OPENSEQ.org - 1503820380 - GREMLIN Submission

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RRP42

ID:	1503820380	Query Sequence MSLSVAEKSYLYDSLASTPSIRPDGRLPHQFRPIEIFTDFLPSSNGSSRIIASDGSECIVSIKSKVVDHHVENELLQVDVDIAGQRDDALVVETITSLLNKVLKSGSGVDSSKLQLTKKYSFKIFVDVLVISSHSHPVSLISFAIYSALNSTYLPKLISAFDDLEVEELPTFHDYDMVKLDINPPLVFILAVVGNNMLLDPAANESEVANNGLIISWSNGKITSPIRSVALNDSNVKSFKPHLLKQGLAMVEKYAPDVVRSLENL	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	265 (249)
Sequences:	3725 (1737.8)
Seq/Len:	14.960
Nf(neff/√len):	110.1

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: 14.960).

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
62_I	148_A	4.641	1.00
27_L	30_Q	3.809	1.00
39_D	151_S	3.764	1.00
60_V	144_A	3.592	1.00
58_C	130_V	3.398	1.00
261_S	264_N	3.257	1.00
183_N	220_G	2.962	1.00
191_A	201_P	2.822	1.00
29_H	253_K	2.805	1.00
102_V	225_P	2.677	1.00
59_I	131_I	2.651	1.00
74_E	100_N	2.567	1.00
199_L	254_Y	2.536	1.00
13_D	17_S	2.522	1.00
219_N	260_R	2.435	1.00
62_I	126_V	2.399	1.00
219_N	263_E	2.189	1.00
66_V	116_L	2.145	1.00
126_V	145_I	2.104	1.00
35_E	51_I	2.081	1.00
62_I	152_T	2.048	1.00
184_P	263_E	2.027	1.00
249_A	253_K	2.027	1.00
36_I	261_S	1.993	1.00
41_L	44_S	1.869	1.00
49_R	57_E	1.852	1.00
31_F	199_L	1.846	1.00
146_Y	184_P	1.837	1.00
190_L	197_M	1.823	1.00
20_S	196_N	1.801	1.00
128_V	145_I	1.793	1.00
60_V	78_V	1.782	1.00
257_D	261_S	1.756	1.00
103_L	145_I	1.747	1.00
139_S	142_S	1.734	1.00
60_V	126_V	1.725	1.00
242_H	246_Q	1.693	1.00
191_A	209_A	1.686	1.00
51_I	57_E	1.684	1.00
228_S	231_L	1.670	1.00
215_I	251_V	1.600	1.00
4_S	7_E	1.578	1.00
106_G	185_P	1.574	1.00
128_V	141_I	1.565	1.00
58_C	144_A	1.552	1.00
192_V	243_L	1.545	1.00
254_Y	257_D	1.522	1.00
48_S	147_S	1.505	1.00
12_Y	210_N	1.499	1.00
39_D	46_G	1.495	1.00
24_D	202_A	1.492	1.00
252_E	256_P	1.492	1.00
253_K	257_D	1.478	1.00
32_R	200_D	1.476	1.00
14_S	19_P	1.466	1.00
29_H	250_M	1.458	1.00
183_N	219_N	1.457	1.00
9_S	13_D	1.450	1.00
28_P	196_N	1.446	1.00
217_W	255_A	1.441	1.00
36_I	147_S	1.438	1.00
81_D	127_D	1.437	1.00
188_F	199_L	1.429	1.00
34_I	261_S	1.388	0.99
146_Y	263_E	1.383	0.99
44_S	61_S	1.353	0.99
257_D	260_R	1.295	0.99
23_P	202_A	1.288	0.99
194_G	232_N	1.287	0.99
240_K	243_L	1.282	0.99
187_V	216_S	1.277	0.99
54_D	134_H	1.274	0.99
76_L	145_I	1.273	0.99
143_F	262_L	1.266	0.99
10_Y	14_S	1.262	0.99
10_Y	13_D	1.255	0.99
22_R	26_R	1.246	0.98
69_H	74_E	1.244	0.98
183_N	218_S	1.226	0.98
111_S	119_K	1.223	0.98
88_D	92_V	1.222	0.98
139_S	189_I	1.219	0.98
31_F	257_D	1.217	0.98
249_A	252_E	1.215	0.98
78_V	145_I	1.210	0.98
72_E	112_S	1.209	0.98
260_R	264_N	1.189	0.98
106_G	156_K	1.164	0.97
7_E	14_S	1.164	0.97
109_V	124_I	1.158	0.97
60_V	145_I	1.153	0.97
23_P	204_N	1.148	0.97
66_V	120_Y	1.122	0.97
82_I	133_S	1.120	0.96
190_L	251_V	1.113	0.96
60_V	128_V	1.108	0.96
48_S	62_I	1.105	0.96
246_Q	250_M	1.105	0.96
46_G	152_T	1.101	0.96
37_F	49_R	1.096	0.96
200_D	205_E	1.079	0.95
128_V	144_A	1.075	0.95
21_I	27_L	1.064	0.95
67_V	123_K	1.060	0.95
38_T	151_S	1.055	0.95
119_K	182_I	1.027	0.94
185_P	218_S	1.027	0.94
17_S	21_I	1.024	0.93
114_L	155_P	1.020	0.93
7_E	10_Y	1.017	0.93
100_N	104_K	1.016	0.93
48_S	60_V	1.012	0.93
22_R	205_E	1.012	0.93
81_D	129_L	1.010	0.93
215_I	248_L	1.008	0.93
7_E	11_L	1.006	0.93

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
4ifdE	1	0.9774	100	0.145	Contact Map
2nn6E	1	0.9321	100	0.177	Contact Map
2wnrA	3	0.9283	100	0.189	Contact Map
2nn6C	1	0.9358	100	0.191	Contact Map
2po1B	1	0.9283	100	0.192	Contact Map
3m7nG	3	0.917	100	0.193	Contact Map
4ifdA	1	0.9283	100	0.203	Contact Map
2je6A	1	0.9245	100	0.204	Contact Map
2nn6A	1	0.9396	100	0.215	Contact Map
4ifdC	1	0.9623	100	0.246	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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