OPENSEQ.org - 1504851007 - GREMLIN Submission

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scEMC2

ID:	1504851007	Query Sequence MLKDLVREKLLTIMNTKAYTQFNPEQLLQLENEMKIYMKSGDSALTEGNYFFLMEMLFYVLVYRNQDVDAQVVYNTLRDRLGENSYKMVIMKATLLQINGNDKGAIEYLENLLNDDLEYETDFVTYVSIAKKLIAIKTTSKNLSQESVLKEVVALTDKFPLDAELWWYASEIYFEMGQFEKACYCLEQVLCITPFNYACFGRLSETLYYEALRSKKQTKTELLEKALKNALRSVELSELYLKGWALVNIISRELGRNKQNDLIKLSASKLKEISAKSNNKDKITAELILNKI	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	292 (276)
Sequences:	1370 (929.4)
Seq/Len:	4.964
Nf(neff/√len):	55.9

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: 4.964).

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
101_N	104_G	4.525	1.00
178_Q	181_K	4.371	1.00
66_Q	69_D	3.168	1.00
144_S	147_S	3.008	1.00
247_V	251_S	2.944	1.00
149_L	169_A	2.355	1.00
227_L	250_I	2.260	1.00
173_Y	181_K	1.986	1.00
166_W	185_C	1.983	1.00
256_R	265_L	1.932	1.00
212_L	215_K	1.918	1.00
282_K	286_E	1.906	1.00
183_C	203_L	1.883	1.00
75_N	92_K	1.843	1.00
203_L	207_L	1.804	1.00
169_A	173_Y	1.781	1.00
222_L	225_K	1.768	1.00
169_A	185_C	1.768	1.00
155_L	165_L	1.696	0.99
231_L	251_S	1.692	0.99
57_L	61_L	1.620	0.99
93_A	109_L	1.601	0.99
106_I	110_E	1.595	0.99
234_V	244_W	1.563	0.99
71_Q	99_N	1.507	0.99
153_V	169_A	1.501	0.98
58_F	74_Y	1.494	0.98
152_V	169_A	1.476	0.98
89_V	108_Y	1.445	0.98
170_S	186_L	1.442	0.98
234_V	243_G	1.432	0.98
145_Q	172_I	1.403	0.97
287_L	290_N	1.375	0.97
231_L	247_V	1.363	0.97
74_Y	91_M	1.358	0.97
183_C	206_T	1.352	0.97
146_E	176_M	1.324	0.96
224_E	254_L	1.319	0.96
156_T	166_W	1.301	0.95
218_T	223_L	1.295	0.95
167_W	202_R	1.279	0.95
173_Y	178_Q	1.267	0.94
183_C	187_E	1.266	0.94
58_F	88_M	1.264	0.94
227_L	247_V	1.259	0.94
189_V	199_C	1.257	0.94
149_L	176_M	1.253	0.94
201_G	205_E	1.247	0.94
15_N	18_A	1.233	0.93
267_A	289_L	1.233	0.93
274_S	282_K	1.220	0.93
30_L	34_M	1.219	0.93
20_T	29_Q	1.217	0.93
107_E	111_N	1.212	0.93
26_Q	33_E	1.206	0.92
137_K	147_S	1.204	0.92
170_S	185_C	1.203	0.92
233_S	236_L	1.203	0.92
149_L	173_Y	1.195	0.92
280_K	283_I	1.195	0.92
28_L	35_K	1.195	0.92
14_M	18_A	1.194	0.92
268_S	272_E	1.189	0.92
250_I	254_L	1.186	0.92
26_Q	29_Q	1.185	0.91
149_L	172_I	1.182	0.91
230_A	246_L	1.172	0.91
286_E	290_N	1.156	0.90
29_Q	36_I	1.156	0.90
22_F	33_E	1.154	0.90
285_A	289_L	1.144	0.89
85_S	88_M	1.140	0.89
230_A	247_V	1.140	0.89
71_Q	92_K	1.139	0.89
233_S	243_G	1.132	0.89
60_V	64_R	1.130	0.89
31_E	35_K	1.123	0.88
18_A	34_M	1.122	0.88
22_F	34_M	1.120	0.88
26_Q	34_M	1.116	0.88
248_N	281_D	1.111	0.88
25_E	28_L	1.107	0.87
284_T	287_L	1.106	0.87
131_K	152_V	1.106	0.87
25_E	29_Q	1.101	0.87
232_R	235_E	1.099	0.87
38_M	42_D	1.096	0.87
281_D	285_A	1.094	0.86
100_G	177_G	1.090	0.86
162_D	165_L	1.081	0.86
27_L	30_L	1.078	0.85
26_Q	32_N	1.078	0.85
32_N	36_I	1.075	0.85
15_N	19_Y	1.071	0.85
155_L	170_S	1.071	0.85
63_Y	93_A	1.068	0.85
24_P	28_L	1.067	0.85
22_F	25_E	1.065	0.84
271_K	275_A	1.065	0.84
138_T	172_I	1.062	0.84
103_K	107_E	1.053	0.84
65_N	177_G	1.052	0.83
32_N	39_K	1.045	0.83
27_L	31_E	1.041	0.83
13_I	23_N	1.033	0.82
137_K	144_S	1.030	0.82
75_N	79_D	1.024	0.81
31_E	34_M	1.014	0.80
89_V	112_L	1.012	0.80
25_E	34_M	1.012	0.80
25_E	30_L	1.010	0.80
160_P	194_P	1.008	0.80
24_P	36_I	1.008	0.80
88_M	226_A	1.008	0.80
283_I	287_L	1.007	0.80
25_E	32_N	1.001	0.79

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
3dssA	1	0.887	100	0.406	Contact Map
3q7aA	1	0.887	100	0.411	Contact Map
4l9pA	1	0.8836	100	0.413	Contact Map
4ui9C	2	0	100	0.42	Contact Map
1w3bA	2	0.9041	100	0.423	Contact Map
2h6fA	1	0.8836	100	0.434	Contact Map
4ui9J	1	0	100	0.437	Contact Map
4eqfA	1	0.8356	100	0.44	Contact Map
3draA	1	0.8767	100	0.444	Contact Map
2xpiA	2	0.9041	100	0.449	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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