OPENSEQ.org - 1419355841 - GREMLIN Submission

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cus-210

ID:	1419355841	Query Sequence MVSKPFQRPFSLATRLTFFISLATIAAFFAFAWIMIHSVKVHFAEQDINDLKEISATLERVLNHPDETQARRLMTLEDIVSGYSNVLISLADSQGKTVYHSPGAPDIREFTRDAIPDKDAQGGEVYLLSGPTMMMPGHGHGHMEHSNWRMINLPVGPLVDGKPIYTLYIALSIDFHLHYINDLMNKLIMTASVISILIVFIVLLAVHKGH	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	210 (204)
Sequences:	284 (243.8)
Seq/Len:	1.392
Nf(neff/√len):	17.1

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: 1.392).

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
90_L	167_L	1.887	0.96
89_S	97_T	1.821	0.95
76_L	203_L	1.665	0.92
92_D	96_K	1.607	0.89
55_S	154_P	1.545	0.87
181_N	185_N	1.526	0.86
15_R	209_G	1.443	0.81
21_S	201_I	1.408	0.79
193_V	200_F	1.393	0.78
76_L	101_S	1.352	0.75
24_T	32_A	1.348	0.75
179_Y	202_V	1.331	0.74
38_S	42_H	1.321	0.73
47_D	179_Y	1.314	0.72
152_N	166_T	1.308	0.72
49_N	88_I	1.297	0.71
179_Y	183_L	1.295	0.71
96_K	204_L	1.278	0.69
69_Q	118_K	1.268	0.68
77_E	163_P	1.266	0.68
20_I	172_S	1.251	0.67
150_M	168_Y	1.244	0.66
173_I	180_I	1.236	0.65
43_F	179_Y	1.228	0.65
15_R	154_P	1.226	0.64
25_I	194_I	1.224	0.64
59_E	153_L	1.224	0.64
16_L	20_I	1.222	0.64
149_R	169_I	1.214	0.63
100_H	122_G	1.211	0.63
11_S	151_I	1.205	0.63
13_A	207_H	1.201	0.62
57_T	182_D	1.199	0.62
16_L	208_K	1.195	0.62
34_I	198_I	1.194	0.61
192_S	207_H	1.192	0.61
188_I	192_S	1.188	0.61
22_L	26_A	1.187	0.61
76_L	92_D	1.177	0.60
42_H	169_I	1.174	0.60
94_Q	162_K	1.172	0.59
33_W	118_K	1.171	0.59
107_I	144_E	1.171	0.59
88_I	205_A	1.167	0.59
186_K	193_V	1.162	0.58
48_I	196_I	1.158	0.58
12_L	209_G	1.153	0.57
95_G	166_T	1.150	0.57
79_I	162_K	1.143	0.56
47_D	173_I	1.142	0.56
53_E	172_S	1.138	0.56
128_L	173_I	1.131	0.55
16_L	197_L	1.130	0.55
62_L	161_G	1.128	0.55
150_M	194_I	1.125	0.55
18_F	155_V	1.122	0.54
43_F	199_V	1.119	0.54
26_A	41_V	1.119	0.54
188_I	201_I	1.119	0.54
15_R	98_V	1.113	0.53
34_I	110_F	1.111	0.53
74_M	94_Q	1.111	0.53
43_F	209_G	1.108	0.53
88_I	190_T	1.108	0.53
24_T	165_Y	1.106	0.53
109_E	145_H	1.104	0.53
167_L	187_L	1.102	0.52
32_A	155_V	1.098	0.52
54_I	169_I	1.097	0.52
120_A	141_G	1.091	0.51
13_A	195_S	1.086	0.51
15_R	47_D	1.083	0.50
12_L	190_T	1.080	0.50
10_F	186_K	1.075	0.50
14_T	26_A	1.073	0.49
90_L	193_V	1.073	0.49
65_P	157_P	1.072	0.49
198_I	208_K	1.069	0.49
12_L	31_F	1.069	0.49
170_A	209_G	1.069	0.49
38_S	47_D	1.067	0.49
206_V	210_H	1.062	0.48
33_W	208_K	1.058	0.48
24_T	36_I	1.056	0.48
26_A	33_W	1.055	0.48
20_I	191_A	1.052	0.47
24_T	34_I	1.051	0.47
25_I	29_F	1.049	0.47
26_A	37_H	1.048	0.47
16_L	79_I	1.046	0.47
82_G	176_H	1.046	0.47
48_I	149_R	1.041	0.46
23_A	176_H	1.039	0.46
17_T	206_V	1.037	0.46
96_K	150_M	1.037	0.46
25_I	28_F	1.036	0.46
24_T	198_I	1.036	0.46
26_A	182_D	1.036	0.46
108_R	157_P	1.033	0.45
15_R	170_A	1.032	0.45
98_V	118_K	1.030	0.45
58_L	68_T	1.028	0.45
27_A	205_A	1.026	0.45
20_I	199_V	1.026	0.45
9_P	206_V	1.025	0.45
155_V	167_L	1.025	0.45
16_L	206_V	1.019	0.44
94_Q	124_E	1.018	0.44
49_N	131_P	1.016	0.44
39_V	198_I	1.013	0.43
128_L	199_V	1.008	0.43
42_H	209_G	1.003	0.42
16_L	82_G	1.002	0.42
13_A	17_T	1.001	0.42
26_A	62_L	1.000	0.42

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: (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
2kseA	1	0.3667	99.3	0.566	Contact Map
3cwfA	2	0.519	97.5	0.746	Contact Map
3e4oA	2	0.7476	96.7	0.778	Contact Map
4cq4A	4	0.1619	96.5	0.781	Contact Map
4onxA	6	0.5952	95	0.807	Contact Map
3by8A	1	0.6048	90.6	0.834	Contact Map
1p0zA	10	0.6	84.3	0.85	Contact Map
3b42A	2	0.5714	74.7	0.864	Contact Map
2f95B	1	0.2524	53.9	0.881	Contact Map
3b47A	1	0.5286	51.3	0.883	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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