OPENSEQ.org - 1496201779 - GREMLIN Submission

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LH32

ID:	1496201779	Query Sequence VNPEKLLVITVATAETEGYLRFLRSAEFFNYTVRTLGLGEEWRGGDVARTVGGGQKVRWLKKEMEKYADREDMIIMFVDSYDVILAGSPTELLKKFVQSGSRLLFSAESFCWPEWGLAEQYPEVGTGKRFLNSGGFIGFATTIHQIVRQWKYKDDDDDQLFYTRLYLDPGLREKLSLNLDHKSRIFQNLNGALDEVVLKFDRNRVRIRNVAYDTLPIVVHGNGPTKLQLNYLG	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	233 (232)
Sequences:	457 (317.1)
Seq/Len:	1.970
Nf(neff/√len):	20.8

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: 1.970).

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
96_F	139_F	2.951	1.00
103_L	146_I	2.452	1.00
102_R	142_T	2.238	1.00
82_D	158_D	1.975	0.99
12_A	81_Y	1.928	0.99
9_I	36_L	1.885	0.98
6_L	89_P	1.820	0.98
166_Y	181_H	1.688	0.96
206_R	215_L	1.666	0.95
102_R	139_F	1.665	0.95
82_D	134_G	1.658	0.95
205_V	212_Y	1.648	0.95
79_D	132_N	1.619	0.94
108_E	188_N	1.603	0.94
74_I	96_F	1.550	0.93
134_G	158_D	1.534	0.92
208_R	215_L	1.500	0.91
76_M	218_V	1.484	0.90
145_Q	175_L	1.448	0.89
79_D	134_G	1.440	0.88
142_T	176_S	1.436	0.88
133_S	159_Q	1.412	0.87
228_Q	231_Y	1.403	0.87
112_W	132_N	1.369	0.85
84_I	233_G	1.363	0.84
113_P	159_Q	1.355	0.84
79_D	82_D	1.349	0.84
200_F	214_T	1.323	0.82
101_S	178_N	1.320	0.82
205_V	210_V	1.306	0.81
6_L	76_M	1.297	0.80
19_Y	35_T	1.294	0.80
201_D	206_R	1.291	0.80
127_G	212_Y	1.284	0.79
146_I	177_L	1.283	0.79
204_R	215_L	1.273	0.78
229_L	233_G	1.270	0.78
102_R	176_S	1.252	0.77
56_K	133_S	1.250	0.77
163_T	188_N	1.249	0.77
31_Y	92_L	1.247	0.76
215_L	231_Y	1.244	0.76
205_V	228_Q	1.240	0.76
205_V	231_Y	1.235	0.75
74_I	93_L	1.217	0.74
199_K	208_R	1.211	0.73
60_L	77_F	1.201	0.72
89_P	92_L	1.200	0.72
112_W	134_G	1.191	0.72
206_R	231_Y	1.187	0.71
75_I	231_Y	1.186	0.71
201_D	217_I	1.186	0.71
71_E	144_H	1.185	0.71
205_V	208_R	1.185	0.71
200_F	205_V	1.177	0.70
197_V	231_Y	1.170	0.70
106_S	161_F	1.167	0.69
111_C	183_S	1.167	0.69
113_P	157_D	1.162	0.69
133_S	158_D	1.158	0.68
220_H	223_G	1.157	0.68
105_F	131_L	1.157	0.68
80_S	83_V	1.151	0.68
77_F	136_F	1.137	0.66
222_N	225_T	1.137	0.66
213_D	228_Q	1.135	0.66
205_V	213_D	1.135	0.66
18_G	21_R	1.131	0.66
211_A	232_L	1.128	0.66
215_L	228_Q	1.120	0.65
199_K	215_L	1.115	0.64
113_P	133_S	1.114	0.64
207_I	231_Y	1.114	0.64
56_K	134_G	1.111	0.64
197_V	201_D	1.101	0.63
56_K	81_Y	1.099	0.63
198_L	212_Y	1.098	0.62
103_L	141_T	1.095	0.62
213_D	231_Y	1.095	0.62
216_P	220_H	1.092	0.62
201_D	205_V	1.091	0.62
202_R	211_A	1.089	0.62
137_I	162_Y	1.085	0.61
205_V	211_A	1.084	0.61
228_Q	233_G	1.082	0.61
64_M	227_L	1.080	0.61
211_A	231_Y	1.079	0.60
37_G	59_W	1.079	0.60
200_F	203_N	1.077	0.60
108_E	191_G	1.076	0.60
203_N	211_A	1.075	0.60
203_N	208_R	1.072	0.60
81_Y	113_P	1.070	0.60
189_L	196_V	1.065	0.59
12_A	19_Y	1.063	0.59
179_L	185_I	1.063	0.59
19_Y	178_N	1.062	0.59
211_A	233_G	1.056	0.58
56_K	158_D	1.052	0.58
202_R	208_R	1.048	0.57
211_A	228_Q	1.040	0.56
36_L	59_W	1.040	0.56
108_E	132_N	1.035	0.56
178_N	207_I	1.033	0.55
75_I	136_F	1.028	0.55
208_R	212_Y	1.023	0.54
26_A	33_V	1.023	0.54
211_A	229_L	1.022	0.54
213_D	232_L	1.020	0.54
197_V	205_V	1.020	0.54
130_F	179_L	1.019	0.54
57_V	64_M	1.019	0.54
113_P	134_G	1.015	0.54
104_L	185_I	1.015	0.54
197_V	206_R	1.007	0.53
15_E	146_I	1.006	0.53
204_R	208_R	1.006	0.53
135_G	186_F	1.006	0.53
201_D	208_R	1.006	0.53
203_N	218_V	1.004	0.52

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
1g9rA	1	0.9227	97.3	0.891	Contact Map
3tztA	2	0.7768	97.2	0.892	Contact Map
4uegA	2	0.8197	95.4	0.91	Contact Map
1ll2A	1	0.824	95.4	0.91	Contact Map
3u2uA	2	0.824	95.2	0.911	Contact Map
2p6wA	1	0.8112	93.9	0.917	Contact Map
1qg8A	1	0.8627	72.5	0.939	Contact Map
3bcvA	2	0.7468	65.7	0.942	Contact Map
3l7iA	4	0	60.3	0.944	Contact Map
4p02A	1	0.9356	51.1	0.947	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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