OPENSEQ.org - 1444166045 - GREMLIN Submission

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rbpms2

ID:	1444166045	Query Sequence MSNLKPDGEHGGSTGTGSGAGSGGALEEEVRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTARQPVGFVIFDSRAGAEAAKNALNGIRFDPENPQTLRLEFAKANTKMAKSKLMATPNPSNVHPALGAHFIARDPYDLMGAALIPASPEAWAPYPLYTTELTPAISHAAFTYPTATAAAAALHAQVRWYPSSDTTQQGWKYRQFC	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	209 (187)
Sequences:	326 (235.3)
Seq/Len:	1.743
Nf(neff/√len):	17.2

HHblits Results: (2015_06)
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: 1.743).

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
84_A	88_L	2.200	0.99
69_P	179_A	2.126	0.99
23_G	26_L	1.851	0.97
38_L	46_E	1.829	0.97
201_Q	205_Y	1.782	0.96
51_F	73_V	1.656	0.94
55_K	156_A	1.529	0.90
35_V	101_L	1.529	0.90
51_F	84_A	1.524	0.90
36_S	70_V	1.502	0.89
35_V	51_F	1.460	0.87
69_P	81_A	1.435	0.86
57_Y	73_V	1.412	0.85
84_A	103_L	1.379	0.83
36_S	136_A	1.372	0.82
147_L	184_A	1.364	0.82
134_F	180_T	1.363	0.82
46_E	94_D	1.354	0.81
51_F	75_F	1.352	0.81
44_P	60_S	1.349	0.81
36_S	106_A	1.321	0.79
22_S	25_A	1.307	0.78
50_L	75_F	1.290	0.76
65_T	143_M	1.281	0.76
62_I	67_R	1.278	0.76
36_S	102_R	1.253	0.74
37_G	90_G	1.251	0.73
56_G	60_S	1.246	0.73
34_F	70_V	1.215	0.70
103_L	113_A	1.208	0.70
30_V	65_T	1.206	0.69
147_L	190_V	1.205	0.69
72_F	186_L	1.204	0.69
33_L	117_L	1.191	0.68
175_T	179_A	1.188	0.68
77_S	80_G	1.179	0.67
99_Q	102_R	1.174	0.66
63_K	75_F	1.172	0.66
93_F	100_T	1.164	0.65
107_K	114_K	1.161	0.65
58_E	103_L	1.152	0.64
77_S	83_A	1.147	0.64
195_S	202_G	1.136	0.63
191_R	194_P	1.134	0.62
38_L	71_G	1.129	0.62
22_S	26_L	1.128	0.62
202_G	206_R	1.125	0.62
47_L	204_K	1.120	0.61
117_L	179_A	1.116	0.61
34_F	71_G	1.113	0.60
36_S	111_K	1.109	0.60
199_T	204_K	1.107	0.60
43_K	149_P	1.102	0.59
33_L	133_H	1.100	0.59
62_I	103_L	1.091	0.58
202_G	208_F	1.089	0.58
35_V	42_I	1.088	0.58
62_I	119_A	1.087	0.58
198_T	202_G	1.082	0.57
196_S	209_C	1.081	0.57
75_F	87_A	1.079	0.57
191_R	199_T	1.076	0.56
43_K	73_V	1.076	0.56
48_Y	184_A	1.074	0.56
168_A	179_A	1.074	0.56
204_K	207_Q	1.073	0.56
39_P	43_K	1.070	0.56
42_I	47_L	1.068	0.56
38_L	152_P	1.067	0.55
135_I	138_D	1.066	0.55
72_F	81_A	1.066	0.55
152_P	188_A	1.065	0.55
39_P	133_H	1.064	0.55
168_A	186_L	1.061	0.55
37_G	123_P	1.061	0.55
85_K	157_P	1.060	0.55
92_R	99_Q	1.058	0.55
178_T	181_A	1.057	0.54
83_A	142_L	1.056	0.54
202_G	205_Y	1.055	0.54
151_S	154_A	1.054	0.54
200_Q	205_Y	1.048	0.53
27_E	38_L	1.044	0.53
66_A	99_Q	1.043	0.53
37_G	51_F	1.038	0.52
125_N	141_D	1.037	0.52
201_Q	204_K	1.037	0.52
38_L	194_P	1.033	0.52
73_V	82_E	1.031	0.52
101_L	109_N	1.029	0.51
60_S	181_A	1.025	0.51
109_N	112_M	1.025	0.51
198_T	204_K	1.023	0.51
198_T	201_Q	1.022	0.51
99_Q	181_A	1.020	0.50
93_F	123_P	1.020	0.50
67_R	115_S	1.019	0.50
84_A	109_N	1.016	0.50
45_R	133_H	1.016	0.50
111_K	184_A	1.013	0.50
183_A	192_W	1.012	0.50
196_S	204_K	1.012	0.50
142_L	203_W	1.012	0.50
75_F	84_A	1.007	0.49
117_L	184_A	1.007	0.49
39_P	69_P	1.007	0.49
88_L	198_T	1.006	0.49

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: (06Aug15)
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
2qfjA	2	0.8469	100	0.404	Contact Map
1l3kA	1	0.7368	100	0.432	Contact Map
3md3A	1	0.7464	100	0.432	Contact Map
2mkhA	1	0.8947	100	0.437	Contact Map
2yh0A	1	0.799	100	0.439	Contact Map
2cjkA	1	0.7416	100	0.442	Contact Map
4pkdB	1	0.8278	100	0.442	Contact Map
3vajA	2	0.7512	100	0.446	Contact Map
4qptA	1	0	100	0.447	Contact Map
4f02A	2	0.7416	100	0.448	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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