OPENSEQ.org - 1405378649 - GREMLIN Submission

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T0830 400-575 -force run

ID:	1405378649	Query Sequence NSFYRAYAVWVAVAFVVMLLGIAVARLLLRRGVLPSVAVYAMGMYLGFTVALLGHETVGRPASGADIAPQIAQKLTPEMPLYGVQMLDHTLPFYLRHPLMMVGQADELTFGATVEPQRVVPDVDSFTKLWKNGQPAMAVMSPDTYLALAPTLSMYVVARDWRRVVVANVASLAGPQ	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	176 (170)
Sequences:	122 (107.7)
Seq/Len:	0.718
Nf(neff/√len):	8.3

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: 0.718).

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
71_I	165_V	2.071	0.93
87_L	97_H	1.984	0.91
89_H	107_E	1.824	0.86
20_L	68_A	1.701	0.80
109_T	113_T	1.631	0.76
84_V	116_P	1.590	0.74
160_D	163_R	1.566	0.72
4_Y	10_W	1.556	0.71
115_E	118_R	1.518	0.69
156_V	159_R	1.464	0.65
66_D	75_L	1.449	0.63
107_E	119_V	1.413	0.60
41_A	95_L	1.412	0.60
92_P	119_V	1.403	0.60
39_V	139_V	1.393	0.59
84_V	138_A	1.387	0.58
139_V	159_R	1.380	0.58
41_A	97_H	1.370	0.57
45_Y	128_K	1.370	0.57
105_A	109_T	1.369	0.57
107_E	110_F	1.357	0.56
88_D	115_E	1.336	0.54
72_A	86_M	1.325	0.53
7_Y	23_A	1.324	0.53
6_A	9_V	1.320	0.53
13_V	150_P	1.306	0.52
67_I	93_F	1.287	0.50
82_Y	136_A	1.281	0.49
72_A	112_A	1.267	0.48
15_F	129_L	1.255	0.47
22_I	126_F	1.254	0.47
98_P	119_V	1.252	0.47
71_I	81_L	1.237	0.46
97_H	158_A	1.237	0.46
124_D	128_K	1.231	0.45
5_R	15_F	1.225	0.45
82_Y	102_V	1.225	0.45
82_Y	98_P	1.211	0.44
80_P	100_M	1.209	0.43
86_M	137_M	1.183	0.41
58_V	62_A	1.177	0.41
8_A	12_A	1.173	0.40
110_F	119_V	1.163	0.40
81_L	136_A	1.150	0.38
126_F	138_A	1.147	0.38
6_A	157_V	1.136	0.37
37_V	165_V	1.136	0.37
109_T	114_V	1.136	0.37
75_L	78_E	1.126	0.37
18_M	148_L	1.125	0.37
80_P	129_L	1.125	0.37
151_T	155_Y	1.121	0.36
2_S	109_T	1.117	0.36
65_A	153_S	1.117	0.36
21_G	42_M	1.100	0.35
64_G	163_R	1.099	0.34
92_P	164_V	1.095	0.34
50_V	53_L	1.087	0.34
89_H	110_F	1.085	0.33
17_V	149_A	1.078	0.33
140_M	166_V	1.068	0.32
115_E	119_V	1.067	0.32
17_V	167_A	1.063	0.32
116_P	120_V	1.060	0.32
11_V	27_L	1.059	0.31
99_L	104_Q	1.055	0.31
68_A	127_T	1.053	0.31
20_L	43_G	1.050	0.31
46_L	145_Y	1.050	0.31
105_A	112_A	1.049	0.31
64_G	160_D	1.048	0.31
51_A	58_V	1.045	0.30
100_M	129_L	1.045	0.30
19_L	71_I	1.042	0.30
70_Q	124_D	1.027	0.29
51_A	117_Q	1.027	0.29
107_E	115_E	1.026	0.29
124_D	167_A	1.026	0.29
84_V	106_D	1.023	0.29
112_A	120_V	1.022	0.29
50_V	125_S	1.020	0.29
24_V	124_D	1.020	0.29
82_Y	116_P	1.019	0.29
25_A	148_L	1.018	0.29
115_E	160_D	1.016	0.28
79_M	167_A	1.015	0.28
66_D	122_D	1.010	0.28
79_M	82_Y	1.010	0.28
73_Q	87_L	1.009	0.28
37_V	101_M	1.008	0.28
112_A	115_E	1.003	0.28
22_I	39_V	1.003	0.28
95_L	130_W	1.000	0.27

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
1ap8A	1	0.6193	10.9	0.953	Contact Map
2l5bA	1	0.1705	10.7	0.953	Contact Map
4tpwA	2	0.5114	10.3	0.954	Contact Map
3hxiA	1	0.5057	9.3	0.955	Contact Map
2idrA	2	0.5114	7.4	0.957	Contact Map
3m94A	1	0.5	5.2	0.96	Contact Map
4b6uA	1	0.6591	5.2	0.96	Contact Map
1igqA	4	0.1875	5.1	0.96	Contact Map
4ue8A	1	0.4602	5	0.96	Contact Map
2zy9A	2	0.5455	4.7	0.961	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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