OPENSEQ.org - 1430407984 - GREMLIN Submission

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TRY2_RAT

ID:	1430407984	Query Sequence IVGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEGNEQFVNAAKIIKHPNFDRKTLNNDIMLIKLSSPVKLNARVATVALPSSCAPAGTQCLISGWGNTLSSGVNEPDLLQCLDAPLLPQADCEASYPGKITDNMVCVGFLEGGKDSCQGDSGGPVVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWI	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	216 (216)
Sequences:	10425 (8051.3)
Seq/Len:	48.264
Nf(neff/√len):	547.8

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: 48.264).

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
116_C	183_C	4.383	1.00
27_G	35_V	3.277	1.00
25_C	41_C	3.135	1.00
34_W	87_L	3.052	1.00
6_T	136_Q	2.948	1.00
11_S	137_C	2.914	1.00
68_A	89_K	2.836	1.00
173_C	197_C	2.741	1.00
12_V	137_C	2.584	1.00
15_Q	119_S	2.576	1.00
17_S	23_H	2.546	1.00
42_Y	86_M	2.544	1.00
34_W	89_K	2.504	1.00
40_H	177_S	2.476	1.00
50_L	94_V	2.394	1.00
29_L	94_V	2.378	1.00
66_N	91_S	2.376	1.00
83_N	212_Y	2.367	1.00
28_S	187_L	2.256	1.00
36_V	187_L	2.211	1.00
69_K	89_K	2.123	1.00
33_Q	93_P	2.106	1.00
90_L	94_V	2.099	1.00
193_W	205_V	1.996	1.00
138_L	170_K	1.995	1.00
148_C	162_C	1.984	1.00
16_V	27_G	1.968	1.00
12_V	119_S	1.942	1.00
33_Q	89_K	1.927	1.00
85_I	212_Y	1.913	1.00
96_L	102_T	1.897	1.00
14_Y	104_A	1.897	1.00
118_I	172_S	1.883	1.00
31_N	34_W	1.849	1.00
171_D	204_G	1.846	1.00
49_R	64_F	1.843	1.00
116_C	142_L	1.823	1.00
67_A	88_I	1.822	1.00
32_D	93_P	1.821	1.00
159_N	211_N	1.816	1.00
119_S	182_V	1.767	1.00
65_V	94_V	1.720	1.00
6_T	134_L	1.718	1.00
103_V	187_L	1.713	1.00
16_V	50_L	1.706	1.00
82_N	159_N	1.693	1.00
161_V	181_V	1.674	1.00
207_T	212_Y	1.594	1.00
118_I	138_L	1.590	1.00
28_S	190_I	1.575	1.00
7_C	12_V	1.563	1.00
1_I	4_G	1.517	1.00
28_S	103_V	1.513	1.00
126_S	199_L	1.509	1.00
65_V	91_S	1.504	1.00
68_A	91_S	1.476	1.00
103_V	182_V	1.459	1.00
49_R	52_E	1.452	1.00
172_S	191_V	1.443	1.00
16_V	35_V	1.442	1.00
132_P	136_Q	1.403	0.99
208_K	211_N	1.397	0.99
77_D	80_T	1.393	0.99
75_N	83_N	1.363	0.99
37_S	42_Y	1.317	0.99
19_N	23_H	1.309	0.99
14_Y	182_V	1.301	0.99
145_Q	208_K	1.297	0.99
15_Q	135_L	1.270	0.99
144_P	147_D	1.268	0.99
116_C	181_V	1.262	0.99
48_V	51_G	1.238	0.98
181_V	206_Y	1.238	0.98
116_C	188_Q	1.226	0.98
191_V	194_G	1.225	0.98
50_L	100_V	1.221	0.98
85_I	207_T	1.216	0.98
12_V	117_L	1.216	0.98
115_Q	139_D	1.214	0.98
117_L	139_D	1.211	0.98
72_K	86_M	1.211	0.98
8_Q	11_S	1.201	0.98
52_E	62_E	1.200	0.98
15_Q	26_G	1.198	0.98
9_E	53_H	1.197	0.98
160_M	193_W	1.183	0.98
112_A	144_P	1.181	0.98
82_N	157_T	1.170	0.97
7_C	137_C	1.159	0.97
29_L	96_L	1.149	0.97
54_N	133_D	1.141	0.97
118_I	191_V	1.141	0.97
115_Q	141_P	1.140	0.97
141_P	164_G	1.138	0.97
10_N	99_R	1.136	0.97
73_H	83_N	1.134	0.97
35_V	48_V	1.120	0.96
118_I	140_A	1.119	0.96
10_N	53_H	1.117	0.96
71_I	89_K	1.090	0.96
65_V	92_S	1.079	0.95
70_I	88_I	1.075	0.95
143_L	203_P	1.071	0.95
159_N	212_Y	1.070	0.95
34_W	71_I	1.063	0.95
38_A	190_I	1.059	0.95
163_V	181_V	1.058	0.95
42_Y	72_K	1.053	0.95
106_P	213_V	1.045	0.94
176_D	179_G	1.043	0.94
15_Q	180_P	1.043	0.94
183_C	188_Q	1.042	0.94
83_N	159_N	1.041	0.94
56_N	133_D	1.038	0.94
18_L	48_V	1.037	0.94
40_H	84_D	1.024	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: (31Jan15)
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
4nzqA	1	1	100	0.015	Contact Map
2f83A	1	0.9028	100	0.023	Contact Map
4i8hA	1	1	100	0.026	Contact Map
3nxpA	1	0.9907	100	0.026	Contact Map
4igdA	1	0.9769	100	0.028	Contact Map
1hj8A	1	0.9954	100	0.029	Contact Map
4kkdA	2	0.9815	100	0.029	Contact Map
2b9lA	1	0.9954	100	0.038	Contact Map
1fxyA	1	1	100	0.04	Contact Map
1tonA	1	0.9861	100	0.045	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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