OPENSEQ.org - 1492603611 - GREMLIN Submission

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2x6u

ID:	1492603611	Query Sequence GAMEGIKVFLHERELWLKFHEVGTEMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKWSVTGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQ	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	203 (194)
Sequences:	708 (482)
Seq/Len:	3.649
Nf(neff/√len):	34.6

HHblits Results: (2016_02)
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: 3.649).

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
13_R	17_L	2.402	1.00
29_T	32_G	2.275	1.00
26_M	29_T	2.157	1.00
178_K	182_N	2.156	1.00
175_T	179_I	2.091	1.00
26_M	32_G	2.089	1.00
182_N	185_A	2.071	1.00
179_I	188_F	1.910	1.00
136_H	155_T	1.895	1.00
26_M	30_K	1.854	1.00
185_A	188_F	1.829	0.99
8_V	43_V	1.780	0.99
50_T	139_K	1.757	0.99
64_H	67_K	1.757	0.99
25_E	32_G	1.754	0.99
27_I	30_K	1.703	0.99
125_L	165_A	1.652	0.99
43_V	54_L	1.624	0.98
16_W	26_M	1.613	0.98
178_K	185_A	1.583	0.98
182_N	186_K	1.575	0.98
97_G	101_M	1.572	0.98
174_I	178_K	1.529	0.97
54_L	135_L	1.528	0.97
179_I	183_P	1.487	0.97
129_H	133_P	1.454	0.96
56_M	110_L	1.446	0.96
117_L	122_H	1.438	0.96
127_S	167_T	1.435	0.96
192_D	195_E	1.423	0.96
175_T	188_F	1.416	0.95
177_L	183_P	1.383	0.95
16_W	25_E	1.372	0.94
95_A	100_W	1.367	0.94
37_P	52_Y	1.363	0.94
19_F	30_K	1.362	0.94
55_L	138_V	1.359	0.94
62_D	66_Y	1.355	0.94
39_Y	135_L	1.340	0.93
175_T	186_K	1.333	0.93
19_F	29_T	1.333	0.93
179_I	185_A	1.318	0.93
184_F	188_F	1.306	0.92
15_L	25_E	1.282	0.91
24_T	32_G	1.281	0.91
183_P	186_K	1.270	0.91
15_L	19_F	1.259	0.90
179_I	184_F	1.254	0.90
19_F	24_T	1.247	0.90
179_I	182_N	1.230	0.89
24_T	28_I	1.229	0.89
90_H	107_F	1.227	0.89
118_D	121_G	1.226	0.89
15_L	24_T	1.226	0.89
57_D	134_R	1.224	0.89
179_I	186_K	1.223	0.88
27_I	32_G	1.213	0.88
111_K	114_N	1.205	0.88
39_Y	68_F	1.200	0.87
19_F	26_M	1.199	0.87
68_F	73_W	1.198	0.87
175_T	184_F	1.181	0.86
166_V	169_Y	1.176	0.86
178_K	184_F	1.168	0.85
15_L	29_T	1.164	0.85
128_M	168_S	1.154	0.84
183_P	188_F	1.149	0.84
193_D	196_L	1.141	0.83
166_V	170_Q	1.139	0.83
167_T	170_Q	1.137	0.83
17_L	21_E	1.136	0.83
130_K	164_I	1.129	0.82
177_L	188_F	1.122	0.82
41_V	135_L	1.121	0.82
15_L	32_G	1.120	0.82
24_T	29_T	1.119	0.82
175_T	185_A	1.108	0.81
19_F	32_G	1.104	0.80
25_E	29_T	1.102	0.80
16_W	32_G	1.098	0.80
57_D	136_H	1.093	0.80
161_T	166_V	1.085	0.79
9_F	42_K	1.084	0.79
25_E	28_I	1.080	0.78
118_D	122_H	1.079	0.78
182_N	188_F	1.077	0.78
33_R	36_F	1.066	0.77
18_K	21_E	1.064	0.77
34_R	37_P	1.064	0.77
52_Y	62_D	1.063	0.77
40_K	51_K	1.060	0.77
178_K	186_K	1.051	0.76
177_L	182_N	1.044	0.75
114_N	167_T	1.032	0.74
182_N	189_R	1.030	0.74
95_A	99_H	1.016	0.72
45_G	52_Y	1.016	0.72
33_R	37_P	1.016	0.72
90_H	93_S	1.012	0.72
46_L	52_Y	1.011	0.72
175_T	182_N	1.009	0.71
43_V	137_I	1.006	0.71
37_P	46_L	1.004	0.71
177_L	185_A	1.004	0.71
25_E	30_K	1.003	0.71
115_N	128_M	1.002	0.71

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
2x6uA	1	0.867	100	-0.011	Contact Map
1h6fA	2	0.9163	100	0.024	Contact Map
4a04A	2	0.9212	100	0.042	Contact Map
1xbrA	2	0.9064	100	0.046	Contact Map
4hwbA	1	0.3842	14.6	0.959	Contact Map
2xn2A	1	0.4483	11.2	0.961	Contact Map
2nqaA	2	0.5419	10.8	0.961	Contact Map
3mi6A	4	0.4877	9.1	0.963	Contact Map
3n06B	1	0.3941	8.5	0.963	Contact Map
1uemA	1	0.3498	7.5	0.964	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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