OPENSEQ.org - 1408008072 - GREMLIN Submission

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Mad2

ID:	1408008072	Query Sequence MALQLSREQGITLRGSAEIVAEFFSFGINSILYQRGIYPSETFTRVQKYGLTLLVTTDLELIKYLNNVVEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSAPREKSQKAIQDEIRSVIRQITATVTFLPLLEVSCSFDLLIYTDKDLVVPEKWEESGPQFITNSEEVRLRSFTTTIHKVNSMVAYKIPVND	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	205 (202)
Sequences:	274 (194.9)
Seq/Len:	1.356
Nf(neff/√len):	13.7

HHblits Results: (2013_03)
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: 1.356).

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
32_L	35_R	1.823	0.95
100_W	133_R	1.709	0.92
99_R	156_Y	1.706	0.92
35_R	38_Y	1.652	0.91
49_Y	164_P	1.576	0.88
137_A	193_V	1.517	0.85
100_W	134_Q	1.505	0.84
149_C	183_L	1.499	0.84
24_F	51_L	1.470	0.82
150_S	153_L	1.432	0.80
128_I	134_Q	1.432	0.80
35_R	43_F	1.432	0.80
56_T	155_I	1.404	0.78
98_E	102_F	1.389	0.77
11_I	18_E	1.363	0.75
19_I	192_K	1.363	0.75
17_A	61_L	1.362	0.75
5_L	8_E	1.338	0.73
61_L	81_V	1.335	0.73
131_V	147_V	1.328	0.73
8_E	201_I	1.314	0.71
3_L	7_R	1.314	0.71
71_Q	75_W	1.313	0.71
32_L	38_Y	1.311	0.71
20_V	156_Y	1.308	0.71
11_I	76_L	1.295	0.70
51_L	100_W	1.281	0.69
56_T	72_L	1.275	0.68
56_T	62_I	1.272	0.68
7_R	94_G	1.271	0.68
119_K	124_I	1.265	0.67
68_V	81_V	1.257	0.67
31_I	35_R	1.256	0.66
35_R	164_P	1.253	0.66
17_A	86_V	1.240	0.65
26_F	53_L	1.235	0.65
10_G	201_I	1.230	0.64
49_Y	52_T	1.215	0.63
9_Q	12_T	1.210	0.62
21_A	61_L	1.208	0.62
65_L	144_L	1.205	0.62
85_V	99_R	1.201	0.61
100_W	138_T	1.201	0.61
125_Q	129_R	1.188	0.60
37_I	132_I	1.181	0.59
142_L	197_V	1.178	0.59
150_S	155_I	1.173	0.59
61_L	65_L	1.165	0.58
28_I	81_V	1.160	0.57
56_T	61_L	1.155	0.57
159_K	172_P	1.153	0.57
128_I	188_T	1.151	0.56
5_L	9_Q	1.144	0.56
164_P	188_T	1.139	0.55
97_L	122_K	1.138	0.55
60_E	64_Y	1.138	0.55
100_W	139_V	1.137	0.55
64_Y	169_E	1.135	0.55
128_I	191_H	1.132	0.55
35_R	98_E	1.128	0.54
122_K	184_R	1.127	0.54
61_L	92_E	1.125	0.54
170_S	193_V	1.123	0.54
75_W	135_I	1.122	0.54
132_I	136_T	1.117	0.53
76_L	200_K	1.117	0.53
76_L	85_V	1.117	0.53
141_F	163_V	1.114	0.53
36_G	40_S	1.111	0.52
101_Q	155_I	1.108	0.52
75_W	156_Y	1.104	0.52
186_F	191_H	1.102	0.52
4_Q	8_E	1.098	0.51
119_K	127_E	1.097	0.51
24_F	84_L	1.088	0.50
29_N	61_L	1.084	0.50
24_F	56_T	1.077	0.49
28_I	104_I	1.073	0.49
47_Q	174_F	1.069	0.48
69_V	201_I	1.068	0.48
23_F	195_S	1.068	0.48
11_I	15_G	1.067	0.48
50_G	183_L	1.066	0.48
3_L	6_S	1.060	0.47
37_I	77_Y	1.056	0.47
31_I	38_Y	1.050	0.46
100_W	143_P	1.049	0.46
184_R	188_T	1.047	0.46
28_I	126_D	1.046	0.46
35_R	39_P	1.046	0.46
17_A	26_F	1.045	0.46
128_I	133_R	1.045	0.46
27_G	131_V	1.043	0.46
35_R	142_L	1.042	0.46
64_Y	68_V	1.042	0.46
15_G	24_F	1.038	0.45
128_I	131_V	1.038	0.45
2_A	6_S	1.037	0.45
164_P	197_V	1.035	0.45
51_L	185_S	1.035	0.45
4_Q	7_R	1.035	0.45
167_W	181_V	1.032	0.45
33_Y	179_E	1.031	0.44
23_F	170_S	1.026	0.44
84_L	136_T	1.022	0.44
33_Y	38_Y	1.020	0.43
56_T	132_I	1.019	0.43
73_K	77_Y	1.019	0.43
3_L	74_D	1.014	0.43
36_G	133_R	1.003	0.42
77_Y	120_S	1.002	0.42
135_I	185_S	1.001	0.41
134_Q	143_P	1.000	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: (17Jul14)
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	0.168	Contact Map
4aezB	3	0.9268	100	0.176	Contact Map
3abdA	2	0.9024	100	0.287	Contact Map
4j2gA	2	0.7366	92.7	0.917	Contact Map
2qyfB	2	0.7659	50.9	0.945	Contact Map
2iojA	2	0.3707	6.1	0.965	Contact Map
2qasA	1	0.4537	4.8	0.967	Contact Map
4k7cA	1	0.678	4.4	0.967	Contact Map
1y96B	2	0.3805	4.3	0.967	Contact Map
4c1lA	2	0.5659	3.5	0.969	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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