OPENSEQ.org - 1452699997 - GREMLIN Submission

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1eq6

ID:	1452699997	Query Sequence SMNNKEVELYGGAITTVVPPGFIDASTLREVPDTQEVYVNSRRDEEEFEDGLATNESIIVDLLETVDKSDLKEAWQFHVEDLTELNGTTKWEALQEDTVQQGTKFTGLVMEVANKWGKPDLAQTVVIGVALIRLTQFDTDVVISINVPLTKEEASQASNKELPARCHAVYQLLQEMVRKFHVVDTSLFA	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	189 (172)
Sequences:	345 (255.9)
Seq/Len:	2.006
Nf(neff/√len):	19.5

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: 2.006).

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
141_V	180_F	2.711	1.00
74_A	131_L	2.580	1.00
132_I	180_F	2.164	1.00
79_V	107_G	2.111	0.99
62_L	139_T	2.106	0.99
9_L	12_G	2.021	0.99
58_I	145_I	1.939	0.99
134_L	139_T	1.870	0.98
182_V	185_T	1.845	0.98
79_V	110_M	1.789	0.97
14_I	187_L	1.767	0.97
137_F	185_T	1.739	0.97
15_T	183_V	1.646	0.95
78_H	131_L	1.640	0.95
182_V	187_L	1.636	0.95
74_A	78_H	1.614	0.94
83_T	107_G	1.571	0.93
57_S	146_N	1.567	0.93
61_D	82_L	1.501	0.91
143_I	180_F	1.471	0.90
66_V	78_H	1.467	0.90
25_A	31_V	1.466	0.90
107_G	110_M	1.456	0.89
61_D	77_F	1.454	0.89
110_M	117_G	1.442	0.89
81_D	85_L	1.388	0.86
110_M	116_W	1.369	0.85
63_L	142_V	1.367	0.85
16_T	179_K	1.351	0.84
78_H	146_N	1.340	0.83
16_T	176_M	1.320	0.82
26_S	29_R	1.303	0.81
82_L	129_V	1.267	0.78
107_G	112_V	1.265	0.78
93_A	100_Q	1.227	0.75
18_V	85_L	1.210	0.74
8_E	15_T	1.207	0.74
18_V	143_I	1.203	0.73
30_E	179_K	1.189	0.72
127_I	131_L	1.180	0.71
130_A	144_S	1.179	0.71
83_T	88_T	1.173	0.70
25_A	39_V	1.159	0.69
10_Y	16_T	1.156	0.69
34_T	64_E	1.156	0.69
88_T	127_I	1.152	0.68
147_V	169_V	1.152	0.68
75_W	107_G	1.151	0.68
141_V	183_V	1.141	0.67
31_V	171_Q	1.138	0.67
37_V	139_T	1.135	0.67
13_A	184_D	1.133	0.67
180_F	183_V	1.123	0.66
140_D	146_N	1.114	0.65
64_E	136_Q	1.112	0.64
172_L	176_M	1.112	0.64
74_A	133_R	1.109	0.64
12_G	24_D	1.105	0.64
79_V	105_F	1.099	0.63
84_E	93_A	1.094	0.63
129_V	170_Y	1.090	0.62
95_Q	171_Q	1.088	0.62
105_F	110_M	1.085	0.62
123_Q	151_K	1.085	0.62
11_G	24_D	1.084	0.62
86_N	144_S	1.061	0.59
134_L	185_T	1.059	0.59
125_V	173_L	1.056	0.59
14_I	182_V	1.056	0.59
83_T	86_N	1.051	0.58
60_V	143_I	1.048	0.58
110_M	127_I	1.046	0.57
141_V	174_Q	1.044	0.57
28_L	88_T	1.039	0.57
141_V	182_V	1.036	0.56
7_V	42_R	1.034	0.56
16_T	28_L	1.025	0.55
55_N	173_L	1.024	0.55
73_E	76_Q	1.023	0.55
9_L	13_A	1.022	0.55
100_Q	129_V	1.017	0.54
7_V	38_Y	1.013	0.54
76_Q	142_V	1.010	0.53
31_V	146_N	1.009	0.53
175_E	178_R	1.007	0.53
108_L	163_P	1.004	0.53

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
1eq6A	1	0.9894	100	0.082	Contact Map
3gioA	2	0.4233	9.4	0.956	Contact Map
2wcrA	2	0.418	8.2	0.957	Contact Map
1j98A	1	0.381	4.7	0.962	Contact Map
2mrnA	2	0.2698	4.6	0.962	Contact Map
2lt4A	1	0.1905	4.6	0.962	Contact Map
1wxaA	1	0.2963	4.5	0.962	Contact Map
4elnA	1	0.3545	4	0.963	Contact Map
1k8rB	1	0.2169	3.4	0.964	Contact Map
3lydA	2	0.8042	3.2	0.965	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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