OPENSEQ.org - 1398962858 - GREMLIN Submission

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T0760

ID:	1398962858	Query Sequence MYMKKLKFITLTLAIIITLPMLQSCLDDNDHQSRSLVISTINQISEDSKEFYFTLDNGKTMFPSNSQAWGGEKFENGQRAFVIFNELEQPVNGYDYNIQVRDITKVLTKEIVTMDDEENTEEKIGDDKINATYMWISKDKKYLTIEFQYYSTHSEDKKHFLNLVINNKEADSAAENEDNTDDEYINLEFRHNSERDSPDHLGEGYVSFKLDKIEEQIEGKKGLNIRVRTLYDGIKNYKVQFP	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	242 (233)
Sequences:	364 (317.8)
Seq/Len:	1.562
Nf(neff/√len):	20.8

Jackhmmer Results: (2014_04_16)
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: 1.562).

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
159_H	191_H	2.693	1.00
147_F	204_G	2.400	1.00
107_L	206_V	2.170	0.99
79_R	144_T	2.105	0.99
159_H	196_D	2.083	0.99
79_R	207_S	1.946	0.98
18_T	22_L	1.818	0.96
41_I	80_A	1.761	0.95
53_F	82_V	1.759	0.95
144_T	207_S	1.734	0.95
56_D	79_R	1.689	0.94
191_H	196_D	1.648	0.93
222_G	240_Q	1.634	0.92
5_K	8_F	1.601	0.91
162_N	208_F	1.598	0.91
58_G	187_L	1.584	0.90
143_L	210_L	1.582	0.90
69_W	72_E	1.577	0.90
134_M	225_I	1.494	0.87
42_N	141_K	1.487	0.86
129_I	239_V	1.454	0.85
109_K	125_G	1.399	0.81
55_L	59_K	1.398	0.81
229_T	233_G	1.359	0.79
11_L	19_L	1.355	0.78
205_Y	229_T	1.332	0.77
7_K	17_I	1.331	0.77
145_I	186_N	1.325	0.76
109_K	162_N	1.323	0.76
222_G	238_K	1.312	0.75
128_K	191_H	1.311	0.75
124_I	164_V	1.303	0.75
75_E	95_D	1.297	0.74
5_K	11_L	1.284	0.73
60_T	225_I	1.279	0.73
5_K	9_I	1.277	0.72
125_G	190_R	1.272	0.72
56_D	127_D	1.265	0.71
132_T	231_Y	1.264	0.71
27_D	32_Q	1.262	0.71
43_Q	84_F	1.254	0.70
56_D	144_T	1.241	0.69
52_Y	60_T	1.241	0.69
23_Q	184_Y	1.235	0.69
189_F	206_V	1.229	0.68
72_E	105_K	1.227	0.68
6_L	18_T	1.227	0.68
43_Q	53_F	1.224	0.68
17_I	22_L	1.221	0.67
49_K	61_M	1.220	0.67
38_I	44_I	1.209	0.66
224_N	238_K	1.205	0.66
39_S	55_L	1.196	0.65
125_G	188_E	1.187	0.64
11_L	15_I	1.183	0.64
84_F	198_P	1.168	0.62
151_S	191_H	1.161	0.62
184_Y	222_G	1.160	0.62
39_S	144_T	1.155	0.61
19_L	156_D	1.152	0.61
5_K	24_S	1.146	0.60
184_Y	221_K	1.144	0.60
29_N	95_D	1.143	0.60
54_T	213_I	1.139	0.60
33_S	52_Y	1.132	0.59
83_I	101_R	1.129	0.59
33_S	89_Q	1.125	0.58
159_H	210_L	1.124	0.58
78_Q	105_K	1.115	0.57
77_G	209_K	1.112	0.57
166_N	186_N	1.112	0.57
5_K	23_Q	1.112	0.57
125_G	163_L	1.108	0.56
63_P	196_D	1.103	0.56
148_Q	203_E	1.097	0.55
111_I	189_F	1.094	0.55
46_E	129_I	1.086	0.54
6_L	12_T	1.084	0.54
130_N	146_E	1.080	0.54
129_I	220_K	1.075	0.53
40_T	168_K	1.071	0.53
193_S	196_D	1.071	0.53
46_E	222_G	1.070	0.52
11_L	14_A	1.062	0.52
147_F	208_F	1.061	0.52
145_I	189_F	1.061	0.52
226_R	234_I	1.061	0.52
163_L	202_G	1.060	0.51
81_F	163_L	1.059	0.51
32_Q	48_S	1.058	0.51
192_N	196_D	1.057	0.51
14_A	17_I	1.052	0.51
143_L	196_D	1.050	0.50
51_F	65_N	1.048	0.50
55_L	61_M	1.046	0.50
160_F	189_F	1.044	0.50
143_L	225_I	1.042	0.50
31_H	35_S	1.041	0.49
30_D	34_R	1.036	0.49
136_I	189_F	1.035	0.49
26_L	31_H	1.035	0.49
61_M	82_V	1.032	0.49
31_H	34_R	1.028	0.48
77_G	80_A	1.025	0.48
66_S	210_L	1.024	0.48
15_I	21_M	1.021	0.47
125_G	192_N	1.019	0.47
4_K	8_F	1.019	0.47
24_S	149_Y	1.017	0.47
49_K	189_F	1.016	0.47
77_G	222_G	1.016	0.47
79_R	127_D	1.013	0.47
227_V	237_Y	1.010	0.46
159_H	190_R	1.006	0.46
114_M	164_V	1.003	0.45
9_I	239_V	1.002	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: (17Apr14)
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	0.7934	100	0.284	Contact Map
3k6oA	2	0.7851	100	0.308	Contact Map
3k0yA	1	0.7562	100	0.325	Contact Map
3qwnA	12	0.8099	100	0.36	Contact Map
3nqiA	4	0.7975	99.9	0.603	Contact Map
4lmhA	4	0.6157	22.8	0.944	Contact Map
3p24A	4	0.6983	13.5	0.949	Contact Map
1d4m1	1	0.186	12.8	0.95	Contact Map
4bbwA	1	0.7934	10.6	0.952	Contact Map
4k3bA	1	0.8223	7.2	0.955	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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