OPENSEQ.org - 1500978587 - GREMLIN Submission

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ID:	1500978587	Query Sequence IVGGEFTEVENQPWFAAIYQKNKGGSPPSFKCGGSLISPCWVASAAHCFIQLPKKENYVVYLGQSKESSYNPGEMKFEVEQLILHEYYREDSLAYHNDIALLKIRTSTGQCAQPSRSIQTIALPPRFTDAPFGSDCEITGFGKESESDYLYPKNLKMSVVKLVSHEQCMQPHYYGSEINYKMLCAADPEWKTDSCKGDSGGPLICNIEGRPTLSGIVSWGRGCAEKNKPGVYTRVSHFLDWIQSHIG	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	247 (243)
Sequences:	14024 (10177.4)
Seq/Len:	57.712
Nf(neff/√len):	652.9

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: 57.712).

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
136_C	205_C	4.374	1.00
32_C	48_C	3.710	1.00
41_W	103_K	3.070	1.00
80_E	103_K	3.011	1.00
41_W	101_L	2.988	1.00
11_N	157_M	2.890	1.00
34_G	42_V	2.763	1.00
6_F	156_K	2.720	1.00
49_F	100_A	2.606	1.00
15_F	139_T	2.604	1.00
35_S	213_L	2.527	1.00
12_Q	157_M	2.512	1.00
78_E	105_R	2.480	1.00
17_A	30_F	2.457	1.00
195_C	223_C	2.287	1.00
40_C	107_S	2.286	1.00
158_S	192_T	2.283	1.00
43_A	213_L	2.276	1.00
36_L	108_T	2.274	1.00
97_N	238_F	2.255	1.00
81_Q	103_K	2.222	1.00
62_L	108_T	2.186	1.00
16_A	34_G	2.182	1.00
6_F	154_N	2.182	1.00
40_C	103_K	2.169	1.00
219_W	231_V	2.126	1.00
12_Q	139_T	2.125	1.00
47_H	199_S	2.095	1.00
38_S	41_W	2.079	1.00
168_C	184_C	2.076	1.00
39_P	107_S	2.053	1.00
138_I	194_S	2.026	1.00
61_Y	76_K	2.017	1.00
104_I	108_T	2.013	1.00
16_A	62_L	2.009	1.00
83_I	245_H	1.954	1.00
99_I	238_F	1.915	1.00
1_I	4_G	1.907	1.00
86_E	245_H	1.899	1.00
79_V	102_L	1.879	1.00
181_K	237_H	1.875	1.00
239_L	243_Q	1.861	1.00
80_E	105_R	1.853	1.00
77_F	105_R	1.840	1.00
96_H	181_K	1.769	1.00
77_F	108_T	1.765	1.00
139_T	204_I	1.748	1.00
136_C	162_L	1.734	1.00
87_Y	97_N	1.688	1.00
114_P	120_T	1.667	1.00
16_A	42_V	1.606	1.00
14_W	204_I	1.554	1.00
233_T	238_F	1.543	1.00
19_Y	30_F	1.533	1.00
138_I	158_S	1.528	1.00
194_S	217_V	1.475	1.00
7_T	12_Q	1.464	1.00
85_H	97_N	1.433	1.00
66_K	153_K	1.431	1.00
193_D	230_G	1.431	1.00
121_I	213_L	1.426	1.00
203_L	232_Y	1.418	1.00
61_Y	64_Q	1.418	1.00
59_V	76_K	1.415	1.00
234_R	237_H	1.408	1.00
205_C	214_S	1.406	0.99
44_S	49_F	1.403	0.99
10_E	65_S	1.383	0.99
83_I	103_K	1.380	0.99
144_E	156_K	1.380	0.99
217_V	220_G	1.375	0.99
135_D	159_V	1.362	0.99
183_L	203_L	1.355	0.99
9_V	65_S	1.354	0.99
14_W	122_A	1.349	0.99
137_E	159_V	1.348	0.99
49_F	84_L	1.347	0.99
15_F	155_L	1.347	0.99
45_A	216_I	1.347	0.99
35_S	121_I	1.326	0.99
146_E	225_E	1.315	0.99
99_I	233_T	1.310	0.99
77_F	106_T	1.294	0.99
84_L	100_A	1.286	0.99
35_S	216_I	1.283	0.99
47_H	98_D	1.282	0.99
163_V	229_P	1.260	0.99
82_L	102_L	1.240	0.98
182_M	219_W	1.240	0.98
15_F	141_F	1.237	0.98
41_W	245_H	1.234	0.98
15_F	33_G	1.232	0.98
36_L	62_L	1.231	0.98
68_S	153_K	1.214	0.98
66_K	154_N	1.207	0.98
121_I	204_I	1.201	0.98
8_E	11_N	1.196	0.98
138_I	160_V	1.192	0.98
35_S	43_A	1.191	0.98
14_W	211_P	1.180	0.98
152_P	156_K	1.172	0.98
18_I	60_V	1.154	0.97
97_N	181_K	1.151	0.97
200_G	203_L	1.146	0.97
5_E	157_M	1.142	0.97
221_R	228_K	1.136	0.97
164_S	167_Q	1.119	0.96
136_C	203_L	1.112	0.96
36_L	42_V	1.108	0.96
12_Q	137_E	1.105	0.96
6_F	65_S	1.103	0.96
42_V	60_V	1.099	0.96
241_W	245_H	1.094	0.96
64_Q	74_E	1.073	0.95
85_H	88_Y	1.056	0.95
7_T	157_M	1.055	0.95
206_N	211_P	1.053	0.95
12_Q	211_P	1.051	0.94
204_I	211_P	1.043	0.94
18_I	102_L	1.040	0.94
49_F	82_L	1.032	0.94
19_Y	61_Y	1.028	0.94
10_E	117_S	1.019	0.93
44_S	100_A	1.000	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

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
2f83A	1	0.8704	100	-0.022	Contact Map
4nzqA	1	0.9555	100	0.005	Contact Map
1rtfB	1	0.9757	100	0.007	Contact Map
4durA	2	0.9109	100	0.008	Contact Map
2vntA	6	0.996	100	0.009	Contact Map
4kkdA	2	0.9595	100	0.012	Contact Map
2xxlA	2	0.9433	100	0.012	Contact Map
3gylB	1	0.9514	100	0.012	Contact Map
1fiwA	1	0.9757	100	0.015	Contact Map
3nxpA	1	0.9474	100	0.015	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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