OPENSEQ.org - 1515673251 - GREMLIN Submission

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ID:	1515673251	Query Sequence NLPNMLRDLRDAFSRVKTFFDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIR	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	139 (136)
Sequences:	230 (126.8)
Seq/Len:	1.691
Nf(neff/√len):	10.9

HHblits Results: (2016_02)
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: 1.691).

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
118_K	122_E	2.156	0.99
13_F	17_K	2.027	0.99
57_M	129_Y	1.693	0.95
31_S	104_V	1.620	0.93
50_Q	54_E	1.562	0.91
111_L	118_K	1.557	0.91
119_A	122_E	1.459	0.86
118_K	126_F	1.445	0.86
16_V	94_C	1.423	0.85
25_N	64_D	1.417	0.84
64_D	104_V	1.414	0.84
119_A	124_D	1.412	0.84
21_D	28_L	1.401	0.83
123_F	127_I	1.400	0.83
129_Y	133_Y	1.398	0.83
6_L	14_S	1.392	0.83
122_E	126_F	1.381	0.82
57_M	78_L	1.377	0.82
52_Y	94_C	1.320	0.78
24_D	71_V	1.308	0.77
121_S	127_I	1.305	0.77
10_R	16_V	1.302	0.77
75_G	78_L	1.297	0.76
118_K	121_S	1.288	0.76
115_G	127_I	1.251	0.72
45_L	80_T	1.238	0.71
51_F	78_L	1.228	0.70
118_K	123_F	1.205	0.68
22_Q	84_R	1.202	0.68
72_N	136_M	1.190	0.67
78_L	123_F	1.178	0.66
48_M	57_M	1.177	0.66
10_R	94_C	1.175	0.66
48_M	126_F	1.174	0.65
43_Q	92_L	1.169	0.65
119_A	129_Y	1.166	0.65
2_L	136_M	1.161	0.64
27_L	51_F	1.148	0.63
25_N	72_N	1.148	0.63
23_L	36_F	1.145	0.63
111_L	121_S	1.137	0.62
130_I	133_Y	1.129	0.61
62_N	90_R	1.091	0.57
77_N	104_V	1.086	0.57
57_M	75_G	1.078	0.56
5_M	10_R	1.077	0.56
56_V	119_A	1.076	0.55
115_G	122_E	1.075	0.55
5_M	16_V	1.075	0.55
15_R	109_N	1.072	0.55
42_C	88_C	1.067	0.55
74_L	108_F	1.059	0.54
73_S	114_K	1.058	0.54
26_L	85_L	1.058	0.54
55_E	78_L	1.048	0.53
27_L	58_P	1.045	0.52
37_K	59_Q	1.038	0.51
116_I	119_A	1.034	0.51
36_F	100_A	1.024	0.50
9_L	16_V	1.024	0.50
12_A	62_N	1.023	0.50
115_G	118_K	1.021	0.50
88_C	94_C	1.019	0.49
83_L	112_Q	1.016	0.49
120_M	126_F	1.008	0.48
12_A	78_L	1.006	0.48
130_I	136_M	1.005	0.48
17_K	66_D	1.002	0.48
4_N	124_D	1.001	0.48
95_E	105_K	1.001	0.48

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
2ilkA	1	1	100	0.089	Contact Map
1lqsL	2	0.9424	100	0.163	Contact Map
4dohA	2	0.964	100	0.17	Contact Map
1n1fA	1	0.9784	100	0.172	Contact Map
3dlqI	1	0.8777	100	0.238	Contact Map
4o6kA	4	0.8777	100	0.246	Contact Map
1fyhA	2	0.8849	36.2	0.923	Contact Map
2rigA	1	0.8058	19.5	0.932	Contact Map
1wb9A	2	0.9353	17.3	0.934	Contact Map
1d9cA	2	0.8201	16.4	0.935	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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