OPENSEQ.org - 1414450648 - GREMLIN Submission

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VX 50-329

ID:	1414450648	Query Sequence VRGLRRARAAGVRTIVDVSTFDIGRDVSLLAEVSRAADVHIVAATGLWFDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKATPFQELVLKAAARASLATGVPVTTHTAASQRDGEQQAAIFESEGLSPSRVCIGHSDDTDDLSYLTALAARGYLIGLDHIPHSAIGLEDNASASALLGIRSWQTRALLIKALIDQGYMKQILVSNDWLFGFSSYVTNIMDVMDRVNPDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLSPTLR	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	280 (231)
Sequences:	3516 (2560.4)
Seq/Len:	15.221
Nf(neff/√len):	168.5

HHblits Results: (2013_03)
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: 15.221).

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 > 50% 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
64_T	110_A	3.961	1.00
91_G	128_Q	3.701	1.00
102_K	135_S	3.287	1.00
105_A	115_V	3.120	1.00
269_T	273_R	2.421	1.00
35_R	69_R	2.410	1.00
98_E	128_Q	2.382	1.00
5_R	9_A	2.248	1.00
106_R	136_E	2.188	1.00
154_L	207_Q	2.168	1.00
87_V	104_A	2.124	1.00
67_F	75_I	2.121	1.00
14_T	272_A	2.056	1.00
134_E	159_A	2.044	1.00
44_A	74_G	2.022	1.00
158_T	162_A	2.003	1.00
210_M	266_I	1.959	1.00
258_V	263_L	1.958	1.00
159_A	162_A	1.956	1.00
119_T	129_Q	1.950	1.00
102_K	136_E	1.948	1.00
265_G	269_T	1.932	1.00
127_E	131_A	1.910	1.00
169_L	205_I	1.906	1.00
32_E	36_A	1.865	1.00
44_A	116_T	1.856	1.00
259_P	262_T	1.824	1.00
268_V	271_P	1.819	1.00
153_D	156_Y	1.771	1.00
18_V	116_T	1.767	1.00
87_V	115_V	1.762	1.00
210_M	256_K	1.761	1.00
134_E	163_R	1.754	1.00
158_T	207_Q	1.751	1.00
166_L	212_Q	1.748	1.00
199_L	203_A	1.713	1.00
214_L	274_F	1.701	1.00
7_A	15_I	1.685	1.00
248_R	251_P	1.684	1.00
203_A	206_D	1.655	1.00
199_L	202_K	1.651	1.00
210_M	258_V	1.633	1.00
131_A	135_S	1.632	1.00
109_L	136_E	1.597	1.00
51_P	93_A	1.593	1.00
91_G	98_E	1.588	1.00
246_P	260_Q	1.573	1.00
6_R	237_V	1.548	1.00
148_S	170_D	1.542	1.00
8_R	40_H	1.536	1.00
103_A	106_R	1.534	1.00
154_L	158_T	1.516	1.00
267_T	271_P	1.501	1.00
102_K	132_I	1.500	1.00
28_S	62_E	1.498	1.00
14_T	42_V	1.491	1.00
143_V	165_Y	1.490	1.00
119_T	126_G	1.476	1.00
98_E	131_A	1.463	1.00
112_G	142_R	1.462	1.00
43_A	72_Q	1.442	1.00
98_E	102_K	1.425	1.00
101_L	129_Q	1.424	1.00
166_L	273_R	1.416	1.00
202_K	255_E	1.406	0.99
67_F	111_T	1.384	0.99
161_A	212_Q	1.371	0.99
64_T	111_T	1.365	0.99
99_L	103_A	1.350	0.99
169_L	213_I	1.346	0.99
16_V	73_Y	1.340	0.99
226_Y	229_N	1.340	0.99
17_D	30_L	1.320	0.99
34_S	43_A	1.295	0.99
32_E	35_R	1.294	0.99
202_K	248_R	1.294	0.99
127_E	156_Y	1.288	0.99
127_E	159_A	1.285	0.99
157_L	167_I	1.283	0.99
126_G	156_Y	1.261	0.99
106_R	110_A	1.250	0.99
101_L	117_T	1.250	0.99
130_A	159_A	1.245	0.98
117_T	129_Q	1.245	0.98
35_R	71_I	1.243	0.98
268_V	272_A	1.231	0.98
209_Y	212_Q	1.217	0.98
98_E	132_I	1.213	0.98
146_G	160_L	1.213	0.98
203_A	207_Q	1.209	0.98
4_L	37_A	1.203	0.98
18_V	44_A	1.201	0.98
191_I	222_G	1.182	0.98
62_E	65_Q	1.182	0.98
30_L	34_S	1.174	0.98
262_T	265_G	1.173	0.98
126_G	152_D	1.172	0.98
236_R	239_P	1.171	0.98
247_L	260_Q	1.167	0.97
249_V	252_F	1.159	0.97
15_I	41_I	1.158	0.97
7_A	12_V	1.142	0.97
37_A	40_H	1.116	0.96
167_I	208_G	1.108	0.96
208_G	213_I	1.107	0.96
130_A	160_L	1.089	0.96
144_C	165_Y	1.084	0.96
246_P	250_I	1.078	0.95
6_R	238_N	1.077	0.95
237_V	241_G	1.076	0.95
105_A	109_L	1.075	0.95
220_L	223_F	1.075	0.95
65_Q	68_L	1.071	0.95
119_T	152_D	1.066	0.95
19_S	27_V	1.063	0.95
205_I	249_V	1.048	0.94
21_F	26_D	1.041	0.94
117_T	146_G	1.036	0.94
16_V	271_P	1.033	0.94
263_L	267_T	1.027	0.94
145_I	274_F	1.025	0.93
28_S	32_E	1.023	0.93
130_A	156_Y	1.002	0.92
30_L	43_A	1.002	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: (06Sep14)
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
3k2gA	4	0.9286	100	0.34	Contact Map
3rhgA	1	0.9321	100	0.383	Contact Map
3e2vA	2	0.8357	100	0.389	Contact Map
1yixA	2	0.8321	100	0.468	Contact Map
3ipwA	1	0.8321	100	0.472	Contact Map
3ovgA	6	0.925	100	0.478	Contact Map
3pnzA	6	0.9036	100	0.478	Contact Map
1j6oA	1	0.8321	100	0.487	Contact Map
3gg7A	1	0.7929	100	0.496	Contact Map
2xioA	1	0.8321	100	0.498	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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