0.89
66_W	75_V	1.531	0.89
199_A	202_L	1.459	0.85
55_A	80_D	1.459	0.85
114_S	118_L	1.456	0.85
120_F	213_N	1.426	0.84
51_V	58_H	1.411	0.83
117_M	121_G	1.408	0.82
180_W	214_K	1.376	0.80
114_S	117_M	1.372	0.80
28_V	31_F	1.365	0.80
85_V	117_M	1.352	0.79
47_V	87_L	1.336	0.78
131_A	136_I	1.328	0.77
200_L	203_N	1.310	0.76
25_A	211_F	1.310	0.76
20_T	60_M	1.293	0.74
22_A	215_I	1.280	0.73
187_Y	194_G	1.274	0.73
87_L	124_G	1.270	0.72
124_G	187_Y	1.265	0.72
55_A	149_L	1.255	0.71
52_T	218_G	1.249	0.71
187_Y	209_A	1.247	0.70
58_H	125_E	1.229	0.69
189_T	205_I	1.223	0.68
24_L	53_G	1.221	0.68
28_V	44_S	1.216	0.68
24_L	56_F	1.215	0.68
116_V	141_A	1.210	0.67
81_W	121_G	1.203	0.66
84_T	214_K	1.202	0.66
31_F	49_G	1.198	0.66
121_G	214_K	1.182	0.64
48_S	145_M	1.180	0.64
190_G	205_I	1.176	0.64
26_S	219_L	1.169	0.63
182_I	189_T	1.167	0.63
28_V	53_G	1.167	0.63
85_V	214_K	1.162	0.63
193_M	202_L	1.161	0.62
17_W	20_T	1.160	0.62
19_V	215_I	1.160	0.62
167_S	171_T	1.156	0.62
123_M	185_V	1.155	0.62
66_W	175_I	1.152	0.62
55_A	84_T	1.149	0.61
48_S	218_G	1.147	0.61
227_K	231_N	1.145	0.61
24_L	211_F	1.145	0.61
55_A	88_L	1.145	0.61
78_Y	86_P	1.144	0.61
214_K	218_G	1.141	0.60
19_V	23_L	1.139	0.60
162_S	211_F	1.132	0.60
101_N	132_W	1.127	0.59
198_S	201_N	1.121	0.58
135_F	145_M	1.121	0.58
51_V	84_T	1.116	0.58
19_V	56_F	1.115	0.58
198_S	203_N	1.115	0.58
19_V	211_F	1.115	0.58
55_A	214_K	1.114	0.58
48_S	91_E	1.108	0.57
60_M	64_G	1.107	0.57
55_A	180_W	1.105	0.57
121_G	217_F	1.103	0.57
29_F	110_L	1.101	0.56
30_F	48_S	1.097	0.56
74_T	125_E	1.095	0.56
82_L	115_L	1.091	0.55
83_L	224_V	1.087	0.55
188_F	195_D	1.087	0.55
143_V	174_Y	1.085	0.55
19_V	115_L	1.080	0.54
55_A	87_L	1.079	0.54
165_V	177_I	1.078	0.54
149_L	177_I	1.077	0.54
89_I	98_A	1.075	0.54
160_T	231_N	1.074	0.54
80_D	213_N	1.073	0.53
190_G	193_M	1.072	0.53
19_V	22_A	1.066	0.53
118_L	215_I	1.064	0.53
176_I	221_I	1.057	0.52
55_A	85_V	1.048	0.51
142_W	145_M	1.047	0.51
23_L	55_A	1.044	0.50
80_D	85_V	1.042	0.50
89_I	126_A	1.041	0.50
28_V	129_M	1.037	0.50
228_E	232_A	1.036	0.50
55_A	62_M	1.035	0.49
118_L	214_K	1.031	0.49
76_F	79_I	1.023	0.48
55_A	117_M	1.019	0.48
32_V	136_I	1.014	0.47
142_W	177_I	1.012	0.47
80_D	87_L	1.011	0.47
85_V	118_L	1.010	0.47
125_E	187_Y	1.009	0.47
78_Y	81_W	1.008	0.47
84_T	114_S	1.008	0.47
84_T	121_G	1.007	0.47
51_V	87_L	1.006	0.46
27_T	139_C	1.005	0.46
137_I	189_T	1.005	0.46

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: (31Jan15)
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
4knfA	5	0.9547	100	0.16	Contact Map
3ddlA	2	0.9506	100	0.19	Contact Map
4jq6A	3	0.8477	100	0.193	Contact Map
1xioA	1	0.8724	100	0.205	Contact Map
4hyjA	2	0.9342	100	0.222	Contact Map
1m0kA	1	0.8683	100	0.234	Contact Map
3qapA	1	0.8807	100	0.237	Contact Map
3wqjA	1	0.9095	100	0.239	Contact Map
4l35A	1	0.9342	100	0.243	Contact Map
3am6A	4	0.893	100	0.243	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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