OPENSEQ.org - 1517967808 - GREMLIN Submission

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3wbf

ID:	1517967808	Query Sequence MDKLRVAVVGYGNVGRYALEAVQAAPDMELVGVVRRKVLAATPPELTGVRVVTDISQLEGVQGALLCVPTRSVPEYAEAMLRRGIHTVDSYDIHGDLADLRRRLDPVAREHGAAAVISAGWDPGTDSIIRALLEFMAPKGITYTNFGPGMSMGHSVAVKAIPGVRDALSMTIPAGMGVHKRAVYVELEPGADFAEVERAIKTDPYFVRDETRVTQVESVSALMDVGHGVVMERKGVSGATHNQLFRFEMRINNPALTAQVMVAALRAAARQKPGCYTMIEIPVIDYLPGDREAWIRKLV	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	299 (299)
Sequences:	426 (239.9)
Seq/Len:	1.425
Nf(neff/√len):	13.9

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: 1.425).

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
187_L	196_V	4.862	1.00
165_R	219_V	3.385	1.00
116_V	268_A	3.274	1.00
194_A	197_E	3.138	1.00
195_E	199_A	3.060	1.00
78_E	100_L	2.993	1.00
187_L	193_F	2.864	1.00
161_I	167_A	2.733	1.00
198_R	202_T	2.587	1.00
105_D	109_R	2.550	1.00
87_T	100_L	2.542	1.00
271_Q	281_I	2.500	1.00
158_V	183_V	2.373	1.00
52_V	58_L	2.349	0.99
193_F	196_V	2.298	0.99
134_E	142_T	2.272	0.99
7_A	61_V	2.254	0.99
128_I	283_V	2.241	0.99
116_V	281_I	2.228	0.99
289_G	297_K	2.213	0.99
18_A	65_L	2.183	0.99
106_P	110_E	2.138	0.99
172_I	184_Y	2.134	0.99
78_E	87_T	2.022	0.98
197_E	201_K	2.011	0.98
162_P	199_A	1.973	0.98
125_T	247_F	1.937	0.97
162_P	195_E	1.911	0.97
96_D	99_D	1.888	0.97
55_I	64_A	1.853	0.96
247_F	283_V	1.833	0.96
132_L	247_F	1.808	0.95
6_V	28_M	1.801	0.95
107_V	111_H	1.790	0.95
165_R	188_E	1.780	0.95
264_A	278_M	1.765	0.94
148_P	172_I	1.762	0.94
32_G	52_V	1.702	0.93
180_K	212_R	1.683	0.92
80_M	83_R	1.633	0.91
86_H	268_A	1.625	0.91
55_I	81_L	1.616	0.90
33_V	42_T	1.530	0.87
87_T	115_A	1.516	0.86
182_A	214_T	1.507	0.85
140_G	233_R	1.482	0.84
7_A	64_A	1.466	0.83
132_L	282_P	1.451	0.82
162_P	188_E	1.447	0.82
293_A	297_K	1.439	0.82
113_A	272_K	1.385	0.78
132_L	283_V	1.377	0.78
131_A	279_I	1.359	0.76
150_M	168_L	1.359	0.76
128_I	247_F	1.359	0.76
116_V	119_A	1.344	0.75
166_D	225_V	1.340	0.75
158_V	167_A	1.336	0.75
87_T	275_C	1.330	0.74
32_G	58_L	1.327	0.74
66_L	246_R	1.324	0.74
8_V	19_L	1.318	0.73
33_V	44_P	1.317	0.73
24_A	139_K	1.301	0.72
161_I	199_A	1.291	0.71
114_A	273_P	1.290	0.71
16_R	33_V	1.283	0.70
236_V	242_N	1.281	0.70
22_V	25_A	1.280	0.70
112_G	162_P	1.280	0.70
33_V	49_V	1.269	0.69
90_S	261_M	1.233	0.66
240_T	291_R	1.232	0.66
131_A	135_F	1.231	0.66
104_L	279_I	1.223	0.65
65_L	261_M	1.218	0.64
57_Q	99_D	1.217	0.64
195_E	201_K	1.217	0.64
93_I	208_R	1.212	0.64
9_V	81_L	1.197	0.62
225_V	241_H	1.196	0.62
102_R	105_D	1.192	0.62
119_A	258_A	1.190	0.62
125_T	240_T	1.187	0.61
22_V	262_V	1.156	0.58
114_A	272_K	1.156	0.58
244_L	250_R	1.140	0.57
168_L	225_V	1.138	0.57
102_R	296_R	1.128	0.56
133_L	245_F	1.115	0.54
268_A	281_I	1.115	0.54
9_V	64_A	1.113	0.54
78_E	104_L	1.112	0.54
167_A	252_N	1.108	0.54
83_R	110_E	1.099	0.53
50_R	165_R	1.095	0.52
64_A	81_L	1.091	0.52
165_R	296_R	1.091	0.52
125_T	132_L	1.086	0.51
191_A	280_E	1.084	0.51
16_R	187_L	1.075	0.50
22_V	28_M	1.070	0.50
137_A	245_F	1.069	0.50
172_I	214_T	1.065	0.49
290_D	293_A	1.064	0.49
119_A	278_M	1.061	0.49
100_L	275_C	1.060	0.49
21_A	196_V	1.053	0.48
119_A	268_A	1.053	0.48
9_V	115_A	1.050	0.48
76_Y	80_M	1.048	0.48
291_R	295_I	1.039	0.47
54_D	57_Q	1.037	0.46
22_V	60_G	1.037	0.46
155_S	159_K	1.028	0.45
44_P	47_T	1.026	0.45
271_Q	282_P	1.025	0.45
198_R	281_I	1.024	0.45
166_D	219_V	1.022	0.45
157_A	161_I	1.019	0.45
9_V	66_L	1.019	0.45
90_S	259_Q	1.010	0.44
5_R	115_A	1.009	0.44
157_A	160_A	1.008	0.43
172_I	175_G	1.007	0.43
55_I	276_Y	1.005	0.43
114_A	268_A	1.000	0.43

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

See coupling matrix (for protein design or mutagenesis)
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
3bioA	2	0.9799	100	0.52	Contact Map
3wgqA	2	0.99	100	0.557	Contact Map
3wycA	2	0	100	0.559	Contact Map
1f06A	2	0.9833	100	0.574	Contact Map
3wb9A	3	0.9933	100	0.588	Contact Map
1p9lA	2	0.7793	99.8	0.847	Contact Map
4ywjA	2	0.8361	99.8	0.85	Contact Map
3ijpA	2	0.806	99.8	0.855	Contact Map
1dihA	1	0.8428	99.7	0.867	Contact Map
2czcA	4	0.8863	99.6	0.877	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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