OPENSEQ.org - 1400766814 - GREMLIN Submission

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MAD2

ID:	1400766814	Query Sequence MALQLSREQGITLRGSAEIVAEFFSFGINSILYQRGIYPSETFTRVQKYGLTLLVTTDLELIKYLNNVVEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSAPREKSQKAIQDEIRSVIRQITATVTFLPLLEVSCSFDLLIYTDKDLVVPEKWEESGPQFITNSEEVRLRSFTTTIHKVNSMVAYKIPVND	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	205 (200)
Sequences:	664 (504.4)
Seq/Len:	3.320
Nf(neff/√len):	35.7

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: 3.320).

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
164_P	167_W	3.314	1.00
76_L	104_I	2.319	1.00
35_R	98_E	2.231	1.00
35_R	142_L	2.027	1.00
98_E	102_F	1.973	1.00
32_L	43_F	1.913	1.00
100_W	138_T	1.777	0.99
56_T	62_I	1.769	0.99
74_D	78_K	1.663	0.98
61_L	64_Y	1.654	0.98
72_L	81_V	1.643	0.98
32_L	38_Y	1.640	0.98
167_W	170_S	1.593	0.98
38_Y	153_L	1.534	0.97
29_N	56_T	1.532	0.97
110_A	114_S	1.488	0.96
128_I	134_Q	1.452	0.95
3_L	37_I	1.445	0.95
75_W	157_T	1.402	0.94
68_V	81_V	1.399	0.94
124_I	131_V	1.396	0.94
28_I	86_V	1.369	0.93
72_L	194_N	1.350	0.93
100_W	139_V	1.348	0.93
16_S	191_H	1.310	0.91
38_Y	43_F	1.264	0.89
111_K	114_S	1.259	0.89
22_E	49_Y	1.256	0.89
56_T	155_I	1.253	0.88
22_E	29_N	1.252	0.88
27_G	102_F	1.247	0.88
56_T	72_L	1.238	0.88
38_Y	151_F	1.232	0.87
23_F	181_V	1.226	0.87
4_Q	7_R	1.220	0.87
31_I	88_I	1.218	0.86
5_L	8_E	1.216	0.86
111_K	115_A	1.214	0.86
35_R	102_F	1.204	0.86
21_A	73_K	1.198	0.85
77_Y	120_S	1.193	0.85
71_Q	75_W	1.192	0.85
47_Q	50_G	1.191	0.85
136_T	184_R	1.189	0.85
28_I	65_L	1.188	0.85
92_E	147_V	1.179	0.84
24_F	104_I	1.178	0.84
3_L	6_S	1.177	0.84
38_Y	64_Y	1.176	0.84
35_R	145_L	1.158	0.82
96_V	100_W	1.155	0.82
21_A	153_L	1.148	0.82
20_V	188_T	1.143	0.81
143_P	199_Y	1.138	0.81
99_R	102_F	1.136	0.81
119_K	127_E	1.135	0.81
158_D	162_V	1.134	0.81
75_W	191_H	1.128	0.80
29_N	38_Y	1.128	0.80
165_E	168_E	1.122	0.80
37_I	149_C	1.116	0.79
164_P	170_S	1.115	0.79
107_D	110_A	1.113	0.79
55_V	59_L	1.106	0.78
69_V	149_C	1.097	0.77
98_E	145_L	1.095	0.77
117_R	160_D	1.092	0.77
102_F	145_L	1.091	0.77
16_S	35_R	1.088	0.77
101_Q	171_G	1.081	0.76
46_V	186_F	1.080	0.76
53_L	132_I	1.080	0.76
5_L	9_Q	1.080	0.76
110_A	116_P	1.080	0.76
112_D	116_P	1.079	0.76
21_A	77_Y	1.076	0.76
160_D	163_V	1.073	0.75
20_V	191_H	1.069	0.75
68_V	153_L	1.069	0.75
50_G	54_L	1.069	0.75
26_F	128_I	1.067	0.75
188_T	191_H	1.062	0.74
134_Q	138_T	1.058	0.74
17_A	155_I	1.050	0.73
137_A	141_F	1.049	0.73
108_K	113_D	1.049	0.73
85_V	156_Y	1.042	0.72
26_F	139_V	1.039	0.72
88_I	142_L	1.036	0.72
46_V	134_Q	1.033	0.71
19_I	22_E	1.033	0.71
127_E	143_P	1.032	0.71
73_K	87_V	1.030	0.71
160_D	170_S	1.029	0.71
67_N	153_L	1.026	0.71
133_R	170_S	1.023	0.70
120_S	123_A	1.015	0.69
187_T	199_Y	1.014	0.69
72_L	127_E	1.012	0.69
113_D	116_P	1.006	0.68
131_V	139_V	1.005	0.68
97_L	145_L	1.005	0.68

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: (10May14)
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
2vfxA	12	1	100	0.116	Contact Map
4aezB	3	0.9268	100	0.145	Contact Map
3abdA	2	0.9073	100	0.199	Contact Map
4j2gA	2	0.7463	84.4	0.907	Contact Map
2qyfB	2	0.7756	71.8	0.917	Contact Map
2jp7A	1	0.2244	5.7	0.954	Contact Map
3rpjA	2	0.6	4.2	0.957	Contact Map
3kh1A	2	0.3902	3.4	0.959	Contact Map
1iycA	1	0.1756	2.8	0.96	Contact Map
1j2pA	7	0.3512	2.8	0.96	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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