OPENSEQ.org - 1402427684 - GREMLIN Submission

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T0812

ID:	1402427684	Query Sequence SEAKGLIRTWVTLKAEQTILPLVDEALQHTTTKGIVFQHPEIVAHMDLMREDLHLEPFYWKLPEQFEGKKLMAYGGKLKYAIYFEAREETGFSTYNPQVIIRGGTPTHARIIVRHMAAPLIGQLTRHEIEMTEKEWKYYGDDPRVHRTVTREDFLDILYDIHYILIKATYGNFMRQSRISEISMEVAEQGRGTTMTPPADLIEK	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	204 (194)
Sequences:	483 (277.2)
Seq/Len:	2.490
Nf(neff/√len):	19.9

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: 2.490).

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
101_I	161_I	3.622	1.00
179_I	182_I	2.537	1.00
199_A	202_I	2.083	1.00
76_G	185_E	1.909	0.99
73_A	186_V	1.891	0.99
80_Y	98_Q	1.884	0.99
62_L	66_F	1.827	0.99
76_G	80_Y	1.737	0.98
79_K	128_E	1.696	0.97
62_L	136_W	1.652	0.97
43_V	46_M	1.651	0.97
152_E	156_D	1.606	0.96
67_E	161_I	1.600	0.96
196_T	200_D	1.557	0.95
24_D	28_Q	1.518	0.94
76_G	151_R	1.515	0.94
94_T	167_K	1.465	0.93
104_G	159_Y	1.453	0.92
101_I	193_T	1.452	0.92
98_Q	167_K	1.372	0.89
77_K	130_E	1.368	0.89
20_L	24_D	1.345	0.88
127_H	169_T	1.345	0.88
101_I	129_I	1.342	0.88
169_T	177_S	1.334	0.87
99_V	182_I	1.305	0.86
101_I	117_A	1.303	0.86
76_G	84_F	1.300	0.86
62_L	164_I	1.284	0.85
104_G	154_F	1.281	0.84
118_A	125_T	1.265	0.83
138_Y	153_D	1.260	0.83
42_I	45_H	1.257	0.83
75_G	80_Y	1.247	0.82
188_E	192_G	1.240	0.82
78_L	184_M	1.240	0.82
16_E	19_I	1.228	0.81
111_I	154_F	1.212	0.80
76_G	149_V	1.208	0.79
38_Q	45_H	1.202	0.79
78_L	182_I	1.192	0.78
14_K	17_Q	1.192	0.78
7_I	10_W	1.186	0.78
69_K	131_M	1.181	0.77
19_I	24_D	1.181	0.77
197_P	200_D	1.175	0.77
131_M	184_M	1.171	0.76
70_K	179_I	1.164	0.76
166_I	170_Y	1.159	0.75
60_W	138_Y	1.151	0.75
159_Y	164_I	1.150	0.74
156_D	159_Y	1.149	0.74
71_L	184_M	1.145	0.74
78_L	99_V	1.135	0.73
135_E	154_F	1.133	0.73
22_L	169_T	1.131	0.73
11_V	19_I	1.123	0.72
157_I	185_E	1.122	0.72
6_L	11_V	1.116	0.71
77_K	128_E	1.107	0.70
132_T	136_W	1.105	0.70
90_T	101_I	1.098	0.70
60_W	136_W	1.098	0.70
138_Y	149_V	1.097	0.69
196_T	199_A	1.095	0.69
117_A	162_H	1.095	0.69
96_N	101_I	1.091	0.69
113_V	176_Q	1.091	0.69
101_I	196_T	1.090	0.69
129_I	192_G	1.077	0.67
113_V	156_D	1.073	0.67
9_T	14_K	1.065	0.66
59_Y	178_R	1.064	0.66
58_F	105_T	1.061	0.66
105_T	160_D	1.059	0.65
46_M	50_R	1.059	0.65
24_D	27_L	1.058	0.65
66_F	163_Y	1.051	0.65
62_L	179_I	1.046	0.64
129_I	136_W	1.039	0.63
97_P	152_E	1.037	0.63
80_Y	97_P	1.036	0.63
150_T	153_D	1.035	0.63
99_V	183_S	1.034	0.63
71_L	151_R	1.033	0.63
18_T	25_E	1.032	0.63
15_A	18_T	1.030	0.62
97_P	166_I	1.024	0.62
117_A	161_I	1.023	0.62
93_S	103_G	1.021	0.61
151_R	155_L	1.018	0.61
80_Y	152_E	1.016	0.61
98_Q	170_Y	1.016	0.61
154_F	157_I	1.015	0.61
111_I	149_V	1.012	0.60
121_I	170_Y	1.010	0.60
61_K	69_K	1.008	0.60
62_L	151_R	1.006	0.60
21_P	30_T	1.004	0.59
69_K	75_G	1.001	0.59
136_W	149_V	1.001	0.59

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: (07Jun14)
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
1fjjA	1	0.652	5.6	0.959	Contact Map
2d7nA	1	0.3627	4.8	0.96	Contact Map
2dn7A	1	0.5	4.2	0.961	Contact Map
4hwbA	1	0.4706	3.6	0.963	Contact Map
1x5lA	1	0.5098	3.2	0.963	Contact Map
3n08A	2	0.6078	2.7	0.965	Contact Map
4goqA	5	0.1814	2.5	0.966	Contact Map
1owwA	1	0.402	2.4	0.966	Contact Map
1eerB	2	0.6373	2.3	0.966	Contact Map
2djsA	1	0.4853	2.2	0.966	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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