OPENSEQ.org - 1435770490 - GREMLIN Submission

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T0760

ID:	1435770490	Query Sequence MYMKKLKFITLTLAIIITLPMLQSCLDDNDHQSRSLVISTINQISEDSKEFYFTLDNGKTMFPSNSQAWGGEKFENGQRAFVIFNELEQPVNGYDYNIQVRDITKVLTKEIVTMDDEENTEEKIGDDKINATYMWISKDKKYLTIEFQYYSTHSEDKKHFLNLVINNKEADSAAENEDNTDDEYINLEFRHNSERDSPDHLGEGYVSFKLDKIEEQIEGKKGLNIRVRTLYDGIKNYKVQFP	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	242 (231)
Sequences:	365 (312.5)
Seq/Len:	1.580
Nf(neff/√len):	20.6

Jackhmmer Results: (2015_01_07)
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: 1.580).

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
161_L	189_F	3.023	1.00
147_F	204_G	2.285	0.99
107_L	206_V	2.284	0.99
159_H	191_H	2.182	0.99
56_D	79_R	2.098	0.99
79_R	144_T	1.842	0.97
41_I	80_A	1.773	0.96
53_F	82_V	1.638	0.92
152_T	191_H	1.539	0.89
61_M	82_V	1.530	0.89
159_H	196_D	1.517	0.88
56_D	207_S	1.493	0.87
24_S	30_D	1.467	0.86
56_D	127_D	1.456	0.85
144_T	207_S	1.446	0.84
222_G	240_Q	1.430	0.84
5_K	8_F	1.429	0.83
229_T	233_G	1.428	0.83
224_N	238_K	1.420	0.83
42_N	141_K	1.418	0.83
143_L	225_I	1.413	0.83
83_I	101_R	1.412	0.82
124_I	164_V	1.403	0.82
159_H	210_L	1.403	0.82
69_W	72_E	1.400	0.82
38_I	44_I	1.395	0.81
109_K	125_G	1.395	0.81
12_T	129_I	1.393	0.81
56_D	144_T	1.390	0.81
125_G	190_R	1.388	0.81
162_N	208_F	1.365	0.79
79_R	127_D	1.364	0.79
39_S	144_T	1.362	0.79
63_P	82_V	1.324	0.76
115_D	120_T	1.324	0.76
222_G	238_K	1.312	0.76
49_K	189_F	1.310	0.75
166_N	188_E	1.300	0.75
114_M	120_T	1.289	0.74
17_I	22_L	1.286	0.73
74_F	202_G	1.265	0.72
84_F	96_Y	1.257	0.71
5_K	11_L	1.250	0.70
79_R	207_S	1.246	0.70
127_D	193_S	1.232	0.69
24_S	187_L	1.228	0.68
52_Y	60_T	1.228	0.68
129_I	239_V	1.227	0.68
130_N	146_E	1.211	0.67
17_I	158_K	1.189	0.65
145_I	239_V	1.186	0.65
161_L	206_V	1.176	0.64
134_M	225_I	1.174	0.63
51_F	65_N	1.171	0.63
80_A	103_I	1.169	0.63
78_Q	105_K	1.169	0.63
17_I	20_P	1.162	0.62
4_K	10_T	1.156	0.62
14_A	17_I	1.147	0.61
19_L	24_S	1.139	0.60
111_I	187_L	1.135	0.60
22_L	110_E	1.133	0.59
143_L	210_L	1.129	0.59
219_G	241_F	1.123	0.58
193_S	199_D	1.113	0.57
15_I	21_M	1.112	0.57
16_I	24_S	1.101	0.56
109_K	147_F	1.100	0.56
168_K	186_N	1.098	0.56
199_D	225_I	1.097	0.56
205_Y	229_T	1.092	0.55
60_T	225_I	1.090	0.55
145_I	189_F	1.087	0.55
23_Q	160_F	1.087	0.55
158_K	164_V	1.086	0.54
9_I	239_V	1.085	0.54
159_H	190_R	1.080	0.54
97_N	164_V	1.080	0.54
122_E	198_P	1.076	0.53
16_I	47_D	1.072	0.53
18_T	22_L	1.072	0.53
84_F	191_H	1.070	0.53
20_P	23_Q	1.066	0.52
55_L	59_K	1.065	0.52
37_V	205_Y	1.063	0.52
11_L	19_L	1.055	0.51
184_Y	222_G	1.051	0.51
5_K	9_I	1.050	0.51
189_F	206_V	1.048	0.51
132_T	146_E	1.045	0.50
112_V	162_N	1.045	0.50
109_K	204_G	1.044	0.50
27_D	114_M	1.042	0.50
40_T	65_N	1.037	0.49
148_Q	201_L	1.036	0.49
127_D	195_R	1.032	0.49
45_S	189_F	1.031	0.49
226_R	234_I	1.029	0.49
168_K	181_D	1.029	0.49
38_I	45_S	1.029	0.49
100_V	159_H	1.026	0.48
135_W	191_H	1.025	0.48
125_G	163_L	1.025	0.48
109_K	162_N	1.024	0.48
148_Q	203_E	1.022	0.48
141_K	179_N	1.021	0.48
5_K	23_Q	1.020	0.48
227_V	237_Y	1.016	0.47
101_R	149_Y	1.015	0.47
44_I	77_G	1.015	0.47
6_L	21_M	1.014	0.47
76_N	195_R	1.010	0.47
72_E	105_K	1.009	0.46
45_S	51_F	1.007	0.46
50_E	234_I	1.006	0.46
80_A	208_F	1.006	0.46
10_T	15_I	1.001	0.46
125_G	162_N	1.000	0.45

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
4j8qA	1	0.7851	100	0.233	Contact Map
3k6oA	2	0.7893	100	0.246	Contact Map
4pqxA	4	0.8264	100	0.268	Contact Map
3k0yA	1	0.7562	100	0.291	Contact Map
3qwnA	12	0.8058	100	0.315	Contact Map
3nqiA	4	0.7975	99.5	0.733	Contact Map
4fajA	1	0.5744	63	0.933	Contact Map
3ombA	1	0.3512	28.4	0.946	Contact Map
4k3bA	1	0.8306	23.9	0.948	Contact Map
3ucpA	1	0.6736	23.2	0.948	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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