OPENSEQ.org - 1491222197 - GREMLIN Submission

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Q1

ID:	1491222197	Query Sequence MPTKTSQHAFAGSERWVVPRYSSKPGTLIRLGSVLTDPEDLESSLNLDSIPPIPPHLLRDATPEVRMSVQTELSKSDSTLAKAAPALEGILTLGGGVEASRSQGVSSSLNISGTVKATVFRADKSYMDVLLKDKNVISYAKRGLGKPMFVVVGVATAGRVEMKETRHVTRKAGVSGKVGVEVIGEGEVGLERERSDKSCNEVRGEGGLDFAYRVREFGYSRVRGTVKDKGDWTGKVLFAGGKGPVVEKGGEVVPVFKEFKEGEVKLRATGSFDVAAKA	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	278 (228)
Sequences:	236 (214.6)
Seq/Len:	1.035
Nf(neff/√len):	14.2

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: 1.035).

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
38_P	214_V	2.897	1.00
117_A	155_A	2.887	1.00
34_V	150_V	2.139	0.97
41_L	212_Y	1.612	0.84
34_V	151_V	1.609	0.84
17_V	151_V	1.604	0.84
15_R	19_P	1.593	0.83
38_P	212_Y	1.556	0.81
160_V	208_L	1.546	0.80
92_T	110_N	1.540	0.80
31_L	120_F	1.508	0.78
87_L	122_A	1.506	0.78
158_G	207_G	1.481	0.76
76_S	105_V	1.467	0.75
66_R	205_E	1.453	0.74
177_K	209_D	1.453	0.74
22_S	41_L	1.430	0.73
85_P	106_S	1.428	0.73
38_P	149_F	1.422	0.72
156_T	207_G	1.411	0.71
201_E	209_D	1.400	0.70
147_P	216_E	1.397	0.70
130_L	150_V	1.396	0.70
15_R	18_V	1.384	0.69
110_N	210_F	1.369	0.68
33_S	151_V	1.354	0.67
150_V	230_G	1.353	0.67
161_E	199_C	1.346	0.66
29_I	42_E	1.324	0.64
152_V	216_E	1.324	0.64
16_W	212_Y	1.321	0.64
18_V	147_P	1.312	0.63
34_V	217_F	1.304	0.62
35_L	214_V	1.303	0.62
72_E	161_E	1.301	0.62
37_D	157_A	1.291	0.61
182_V	211_A	1.275	0.60
123_D	165_T	1.271	0.60
85_P	174_V	1.266	0.59
88_E	217_F	1.262	0.59
94_G	150_V	1.254	0.58
29_I	58_L	1.249	0.58
130_L	151_V	1.243	0.57
151_V	184_G	1.242	0.57
128_D	151_V	1.236	0.56
132_K	137_I	1.226	0.55
33_S	130_L	1.226	0.55
68_S	203_R	1.213	0.54
115_V	157_A	1.208	0.54
156_T	163_K	1.200	0.53
17_V	217_F	1.199	0.53
16_W	211_A	1.194	0.52
16_W	33_S	1.193	0.52
208_L	213_R	1.175	0.51
65_V	105_V	1.172	0.50
166_R	209_D	1.168	0.50
67_M	203_R	1.154	0.49
18_V	21_Y	1.150	0.48
28_L	85_P	1.148	0.48
27_T	154_V	1.147	0.48
91_L	110_N	1.146	0.48
125_S	135_N	1.144	0.48
55_P	154_V	1.140	0.47
104_G	167_H	1.134	0.47
146_K	210_F	1.132	0.47
59_R	221_R	1.122	0.46
125_S	159_R	1.120	0.46
208_L	234_G	1.105	0.44
74_S	116_K	1.104	0.44
94_G	98_E	1.103	0.44
37_D	214_V	1.101	0.44
15_R	20_R	1.099	0.44
38_P	41_L	1.097	0.43
45_L	146_K	1.091	0.43
84_A	89_G	1.090	0.43
118_T	231_D	1.089	0.43
34_V	154_V	1.088	0.43
15_R	155_A	1.088	0.43
190_L	235_K	1.087	0.42
22_S	114_T	1.085	0.42
21_Y	33_S	1.085	0.42
15_R	56_H	1.084	0.42
131_L	210_F	1.081	0.42
209_D	239_A	1.077	0.42
126_Y	130_L	1.076	0.41
91_L	210_F	1.074	0.41
89_G	100_S	1.064	0.40
29_I	50_I	1.058	0.40
15_R	46_N	1.053	0.39
46_N	93_L	1.053	0.39
160_V	235_K	1.049	0.39
47_L	238_F	1.049	0.39
22_S	237_L	1.049	0.39
113_G	161_E	1.049	0.39
30_R	128_D	1.040	0.38
153_G	213_R	1.040	0.38
101_R	192_R	1.039	0.38
127_M	167_H	1.036	0.38
157_A	212_Y	1.035	0.38
35_L	116_K	1.032	0.38
152_V	236_V	1.029	0.37
33_S	50_I	1.028	0.37
16_W	41_L	1.027	0.37
89_G	97_V	1.020	0.36
17_V	207_G	1.020	0.36
215_R	231_D	1.018	0.36
16_W	53_I	1.016	0.36
48_D	126_Y	1.009	0.36
148_M	160_V	1.007	0.35
22_S	68_S	1.006	0.35
36_T	150_V	1.006	0.35
46_N	148_M	1.005	0.35
19_P	120_F	1.004	0.35
136_V	217_F	1.003	0.35
156_T	178_V	1.003	0.35

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
3obqA	1	0.1691	8.3	0.968	Contact Map
4gprA	1	0.2446	4.4	0.972	Contact Map
2l0eA	1	0.1115	4	0.972	Contact Map
3mb2B	6	0.2086	3.8	0.973	Contact Map
2e2cA	1	0.2446	3.7	0.973	Contact Map
2aakA	1	0.2518	3	0.974	Contact Map
2ayvA	1	0.2374	3	0.974	Contact Map
2f4zA	2	0.2554	2.9	0.974	Contact Map
1i7kA	2	0.241	2.9	0.974	Contact Map
3rz3A	4	0.3058	2.8	0.974	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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