OPENSEQ.org - 1406133372 - GREMLIN Submission

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Ts814_d03 -force run

ID:	1406133372	Query Sequence PAGNEYRRMEFLSNKYNGMHVENISFHNPYYNVELMTDYRRDKGTYQYDQDQDGRFFIRCSDCNDPDTEADYYIVHFTLACDPLPDGSVYLNGELFNNVLDEKSKMGYNFETKQYEKAVLLKQGSYNYQYLFVPTGSSVGQTGPIEGNYYQ	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	151 (150)
Sequences:	139 (127.7)
Seq/Len:	0.927
Nf(neff/√len):	10.4

HHblits Results: (2013_03)
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: 0.927).

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
109_N	116_E	5.893	1.00
38_D	130_Y	3.057	1.00
106_M	117_K	2.054	0.96
41_R	146_E	1.940	0.94
5_E	51_D	1.925	0.93
88_S	105_K	1.876	0.92
13_S	71_D	1.834	0.91
90_Y	104_S	1.832	0.91
76_H	126_Y	1.807	0.90
121_L	126_Y	1.645	0.83
41_R	130_Y	1.620	0.82
48_Y	76_H	1.607	0.81
18_G	136_G	1.501	0.75
91_L	119_V	1.368	0.65
12_L	125_S	1.353	0.63
96_F	104_S	1.330	0.61
63_C	70_A	1.327	0.61
7_R	146_E	1.315	0.60
8_R	125_S	1.302	0.59
95_L	104_S	1.301	0.59
79_L	145_I	1.299	0.59
2_A	119_V	1.294	0.58
58_I	75_V	1.290	0.58
5_E	53_D	1.281	0.57
52_Q	125_S	1.281	0.57
32_N	76_H	1.265	0.56
24_I	65_D	1.237	0.53
79_L	130_Y	1.235	0.53
46_Y	126_Y	1.217	0.51
87_G	136_G	1.215	0.51
10_E	131_L	1.204	0.50
48_Y	148_N	1.200	0.50
109_N	112_T	1.190	0.49
84_L	151_Q	1.180	0.48
5_E	79_L	1.161	0.46
86_D	135_T	1.158	0.46
61_S	125_S	1.157	0.46
11_F	73_Y	1.124	0.43
8_R	150_Y	1.124	0.43
89_V	119_V	1.110	0.42
2_A	111_E	1.094	0.40
81_C	106_M	1.092	0.40
109_N	113_K	1.081	0.39
43_K	149_Y	1.081	0.39
13_S	18_G	1.076	0.39
21_V	35_L	1.072	0.38
35_L	78_T	1.072	0.38
14_N	53_D	1.068	0.38
10_E	150_Y	1.062	0.37
106_M	123_Q	1.061	0.37
60_C	106_M	1.060	0.37
65_D	82_D	1.059	0.37
65_D	105_K	1.057	0.37
12_L	26_F	1.052	0.37
7_R	38_D	1.046	0.36
31_Y	130_Y	1.039	0.36
75_V	87_G	1.039	0.36
53_D	130_Y	1.033	0.35
2_A	78_T	1.030	0.35
10_E	104_S	1.026	0.34
46_Y	56_F	1.023	0.34
108_Y	114_Q	1.022	0.34
74_I	118_A	1.019	0.34
100_L	127_N	1.018	0.34
12_L	59_R	1.016	0.34
9_M	46_Y	1.007	0.33
12_L	95_L	1.006	0.33
7_R	33_V	1.004	0.33

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
4aefA	2	0.5762	96.1	0.881	Contact Map
4aeeA	2	0.5828	96.1	0.881	Contact Map
2qlvB	2	0.4967	95.7	0.885	Contact Map
2lu3A	1	0.5762	94.4	0.893	Contact Map
1ac0A	1	0.5497	92.9	0.899	Contact Map
1z0nA	3	0.4636	92	0.902	Contact Map
4pyhA	1	0.9007	88.9	0.908	Contact Map
4cfeB	2	0.4503	87.3	0.911	Contact Map
2z0bA	6	0.5497	85	0.914	Contact Map
1m7xA	4	0.6225	84.6	0.914	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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