OPENSEQ.org - 1485262091 - GREMLIN Submission

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PP3 Gremlin

ID:	1485262091	Query Sequence MKRSEINAVMKDALNLFKEYKISLPEFVLWTADEWKTKGEETREIKDNMLGWDITDFGSGDFNDTGLFLITLRNGNQKNKEKYPKPYAEKLMIVKEKQITPMHFHWSKMEDIINCGGGNLIIKLYNSTADEQLADTDVEISVDGVKHIYPAGYELCLKPGDSVTLTPGLYHRFWGEEGKGTVIVREVSMCNDDANDNRFYDKVGRFPEIVEDEAPLYLLCNEYNK	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	225 (225)
Sequences:	294 (185)
Seq/Len:	1.307
Nf(neff/√len):	12.3

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: 1.307).

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
61_D	64_D	4.162	1.00
49_M	194_A	2.370	0.99
57_F	100_T	2.314	0.99
33_D	36_K	2.068	0.98
95_K	181_T	1.948	0.97
29_L	217_Y	1.909	0.96
14_L	29_L	1.909	0.96
28_V	70_I	1.890	0.96
48_N	76_N	1.875	0.96
106_W	198_R	1.670	0.91
156_C	176_E	1.655	0.90
132_Q	201_D	1.647	0.90
11_K	213_E	1.616	0.89
150_P	153_Y	1.579	0.87
17_F	92_M	1.578	0.87
35_W	104_F	1.563	0.86
126_N	138_V	1.552	0.86
133_L	200_Y	1.514	0.84
128_T	132_Q	1.468	0.81
213_E	216_L	1.465	0.81
31_T	47_D	1.460	0.81
118_G	180_G	1.436	0.79
14_L	217_Y	1.428	0.79
104_F	198_R	1.423	0.79
99_I	172_R	1.396	0.77
109_M	189_M	1.394	0.77
87_Y	189_M	1.370	0.75
126_N	136_T	1.369	0.75
30_W	42_T	1.351	0.73
69_L	173_F	1.341	0.73
122_I	217_Y	1.334	0.72
47_D	83_Y	1.324	0.71
165_L	189_M	1.319	0.71
119_N	176_E	1.317	0.71
38_K	49_M	1.309	0.70
10_M	156_C	1.306	0.70
155_L	163_V	1.303	0.69
47_D	50_L	1.296	0.69
96_E	180_G	1.290	0.68
46_K	222_E	1.287	0.68
119_N	158_K	1.275	0.67
15_N	19_E	1.270	0.67
96_E	178_G	1.269	0.66
59_S	65_T	1.265	0.66
121_I	154_E	1.259	0.66
94_V	100_T	1.253	0.65
10_M	22_I	1.244	0.64
11_K	216_L	1.231	0.63
113_I	162_S	1.218	0.62
5_E	63_N	1.216	0.62
35_W	50_L	1.211	0.61
119_N	156_C	1.207	0.61
199_F	205_R	1.194	0.60
71_T	223_Y	1.193	0.59
87_Y	109_M	1.185	0.59
73_R	143_D	1.185	0.59
48_N	83_Y	1.160	0.56
72_L	91_L	1.157	0.56
138_V	151_A	1.153	0.56
102_M	134_A	1.148	0.55
24_L	69_L	1.145	0.55
124_L	165_L	1.145	0.55
16_L	93_I	1.144	0.55
142_V	163_V	1.141	0.54
104_F	170_Y	1.139	0.54
126_N	137_D	1.132	0.53
26_E	161_D	1.125	0.53
29_L	96_E	1.120	0.52
22_I	72_L	1.119	0.52
194_A	224_N	1.117	0.52
34_E	38_K	1.116	0.52
73_R	183_I	1.114	0.52
3_R	7_N	1.113	0.52
126_N	151_A	1.112	0.51
11_K	15_N	1.112	0.51
79_N	82_K	1.107	0.51
100_T	173_F	1.105	0.51
15_N	128_T	1.102	0.50
137_D	169_L	1.098	0.50
218_L	223_Y	1.095	0.50
49_M	83_Y	1.094	0.50
9_V	16_L	1.089	0.49
126_N	169_L	1.088	0.49
92_M	95_K	1.087	0.49
67_L	100_T	1.087	0.49
120_L	165_L	1.084	0.49
114_N	159_P	1.081	0.48
121_I	156_C	1.081	0.48
156_C	174_W	1.081	0.48
117_G	157_L	1.073	0.48
30_W	45_I	1.071	0.47
1_M	4_S	1.069	0.47
88_A	125_Y	1.067	0.47
35_W	44_E	1.063	0.47
77_Q	80_K	1.060	0.46
122_I	149_Y	1.059	0.46
137_D	150_P	1.057	0.46
62_F	95_K	1.055	0.46
173_F	185_R	1.055	0.46
4_S	211_E	1.054	0.46
4_S	52_W	1.054	0.46
4_S	7_N	1.053	0.46
69_L	220_C	1.051	0.45
87_Y	190_C	1.047	0.45
14_L	216_L	1.044	0.45
166_T	169_L	1.041	0.44
46_K	50_L	1.038	0.44
141_S	146_K	1.037	0.44
3_R	62_F	1.034	0.44
125_Y	128_T	1.032	0.44
4_S	143_D	1.030	0.43
127_S	168_G	1.029	0.43
22_I	91_L	1.021	0.42
175_G	182_V	1.018	0.42
46_K	224_N	1.017	0.42
52_W	55_T	1.015	0.42
45_I	164_T	1.015	0.42
68_F	203_V	1.012	0.42
92_M	165_L	1.011	0.41
69_L	185_R	1.011	0.41
43_R	224_N	1.008	0.41
78_K	82_K	1.008	0.41
67_L	120_L	1.006	0.41
104_F	131_E	1.005	0.41
65_T	99_I	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: (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
3kmhA	2	0.9867	100	0.095	Contact Map
2y0oA	1	0.7333	100	0.57	Contact Map
3d0jA	1	0.5911	97.7	0.919	Contact Map
3ww3A	2	0	97.4	0.923	Contact Map
4ieuA	1	0.7822	97.3	0.925	Contact Map
2oa2A	1	0.5867	96.9	0.929	Contact Map
1v70A	1	0.4622	96.9	0.929	Contact Map
4zu4A	6	0	96.8	0.93	Contact Map
4qm9A	2	0.6444	96.8	0.93	Contact Map
3ht1A	1	0.6311	96.7	0.931	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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