OPENSEQ.org - 1402957828 - GREMLIN Submission

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T0774 - TR274

ID:	1402957828	Query Sequence TRHVLTQIANIKVKPDVNLGTDTKIFVTGLKLDPGSTTLYNKAVYKFDNDTWEAISPDASYFSTEQDLSDFLNKTTTDQWGYNKSSINVSDDQNATALFSDTEALYFIPVNNKNGTTNAGDLKLKINYDIVTKVTDTSNLTSTITNKEVSLPKNTFKKGTKHTYVLTIKMNAIKITVEDNMEGWTDDSDSDINVEK	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	196 (188)
Sequences:	213 (195.4)
Seq/Len:	1.133
Nf(neff/√len):	14.3

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: 1.133).

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
156_F	164_Y	4.430	1.00
6_T	162_H	2.995	1.00
7_Q	166_L	2.496	0.99
157_K	160_T	2.371	0.99
172_A	175_I	2.112	0.98
5_L	106_Y	1.929	0.95
128_Y	162_H	1.715	0.90
7_Q	161_K	1.707	0.90
11_I	30_L	1.683	0.89
106_Y	166_L	1.671	0.88
7_Q	107_F	1.671	0.88
39_L	43_A	1.638	0.87
10_N	161_K	1.636	0.87
27_V	177_V	1.618	0.86
7_Q	106_Y	1.500	0.80
107_F	128_Y	1.488	0.79
46_K	50_D	1.483	0.79
6_T	30_L	1.418	0.74
39_L	124_L	1.389	0.72
10_N	162_H	1.381	0.72
114_N	117_T	1.373	0.71
8_I	164_Y	1.372	0.71
7_Q	104_A	1.369	0.71
12_K	163_T	1.366	0.70
151_L	165_V	1.365	0.70
110_V	156_F	1.334	0.68
107_F	156_F	1.327	0.67
45_Y	110_V	1.307	0.65
23_T	177_V	1.279	0.63
13_V	108_I	1.267	0.62
6_T	110_V	1.250	0.60
8_I	161_K	1.243	0.60
12_K	165_V	1.235	0.59
11_I	16_D	1.234	0.59
43_A	156_F	1.232	0.59
173_I	177_V	1.230	0.59
14_K	164_Y	1.229	0.58
5_L	27_V	1.207	0.56
122_L	126_I	1.206	0.56
32_L	119_A	1.203	0.56
128_Y	166_L	1.201	0.56
32_L	174_K	1.201	0.56
45_Y	105_L	1.197	0.55
23_T	108_I	1.191	0.55
2_R	27_V	1.188	0.55
25_I	168_I	1.187	0.54
28_T	128_Y	1.180	0.54
52_W	108_I	1.170	0.53
11_I	156_F	1.167	0.53
8_I	50_D	1.163	0.52
127_N	146_N	1.149	0.51
175_I	181_M	1.137	0.50
7_Q	47_F	1.134	0.49
25_I	108_I	1.127	0.49
93_Q	173_I	1.125	0.49
128_Y	151_L	1.124	0.48
4_V	163_T	1.118	0.48
120_G	131_V	1.117	0.48
70_D	73_N	1.114	0.48
162_H	183_G	1.108	0.47
69_S	74_K	1.101	0.46
58_D	62_F	1.100	0.46
15_P	175_I	1.099	0.46
14_K	25_I	1.097	0.46
137_T	191_D	1.087	0.45
45_Y	147_K	1.077	0.44
87_I	155_T	1.074	0.44
113_K	116_T	1.066	0.43
4_V	156_F	1.063	0.43
7_Q	128_Y	1.059	0.42
2_R	190_S	1.055	0.42
8_I	156_F	1.054	0.42
69_S	73_N	1.048	0.41
85_S	126_I	1.046	0.41
88_N	158_K	1.042	0.41
126_I	137_T	1.042	0.41
6_T	45_Y	1.040	0.41
152_P	182_E	1.023	0.39
23_T	52_W	1.018	0.39
60_S	63_S	1.018	0.39
191_D	194_V	1.018	0.39
111_N	165_V	1.016	0.38
43_A	170_M	1.016	0.38
4_V	50_D	1.016	0.38
177_V	181_M	1.014	0.38
7_Q	167_T	1.008	0.38
73_N	77_T	1.005	0.37
10_N	128_Y	1.005	0.37
11_I	46_K	1.000	0.37

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: (14Jun14)
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
3t2lA	1	0.7398	99.7	0.525	Contact Map
3sy6A	2	0.7092	99.7	0.526	Contact Map
3ufiA	1	0.6173	99.6	0.537	Contact Map
4k4kA	2	0.6531	99.6	0.554	Contact Map
4epsA	1	0.6582	98	0.753	Contact Map
4jg5A	1	0.7908	96.9	0.802	Contact Map
4dguA	2	0.6122	96.7	0.806	Contact Map
4gpvA	2	0.8367	93.2	0.844	Contact Map
3liuA	2	0.8878	91.3	0.853	Contact Map
3up6A	2	0.8265	90.5	0.856	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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