OPENSEQ.org - 1486175277 - GREMLIN Submission

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ID:	1486175277	Query Sequence MGVDIEKGVAWMQARKGRVSYSMDFRDGPDSYDCSSSMYYALRSAGASSAGWAVNTEYMHAWLIENGYELISENAPWDAKRGDIFIWGRKGASAGAGGHTGMFIDSDNIIHCNYAYDGISVNPAEKKLGWQKDATGFWYARANGTYPKDEFEYIEENKSWFYFDDQGYMLAEKWLKHTDGNWYWFDRDGYMATSWKRIGESWYYFNRDGSMVTGWIKYYDNWYYCDATNGDMKSNAFIRYNDGWYLLLPDGRLADKPQFTVEPDGLITAKV	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	271 (210)
Sequences:	690 (529.7)
Seq/Len:	3.286
Nf(neff/√len):	36.6

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: 3.286).

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
154_I	163_F	2.832	1.00
153_Y	160_W	2.388	1.00
254_A	261_V	2.234	1.00
198_I	205_F	2.148	1.00
218_Y	225_C	2.006	1.00
217_K	222_W	1.996	1.00
195_W	204_Y	1.946	1.00
182_W	211_M	1.851	0.99
243_G	266_L	1.739	0.99
197_R	202_W	1.731	0.99
174_W	182_W	1.723	0.99
182_W	222_W	1.720	0.99
138_W	168_Y	1.718	0.99
133_D	140_A	1.672	0.98
130_W	137_F	1.667	0.98
186_D	192_A	1.662	0.98
132_K	137_F	1.636	0.98
226_D	233_K	1.625	0.98
136_G	168_Y	1.623	0.98
240_Y	247_L	1.593	0.98
254_A	257_P	1.583	0.98
195_W	202_W	1.582	0.98
151_F	160_W	1.575	0.97
182_W	244_W	1.573	0.97
260_T	267_I	1.538	0.97
256_K	261_V	1.532	0.97
262_E	268_T	1.526	0.97
185_F	191_M	1.524	0.97
215_W	222_W	1.519	0.97
178_T	199_G	1.503	0.96
185_F	247_L	1.488	0.96
138_W	146_Y	1.474	0.96
154_I	198_I	1.470	0.96
181_N	210_S	1.462	0.96
160_W	202_W	1.441	0.95
151_F	195_W	1.437	0.95
260_T	268_T	1.430	0.95
202_W	222_W	1.426	0.95
216_I	225_C	1.413	0.94
151_F	215_W	1.407	0.94
238_I	247_L	1.391	0.94
258_Q	267_I	1.343	0.92
137_F	169_M	1.339	0.92
225_C	232_M	1.291	0.90
174_W	211_M	1.290	0.90
248_L	252_R	1.270	0.89
146_Y	168_Y	1.266	0.89
262_E	266_L	1.265	0.89
239_R	244_W	1.265	0.89
248_L	254_A	1.262	0.89
221_N	252_R	1.261	0.89
247_L	253_L	1.257	0.88
151_F	174_W	1.256	0.88
169_M	189_G	1.253	0.88
255_D	261_V	1.242	0.88
133_D	138_W	1.235	0.87
138_W	147_P	1.221	0.86
237_F	244_W	1.210	0.86
176_K	197_R	1.206	0.86
185_F	205_F	1.205	0.85
260_T	270_K	1.200	0.85
261_V	267_I	1.186	0.84
194_S	214_G	1.179	0.84
244_W	267_I	1.168	0.83
253_L	256_K	1.158	0.82
133_D	136_G	1.152	0.82
181_N	208_D	1.144	0.81
212_V	216_I	1.138	0.81
127_K	140_A	1.138	0.81
153_Y	158_K	1.126	0.80
241_N	245_Y	1.124	0.80
140_A	147_P	1.111	0.78
237_F	246_L	1.103	0.78
202_W	244_W	1.102	0.78
160_W	191_M	1.098	0.77
151_F	237_F	1.094	0.77
177_H	218_Y	1.091	0.77
192_A	196_K	1.075	0.75
167_G	251_G	1.071	0.75
197_R	201_S	1.068	0.75
217_K	239_R	1.067	0.74
195_W	223_Y	1.066	0.74
153_Y	197_R	1.061	0.74
183_Y	223_Y	1.061	0.74
129_G	140_A	1.049	0.73
209_G	265_G	1.047	0.72
188_D	208_D	1.047	0.72
174_W	215_W	1.040	0.72
197_R	217_K	1.038	0.71
153_Y	159_S	1.036	0.71
232_M	251_G	1.027	0.70
236_A	247_L	1.018	0.69
195_W	215_W	1.016	0.69
211_M	214_G	1.015	0.69
155_E	158_K	1.013	0.69
259_F	267_I	1.012	0.69
197_R	239_R	1.008	0.68
154_I	199_G	1.007	0.68
160_W	244_W	1.005	0.68
128_L	140_A	1.000	0.67

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
4x36A	1	0	100	0.489	Contact Map
2bibA	1	0.9077	100	0.49	Contact Map
2j8gA	1	0.9188	100	0.493	Contact Map
4tvcA	1	0	100	0.523	Contact Map
4np4A	1	0.583	100	0.53	Contact Map
2g7cA	2	0.6015	100	0.534	Contact Map
2qj6A	2	0.6753	100	0.537	Contact Map
2v05A	1	0.9151	100	0.545	Contact Map
2ww5A	1	0.5756	100	0.556	Contact Map
4nbxA	1	0.4834	100	0.583	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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