OPENSEQ.org - 1494890521 - GREMLIN Submission

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ID:	1494890521	Query Sequence MANYYEVLGVQASASPEDIKKAYRKLALRWHPDKNPDNKEEAEKKFKLVSEAYEVLSDSKKRSLYDRAGCDSWRAGGGASTPYHSPFDTGYTFRNPEDIFREFFGGLDPFSFEFWDSPFNSDRGGRGHGLRGAFSAGFGEFPAFMEAFSSFNMLGCSGGSHTTFSSTSFGGSSSGSSGFKSVMSSTEMINGHKVTTKRIVENGQERVEVEEDGQLKSVTVNGKEQLKWMDSK	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	232 (232)
Sequences:	306 (203.7)
Seq/Len:	1.319
Nf(neff/√len):	13.4

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: 1.319).

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
8_L	19_I	2.433	1.00
5_Y	8_L	2.409	0.99
5_Y	19_I	2.363	0.99
10_V	19_I	2.214	0.99
222_G	225_Q	1.998	0.97
51_E	70_C	1.779	0.94
68_A	72_S	1.775	0.94
8_L	14_A	1.744	0.93
5_Y	66_D	1.727	0.93
12_A	64_L	1.689	0.91
8_L	20_K	1.643	0.90
106_G	109_P	1.619	0.89
11_Q	18_D	1.569	0.87
8_L	21_K	1.559	0.86
8_L	22_A	1.544	0.86
186_T	195_T	1.542	0.86
15_S	18_D	1.525	0.85
14_A	19_I	1.519	0.85
199_I	208_E	1.491	0.83
5_Y	10_V	1.488	0.83
178_G	190_N	1.462	0.81
206_R	218_V	1.460	0.81
70_C	73_W	1.438	0.80
10_V	15_S	1.431	0.79
23_Y	32_P	1.421	0.79
37_D	189_I	1.386	0.76
95_N	208_E	1.379	0.76
192_H	214_Q	1.370	0.75
69_G	73_W	1.368	0.75
203_G	222_G	1.366	0.75
4_Y	55_V	1.336	0.72
50_S	97_E	1.331	0.72
27_A	31_H	1.331	0.72
35_N	38_N	1.331	0.72
98_D	157_S	1.317	0.71
208_E	215_L	1.315	0.71
66_D	93_F	1.278	0.68
24_R	94_R	1.265	0.66
96_P	189_I	1.254	0.65
64_L	73_W	1.254	0.65
197_K	215_L	1.252	0.65
4_Y	8_L	1.251	0.65
29_R	41_E	1.247	0.65
72_S	75_A	1.243	0.64
43_E	213_G	1.239	0.64
94_R	102_E	1.237	0.64
45_K	59_S	1.232	0.63
4_Y	20_K	1.221	0.62
211_E	216_K	1.215	0.62
210_E	213_G	1.208	0.61
50_S	219_T	1.199	0.60
23_Y	31_H	1.198	0.60
203_G	207_V	1.193	0.60
221_N	225_Q	1.192	0.60
2_A	7_V	1.189	0.59
10_V	59_S	1.179	0.58
4_Y	51_E	1.169	0.57
45_K	48_L	1.168	0.57
19_I	22_A	1.168	0.57
198_R	205_E	1.163	0.57
27_A	32_P	1.159	0.56
5_Y	21_K	1.156	0.56
30_W	103_F	1.155	0.56
138_F	148_F	1.154	0.56
103_F	211_E	1.150	0.56
54_E	99_I	1.140	0.55
34_K	42_A	1.139	0.54
16_P	49_V	1.136	0.54
68_A	73_W	1.131	0.54
228_W	231_S	1.128	0.53
39_K	213_G	1.125	0.53
5_Y	14_A	1.122	0.53
105_G	110_F	1.120	0.53
53_Y	56_L	1.118	0.52
217_S	221_N	1.118	0.52
9_G	22_A	1.114	0.52
30_W	34_K	1.112	0.52
27_A	33_D	1.110	0.52
15_S	107_L	1.109	0.51
1_M	15_S	1.104	0.51
57_S	61_K	1.100	0.51
39_K	43_E	1.095	0.50
42_A	194_V	1.091	0.50
221_N	224_E	1.090	0.50
5_Y	22_A	1.085	0.49
58_D	61_K	1.085	0.49
124_G	129_G	1.084	0.49
14_A	21_K	1.083	0.49
5_Y	20_K	1.077	0.48
163_T	188_M	1.077	0.48
49_V	189_I	1.074	0.48
17_E	195_T	1.064	0.47
43_E	50_S	1.063	0.47
95_N	193_K	1.057	0.46
164_F	186_T	1.056	0.46
45_K	57_S	1.052	0.46
94_R	205_E	1.049	0.45
85_S	119_F	1.049	0.45
198_R	214_Q	1.049	0.45
72_S	91_Y	1.047	0.45
118_P	128_H	1.043	0.45
26_L	35_N	1.041	0.45
94_R	99_I	1.036	0.44
75_A	207_V	1.036	0.44
18_D	97_E	1.035	0.44
20_K	182_V	1.035	0.44
11_Q	15_S	1.030	0.44
48_L	99_I	1.026	0.43
27_A	56_L	1.023	0.43
8_L	15_S	1.022	0.43
14_A	22_A	1.021	0.43
158_G	161_H	1.021	0.43
102_E	205_E	1.020	0.43
39_K	212_D	1.017	0.42
35_N	57_S	1.016	0.42
55_V	209_V	1.012	0.42
30_W	35_N	1.010	0.42
205_E	220_V	1.006	0.41
24_R	103_F	1.006	0.41
49_V	206_R	1.004	0.41
49_V	103_F	1.004	0.41
41_E	45_K	1.003	0.41
38_N	55_V	1.001	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
4j7zA	6	0.4483	100	0.672	Contact Map
3lz8A	2	0.3017	100	0.674	Contact Map
4j80A	4	0.7198	100	0.674	Contact Map
1bq0A	1	0.3276	100	0.684	Contact Map
2dmxA	1	0.3664	100	0.69	Contact Map
2lgwA	1	0.306	100	0.691	Contact Map
2ej7A	1	0.3233	100	0.697	Contact Map
3apoA	1	0.5905	99.9	0.706	Contact Map
2ctqA	1	0.4052	99.9	0.707	Contact Map
2ctrA	1	0.3578	99.9	0.711	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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