OPENSEQ.org - 1444380618 - GREMLIN Submission

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ID:	1444380618	Query Sequence RQLYYQVLNFGMIVSSALMIWKGLMVITGSESPIVVVLSGSMEPAFHRGDLLFLTNRVEDPIRVGEIVVFRIEGREIPIVHRVLKIHEKQNGHIKFLTKGDNNAVDDRGLYKQGQHWLEKKDVVGRARGFVPYIGIVTILMNDYPKFKYAVLFLLGLFVLVHRE	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	164 (164)
Sequences:	646 (416.3)
Seq/Len:	3.939
Nf(neff/√len):	32.5

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: 3.939).

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
62_I	83_V	3.558	1.00
69_V	80_V	2.700	1.00
46_F	67_I	1.908	1.00
47_H	50_D	1.872	1.00
37_V	52_L	1.693	0.99
40_G	43_E	1.630	0.99
82_R	101_D	1.627	0.99
80_V	127_A	1.619	0.99
2_Q	163_R	1.491	0.97
105_V	109_G	1.457	0.97
40_G	102_N	1.446	0.97
21_W	69_V	1.444	0.97
112_K	115_Q	1.411	0.96
38_L	69_V	1.409	0.96
155_L	160_L	1.402	0.96
49_G	132_P	1.375	0.95
25_M	29_G	1.375	0.95
159_V	163_R	1.370	0.95
154_L	158_F	1.352	0.95
152_L	156_G	1.329	0.94
75_R	85_K	1.324	0.94
68_V	96_F	1.300	0.93
99_K	103_N	1.300	0.93
158_F	161_V	1.300	0.93
157_L	164_E	1.289	0.93
2_Q	6_Q	1.287	0.93
57_R	126_R	1.280	0.92
99_K	106_D	1.274	0.92
108_R	117_W	1.256	0.91
38_L	110_L	1.255	0.91
68_V	152_L	1.247	0.91
66_E	160_L	1.238	0.90
84_L	105_V	1.234	0.90
154_L	162_H	1.234	0.90
115_Q	122_D	1.220	0.90
149_Y	158_F	1.216	0.89
136_I	144_Y	1.210	0.89
96_F	127_A	1.210	0.89
10_F	17_A	1.188	0.88
37_V	125_G	1.186	0.88
44_P	132_P	1.175	0.87
44_P	49_G	1.165	0.87
35_V	78_P	1.161	0.86
132_P	135_G	1.155	0.86
50_D	69_V	1.155	0.86
96_F	123_V	1.150	0.86
69_V	78_P	1.146	0.85
96_F	118_L	1.135	0.85
54_L	69_V	1.135	0.85
43_E	48_R	1.132	0.84
158_F	163_R	1.127	0.84
8_L	150_A	1.117	0.83
154_L	159_V	1.109	0.83
149_Y	156_G	1.107	0.83
68_V	98_T	1.102	0.82
48_R	80_V	1.100	0.82
41_S	81_H	1.097	0.82
45_A	53_F	1.096	0.82
98_T	125_G	1.093	0.81
3_L	163_R	1.085	0.81
81_H	103_N	1.081	0.80
44_P	107_D	1.079	0.80
44_P	99_K	1.069	0.79
39_S	48_R	1.069	0.79
49_G	65_G	1.064	0.79
158_F	162_H	1.062	0.79
155_L	162_H	1.060	0.79
159_V	164_E	1.054	0.78
137_V	142_N	1.054	0.78
43_E	47_H	1.045	0.77
153_F	157_L	1.033	0.76
150_A	156_G	1.031	0.76
82_R	100_G	1.030	0.76
152_L	155_L	1.030	0.76
149_Y	160_L	1.028	0.76
1_R	6_Q	1.026	0.75
37_V	98_T	1.023	0.75
157_L	161_V	1.020	0.75
2_Q	116_H	1.020	0.75
100_G	107_D	1.017	0.74
81_H	99_K	1.015	0.74
78_P	139_I	1.007	0.73
3_L	7_V	1.004	0.73
2_Q	70_F	1.001	0.73

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
4n31A	2	0.6402	99.6	0.61	Contact Map
4me8A	1	0.4085	99.6	0.616	Contact Map
4nv4A	2	0.4085	99.6	0.617	Contact Map
4k8wA	1	0.4939	99.6	0.621	Contact Map
1b12A	4	0.7439	99.5	0.65	Contact Map
1umuA	2	0.6402	98	0.795	Contact Map
1kcaA	8	0.5793	97.8	0.802	Contact Map
2hnfA	1	0.6951	97.5	0.814	Contact Map
1jhfA	2	0.7012	97.5	0.817	Contact Map
3k2zA	2	0.7195	96.6	0.838	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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