OPENSEQ.org - 1465836574 - GREMLIN Submission

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4Q2EAPDBIDCHAINSEQUENCE

ID:	1465836574	Query Sequence MGSSHHHHHHSSGLVPRGSHMDDLKTRVITASVVAPFVVLCFVSYESLIGLVSAILILAGYELITLEMKERDARFFYVILLALYPVLYGLVFEEPTQPLSILFITGVVFSLITDKDPSQVFKTVAAFSIALIYVTFFLSFFLPIYRDFGAANALLVLTSTWVFDSFAYFTGLKFGRTRISPRYSPRKSLEGVIGGFLGVVIYTFLYRLVVNDLLSVNVICFRTFLPFAATVAIMDTFGDIFECALKRHYGVKDSGKTLPGHGGMLDRIDGLLFVAPVSYIVFKILEGVVR	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	290 (265)
Sequences:	3087 (2075.6)
Seq/Len:	11.649
Nf(neff/√len):	127.5

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: 11.649).

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
30_T	258_L	5.805	1.00
166_F	198_G	4.601	1.00
170_T	194_G	4.101	1.00
177_T	190_E	3.937	1.00
192_V	236_T	3.447	1.00
242_E	254_S	3.113	1.00
261_H	267_R	2.623	1.00
176_R	190_E	2.595	1.00
172_L	188_S	2.491	1.00
162_V	202_Y	2.436	1.00
59_A	264_M	2.431	1.00
163_F	236_T	2.429	1.00
170_T	174_F	2.409	1.00
63_L	130_A	2.328	1.00
157_L	161_W	2.303	1.00
66_L	251_V	2.183	1.00
169_F	173_K	2.166	1.00
31_A	36_P	2.155	1.00
66_L	254_S	2.102	1.00
24_L	169_F	2.028	1.00
203_T	228_A	1.955	1.00
156_V	275_A	1.950	1.00
179_I	240_I	1.853	1.00
170_T	198_G	1.818	1.00
163_F	235_D	1.783	1.00
163_F	232_A	1.782	1.00
58_L	264_M	1.747	1.00
59_A	265_L	1.718	1.00
64_I	77_Y	1.699	1.00
54_A	58_L	1.698	1.00
179_I	189_L	1.687	1.00
29_I	33_V	1.658	1.00
28_V	169_F	1.648	1.00
177_T	189_L	1.644	1.00
227_F	281_V	1.644	1.00
24_L	28_V	1.617	1.00
31_A	35_A	1.614	1.00
223_T	281_V	1.577	1.00
189_L	193_I	1.567	1.00
66_L	249_Y	1.539	1.00
60_G	64_I	1.535	1.00
178_R	186_R	1.531	1.00
25_K	29_I	1.501	1.00
61_Y	255_G	1.486	1.00
179_I	192_V	1.480	1.00
158_T	202_Y	1.475	1.00
193_I	197_L	1.454	1.00
161_W	261_H	1.443	1.00
200_V	225_L	1.437	1.00
167_A	195_G	1.417	1.00
159_S	199_V	1.411	1.00
159_S	203_T	1.406	0.99
61_Y	65_T	1.388	0.99
234_M	277_V	1.364	0.99
137_F	140_F	1.362	0.99
170_T	173_K	1.362	0.99
32_S	36_P	1.347	0.99
59_A	268_I	1.344	0.99
140_F	279_Y	1.342	0.99
160_T	274_V	1.327	0.99
161_W	267_R	1.324	0.99
55_I	264_M	1.322	0.99
50_G	54_A	1.317	0.99
180_S	183_Y	1.309	0.99
140_F	280_I	1.299	0.99
64_I	130_A	1.289	0.99
196_F	232_A	1.284	0.99
160_T	271_L	1.273	0.99
34_V	268_I	1.270	0.99
234_M	274_V	1.268	0.99
170_T	197_L	1.260	0.99
200_V	229_A	1.260	0.99
170_T	188_S	1.254	0.99
178_R	181_P	1.253	0.99
178_R	188_S	1.250	0.99
36_P	40_L	1.249	0.99
163_F	195_G	1.237	0.98
196_F	229_A	1.237	0.98
41_C	51_L	1.230	0.98
166_F	194_G	1.223	0.98
156_V	278_S	1.218	0.98
162_V	198_G	1.216	0.98
56_L	138_L	1.194	0.98
160_T	270_G	1.190	0.98
268_I	271_L	1.188	0.98
192_V	233_I	1.180	0.98
63_L	67_E	1.164	0.97
224_F	228_A	1.157	0.97
155_L	228_A	1.151	0.97
160_T	235_D	1.134	0.97
27_R	30_T	1.134	0.97
242_E	265_L	1.133	0.97
231_V	278_S	1.128	0.97
195_G	232_A	1.120	0.96
172_L	186_R	1.120	0.96
34_V	37_F	1.118	0.96
143_P	279_Y	1.113	0.96
235_D	270_G	1.113	0.96
39_V	43_V	1.103	0.96
189_L	192_V	1.102	0.96
166_F	170_T	1.093	0.96
175_G	190_E	1.089	0.96
42_F	153_A	1.082	0.96
25_K	28_V	1.080	0.95
58_L	61_Y	1.080	0.95
133_Y	242_E	1.078	0.95
241_F	245_L	1.066	0.95
36_P	161_W	1.064	0.95
232_A	236_T	1.062	0.95
177_T	193_I	1.060	0.95
204_F	225_L	1.059	0.95
160_T	254_S	1.059	0.95
23_D	26_T	1.056	0.95
140_F	275_A	1.038	0.94
114_D	183_Y	1.033	0.94
222_R	226_P	1.033	0.94
60_G	130_A	1.030	0.94
163_F	199_V	1.023	0.93
201_I	205_L	1.019	0.93
66_L	245_L	1.018	0.93
241_F	244_A	1.014	0.93
174_F	190_E	1.013	0.93
34_V	258_L	1.012	0.93
26_T	30_T	1.008	0.93
24_L	168_Y	1.001	0.92

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

See coupling matrix (for protein design or mutagenesis)
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
4q2eA	2	0.9138	100	0.1	Contact Map
2kogA	1	0.1621	3.3	0.97	Contact Map
4c48C	1	0.1586	2.7	0.971	Contact Map
3hd7A	2	0.1621	1.5	0.975	Contact Map
3fymA	1	0.0379	1.5	0.975	Contact Map
1skhA	1	0.1034	1.5	0.975	Contact Map
2i68A	2	0.0103	1.4	0.975	Contact Map
3tx3A	2	0.2483	1.4	0.975	Contact Map
4ev6A	5	0.2828	1.4	0.975	Contact Map
2mdfA	1	0.1931	1.4	0.975	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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