OPENSEQ.org - 1406624666 - GREMLIN Submission

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TRAP -force run

ID:	1406624666	Query Sequence MAPKGSSKQQSEEDLLLQDFSRNLSAKSSALFFGNAFIVSAIPIWLYWRIWHMDLIQSAVLYSVMTLVSTYLVAFAYKNVKFVLKHKVAQKREDAVSKEVTRKLSEADNRKMSRKEKDERILWKKNEVADYEATTFSIFYNNTLFLVVVIVASFFILKNFNPTVNYILSISASSGLIALLSTGSK	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	185 (182)
Sequences:	86 (67.3)
Seq/Len:	0.473
Nf(neff/√len):	5.0

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: 0.473).

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
165_N	181_S	2.296	0.93
128_V	138_I	1.963	0.83
113_S	145_F	1.920	0.81
166_Y	169_S	1.745	0.72
76_A	79_N	1.661	0.66
88_V	94_D	1.651	0.65
124_K	135_T	1.533	0.57
131_Y	134_T	1.519	0.56
45_W	49_R	1.519	0.56
75_F	87_K	1.509	0.55
24_L	133_A	1.503	0.55
151_V	156_I	1.475	0.53
155_F	158_K	1.475	0.53
45_W	89_A	1.442	0.50
12_E	115_K	1.425	0.49
50_I	73_V	1.402	0.47
65_M	149_V	1.387	0.46
31_L	133_A	1.377	0.45
80_V	83_V	1.354	0.43
53_M	59_A	1.302	0.40
84_L	115_K	1.290	0.39
43_P	76_A	1.289	0.39
15_L	18_Q	1.285	0.38
147_V	159_N	1.269	0.37
23_N	38_I	1.246	0.36
147_V	158_K	1.246	0.36
73_V	161_N	1.237	0.35
175_G	178_A	1.237	0.35
5_G	10_Q	1.236	0.35
125_K	133_A	1.231	0.35
60_V	173_S	1.219	0.34
83_V	105_S	1.208	0.33
129_A	132_E	1.207	0.33
23_N	44_I	1.207	0.33
63_S	94_D	1.206	0.33
53_M	58_S	1.192	0.32
83_V	87_K	1.191	0.32
120_R	127_E	1.189	0.32
120_R	123_W	1.175	0.31
14_D	62_Y	1.166	0.30
88_V	145_F	1.166	0.30
26_A	40_S	1.156	0.30
80_V	148_V	1.146	0.29
79_N	88_V	1.142	0.29
40_S	70_T	1.139	0.29
67_L	97_S	1.135	0.28
83_V	91_K	1.131	0.28
130_D	134_T	1.129	0.28
37_F	183_G	1.128	0.28
155_F	173_S	1.125	0.28
174_S	184_S	1.119	0.27
87_K	91_K	1.114	0.27
165_N	169_S	1.113	0.27
168_L	173_S	1.111	0.27
178_A	183_G	1.110	0.27
145_F	149_V	1.107	0.27
122_L	126_N	1.106	0.27
127_E	132_E	1.105	0.27
64_V	88_V	1.103	0.26
78_K	81_K	1.102	0.26
37_F	145_F	1.100	0.26
56_I	62_Y	1.098	0.26
134_T	176_L	1.090	0.26
66_T	179_L	1.086	0.25
94_D	156_I	1.083	0.25
120_R	162_P	1.079	0.25
52_H	148_V	1.079	0.25
98_K	184_S	1.078	0.25
137_S	141_N	1.077	0.25
58_S	112_M	1.075	0.25
31_L	157_L	1.073	0.25
62_Y	74_A	1.071	0.25
44_I	49_R	1.068	0.24
167_I	180_L	1.067	0.24
18_Q	86_H	1.064	0.24
9_Q	80_V	1.057	0.24
22_R	62_Y	1.055	0.24
10_Q	14_D	1.053	0.24
75_F	183_G	1.052	0.24
173_S	177_I	1.040	0.23
39_V	49_R	1.039	0.23
36_A	40_S	1.033	0.22
15_L	40_S	1.032	0.22
60_V	67_L	1.029	0.22
95_A	175_G	1.026	0.22
42_I	73_V	1.026	0.22
145_F	167_I	1.023	0.22
61_L	147_V	1.023	0.22
20_F	49_R	1.021	0.22
5_G	156_I	1.017	0.22
122_L	142_N	1.015	0.22
11_S	43_P	1.015	0.22
131_Y	136_F	1.014	0.22
54_D	57_Q	1.011	0.21
124_K	172_A	1.010	0.21
5_G	8_K	1.009	0.21
55_L	150_I	1.008	0.21
35_N	38_I	1.005	0.21
177_I	180_L	1.005	0.21
147_V	151_V	1.005	0.21
123_W	135_T	1.004	0.21

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: (12Jul14)
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
1m93A	1	0.173	20.4	0.959	Contact Map
3tx3A	2	0.7081	20	0.959	Contact Map
3b60A	4	0.9081	15	0.962	Contact Map
3b5xA	2	0.9081	12.7	0.963	Contact Map
4afxA	1	0.2973	9.9	0.965	Contact Map
4pl0A	2	0.9243	9.8	0.965	Contact Map
4c7rA	3	0.5081	7.4	0.967	Contact Map
4ajtA	1	0.2811	6.9	0.967	Contact Map
4pypA	1	0.4216	6.9	0.967	Contact Map
1yxaA	2	0.2486	5.5	0.968	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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