OPENSEQ.org - 1400779738 - GREMLIN Submission

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T0790

ID:	1400779738	Query Sequence MGPNAVELTTDQAWCLADVLGAGSYPWVLAITPPYSDHSQRSAFLAAQSAELTRMGVVNSAGAVDPRVAQWITTVCRATQWLDLRFVSGPGDLLRGMVARRSEETVVALRNAQLVTFTAMDIGHQHALVPVLTAGLSGRKPARFDDFALPAAAGARADEQIRNGAPLAEVLEFLGVPPSARPLVESVFDGRRTYVEIVAGEHRDGHRVTTEVGVSIIDTPHGRILVHPTKAFDGEWISTFTPGSADAIAMAVERLTASLPSGSWFPDQPLTRDFDEDAATHREPVLQRRTQKA	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	293 (264)
Sequences:	447 (387.5)
Seq/Len:	1.693
Nf(neff/√len):	23.8

Jackhmmer Results: (2014_04_16)
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: 1.693).

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
142_A	224_I	3.592	1.00
218_D	223_R	2.797	1.00
75_V	108_A	2.472	1.00
12_Q	51_E	2.281	1.00
28_V	216_I	2.244	0.99
14_W	41_R	1.994	0.98
8_L	128_L	1.983	0.98
195_V	216_I	1.932	0.98
22_A	72_I	1.900	0.98
12_Q	55_M	1.889	0.98
13_A	17_A	1.835	0.97
112_A	115_V	1.816	0.97
144_F	224_I	1.790	0.96
26_P	83_D	1.776	0.96
14_W	33_P	1.675	0.94
44_F	48_Q	1.639	0.93
19_V	49_S	1.569	0.91
28_V	85_R	1.558	0.91
75_V	117_F	1.549	0.90
83_D	198_V	1.533	0.90
16_L	68_V	1.528	0.90
26_P	132_L	1.515	0.89
110_R	216_I	1.514	0.89
99_A	106_V	1.502	0.89
9_T	12_Q	1.500	0.88
86_F	137_S	1.490	0.88
199_A	205_G	1.462	0.87
33_P	55_M	1.440	0.86
142_A	251_A	1.439	0.85
13_A	25_Y	1.427	0.85
28_V	110_R	1.412	0.84
99_A	108_A	1.393	0.83
96_G	135_G	1.385	0.82
14_W	44_F	1.371	0.81
72_I	99_A	1.350	0.80
74_T	99_A	1.337	0.79
59_N	63_A	1.324	0.78
12_Q	48_Q	1.295	0.76
48_Q	68_V	1.294	0.76
138_G	184_V	1.292	0.76
195_V	199_A	1.287	0.75
81_W	113_Q	1.275	0.75
216_I	224_I	1.262	0.73
27_W	30_A	1.256	0.73
35_Y	41_R	1.256	0.73
7_E	252_V	1.253	0.73
17_A	142_A	1.250	0.72
233_D	239_T	1.248	0.72
190_G	220_P	1.237	0.71
47_A	51_E	1.233	0.71
17_A	23_G	1.230	0.71
14_W	35_Y	1.219	0.70
32_T	35_Y	1.213	0.69
144_F	243_G	1.213	0.69
79_T	101_R	1.200	0.68
141_P	199_A	1.195	0.67
26_P	95_R	1.193	0.67
20_L	95_R	1.192	0.67
101_R	258_S	1.184	0.66
17_A	26_P	1.182	0.66
110_R	224_I	1.180	0.66
233_D	236_W	1.177	0.66
43_A	47_A	1.173	0.65
208_V	243_G	1.171	0.65
196_E	200_G	1.161	0.64
78_A	138_G	1.157	0.64
243_G	247_A	1.152	0.63
143_R	247_A	1.139	0.62
195_V	218_D	1.135	0.62
113_Q	173_F	1.132	0.61
13_A	68_V	1.131	0.61
15_C	144_F	1.125	0.61
152_A	252_V	1.124	0.61
9_T	52_L	1.124	0.61
17_A	25_Y	1.114	0.59
141_P	152_A	1.113	0.59
21_G	115_V	1.103	0.58
144_F	242_P	1.101	0.58
29_L	154_G	1.099	0.58
141_P	245_A	1.097	0.58
187_V	191_R	1.091	0.57
107_V	142_A	1.090	0.57
16_L	64_V	1.090	0.57
105_T	196_E	1.085	0.56
52_L	59_N	1.085	0.56
167_L	173_F	1.083	0.56
72_I	244_S	1.082	0.56
184_V	217_I	1.081	0.56
116_T	135_G	1.080	0.56
82_L	256_T	1.075	0.55
78_A	81_W	1.064	0.54
171_L	175_G	1.062	0.54
58_V	106_V	1.061	0.54
82_L	95_R	1.059	0.54
107_V	131_V	1.055	0.53
17_A	22_A	1.054	0.53
239_T	252_V	1.048	0.53
88_S	214_V	1.047	0.52
180_A	214_V	1.046	0.52
27_W	81_W	1.044	0.52
17_A	76_C	1.043	0.52
31_I	35_Y	1.041	0.52
27_W	216_I	1.041	0.52
75_V	162_R	1.041	0.52
244_S	247_A	1.040	0.52
195_V	202_H	1.040	0.52
28_V	35_Y	1.040	0.52
213_G	243_G	1.038	0.51
14_W	147_F	1.035	0.51
65_D	126_H	1.035	0.51
141_P	164_G	1.034	0.51
202_H	206_H	1.025	0.50
148_A	248_I	1.022	0.50
99_A	109_L	1.022	0.50
152_A	235_E	1.021	0.50
37_D	40_Q	1.021	0.50
99_A	146_D	1.018	0.49
172_E	178_P	1.018	0.49
108_A	241_T	1.016	0.49
157_A	175_G	1.015	0.49
263_S	266_P	1.014	0.49
155_A	204_D	1.012	0.49
157_A	167_L	1.009	0.48
66_P	69_A	1.006	0.48
12_Q	83_D	1.000	0.47
58_V	198_V	1.000	0.47

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: (10May14)
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
1tvlA	1	0.2423	2.3	0.973	Contact Map
3proC	2	0.3823	2.2	0.973	Contact Map
2phnA	2	0.5529	2.1	0.973	Contact Map
3h8dA	4	0.1638	2.1	0.973	Contact Map
3c3dA	4	0.314	1.9	0.974	Contact Map
3sdoA	2	0.2594	1.6	0.975	Contact Map
3fk4A	2	0.2457	1.6	0.975	Contact Map
3vmtA	2	0.2253	1.6	0.975	Contact Map
1ez0A	4	0.2389	1.5	0.975	Contact Map
3i0yA	4	0.1672	1.4	0.976	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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