OPENSEQ.org - 1513798384 - GREMLIN Submission

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av1_cp 30-238 1-205 20-205 -force run

ID:	1513798384	Query Sequence RGCEGPCKVQSFESRHDIQHIGKVMCVSDVTRGTGLTHRVGKRFCVKSVYVLGKIWMDENIKTKNHTNSVMFFLVRDRRPVDKPQDFGEVFNMFDNEPSTATVKNVHRDRYQVLRKWYATVTGGQYASKEQALVKKFIRVNNYVVYNQQEAGKYENHSENALMLYMACTHASNPVYATLKIRIYFY	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	186 (186)
Sequences:	169 (59)
Seq/Len:	0.909
Nf(neff/√len):	4.3

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: 0.909).

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
82_D	89_E	1.786	0.89
120_T	129_K	1.781	0.89
85_Q	114_L	1.676	0.84
73_F	115_R	1.634	0.82
115_R	120_T	1.570	0.79
114_L	120_T	1.485	0.73
114_L	139_R	1.431	0.69
142_N	145_V	1.424	0.69
81_V	89_E	1.415	0.68
144_V	147_N	1.384	0.65
88_G	93_M	1.379	0.65
148_Q	163_M	1.377	0.65
154_Y	160_N	1.347	0.62
175_V	178_T	1.346	0.62
73_F	94_F	1.338	0.61
12_F	27_V	1.336	0.61
81_V	106_V	1.324	0.60
7_C	10_Q	1.318	0.60
3_C	10_Q	1.313	0.59
73_F	83_K	1.307	0.59
178_T	185_F	1.292	0.57
121_V	130_E	1.287	0.57
182_R	186_Y	1.283	0.57
167_A	171_A	1.281	0.56
167_A	170_H	1.281	0.56
10_Q	20_H	1.280	0.56
65_N	68_N	1.278	0.56
173_N	176_Y	1.269	0.55
178_T	184_Y	1.264	0.55
98_P	101_A	1.259	0.54
147_N	150_E	1.257	0.54
16_H	25_M	1.251	0.54
109_D	112_Q	1.234	0.52
146_Y	149_Q	1.233	0.52
54_K	67_T	1.231	0.52
1_R	59_E	1.218	0.51
165_Y	170_H	1.214	0.50
115_R	129_K	1.214	0.50
36_L	107_H	1.214	0.50
169_T	177_A	1.205	0.50
3_C	6_P	1.193	0.49
122_T	126_Y	1.186	0.48
73_F	107_H	1.186	0.48
122_T	125_Q	1.182	0.48
38_H	42_K	1.180	0.47
162_L	177_A	1.180	0.47
172_S	175_V	1.167	0.46
3_C	7_C	1.167	0.46
122_T	127_A	1.159	0.45
59_E	62_K	1.159	0.45
144_V	149_Q	1.159	0.45
16_H	23_K	1.154	0.45
122_T	128_S	1.154	0.45
37_T	42_K	1.152	0.45
7_C	20_H	1.151	0.45
121_V	131_Q	1.142	0.44
175_V	185_F	1.142	0.44
13_E	27_V	1.135	0.43
116_K	120_T	1.135	0.43
178_T	182_R	1.130	0.43
78_R	84_P	1.129	0.43
10_Q	29_D	1.122	0.42
153_K	156_N	1.122	0.42
101_A	109_D	1.120	0.42
171_A	177_A	1.115	0.42
51_V	107_H	1.111	0.41
86_D	89_E	1.103	0.41
146_Y	150_E	1.099	0.40
40_V	44_F	1.098	0.40
83_K	94_F	1.089	0.39
4_E	11_S	1.084	0.39
1_R	30_V	1.080	0.39
6_P	10_Q	1.078	0.38
76_R	79_R	1.074	0.38
39_R	47_K	1.071	0.38
81_V	114_L	1.056	0.36
177_A	180_K	1.056	0.36
16_H	19_Q	1.049	0.36
89_E	106_V	1.048	0.36
4_E	24_V	1.043	0.35
3_C	20_H	1.040	0.35
151_A	158_S	1.034	0.35
112_Q	129_K	1.034	0.35
115_R	139_R	1.033	0.35
38_H	43_R	1.033	0.35
5_G	20_H	1.032	0.34
104_K	112_Q	1.031	0.34
167_A	177_A	1.022	0.34
93_M	96_N	1.022	0.34
145_V	149_Q	1.020	0.34
77_D	87_F	1.019	0.33
86_D	90_V	1.011	0.33
106_V	148_Q	1.010	0.33
156_N	160_N	1.009	0.33
10_Q	17_D	1.009	0.33
81_V	107_H	1.008	0.33
168_C	177_A	1.007	0.32
37_T	43_R	1.007	0.32
6_P	20_H	1.006	0.32
54_K	58_D	1.005	0.32
1_R	4_E	1.004	0.32
144_V	150_E	1.003	0.32
4_E	10_Q	1.003	0.32
143_Y	152_G	1.001	0.32
120_T	139_R	1.000	0.32

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
2h8eA	1	0.3333	5.3	0.98	Contact Map
3i9v2	2	0.3065	4.5	0.981	Contact Map
3k7lA	1	0.3118	3.9	0.981	Contact Map
3u4vA	2	0.3763	3.2	0.982	Contact Map
1e3pA	1	0.2903	2.9	0.982	Contact Map
3rjrA	4	0.371	2.8	0.982	Contact Map
1wqeA	1	0.043	2.8	0.982	Contact Map
2plxB	1	0.1398	2.6	0.983	Contact Map
3u58A	4	0.3333	2.2	0.983	Contact Map
1vtze	30	0.7849	2.1	0.983	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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