OPENSEQ.org - 1404255310 - GREMLIN Submission

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Q9HYR3_1Z1S -force run

ID:	1404255310	Query Sequence MNAKEILVHSLRLLENGDARGWCDLFHPEGVLEFPYAPPGWKTRFEGRETIWAHMRLFPEHLTVRFTDVQFYETADPDLAIGEFHGDGVATVSGGKLAQDYISVLRTRDGQILLYRDFWNPLRHLEALGGVEAAAKIVQGA	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	141 (136)
Sequences:	94 (90.4)
Seq/Len:	0.691
Nf(neff/√len):	7.8

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: 0.691).

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
36_Y	99_Q	2.302	0.97
34_F	119_W	1.872	0.87
84_F	117_D	1.868	0.87
104_V	117_D	1.775	0.83
33_E	44_R	1.689	0.79
51_I	82_G	1.602	0.73
101_Y	119_W	1.576	0.72
131_V	134_A	1.529	0.68
30_G	51_I	1.506	0.67
90_A	128_L	1.470	0.64
84_F	103_S	1.458	0.63
78_D	108_R	1.434	0.61
22_W	55_M	1.417	0.60
28_P	46_E	1.406	0.59
132_E	135_A	1.401	0.58
6_I	70_Q	1.391	0.58
34_F	101_Y	1.367	0.56
38_P	120_N	1.338	0.53
108_R	113_L	1.326	0.52
55_M	88_G	1.318	0.51
94_G	127_A	1.316	0.51
25_L	66_F	1.302	0.50
34_F	115_Y	1.290	0.49
28_P	50_T	1.286	0.49
28_P	49_E	1.281	0.48
79_L	106_R	1.279	0.48
37_A	118_F	1.242	0.45
22_W	66_F	1.240	0.45
10_S	22_W	1.233	0.44
45_F	118_F	1.216	0.43
11_L	111_Q	1.207	0.42
115_Y	121_P	1.195	0.41
83_E	116_R	1.187	0.41
10_S	55_M	1.185	0.40
15_E	118_F	1.179	0.40
74_T	77_P	1.176	0.40
71_F	120_N	1.160	0.38
133_A	137_I	1.152	0.38
24_D	100_D	1.132	0.36
40_G	76_D	1.131	0.36
72_Y	75_A	1.124	0.36
78_D	90_A	1.118	0.35
24_D	132_E	1.116	0.35
63_T	117_D	1.111	0.35
51_I	84_F	1.101	0.34
32_L	120_N	1.099	0.34
5_E	28_P	1.093	0.33
26_F	82_G	1.083	0.32
134_A	137_I	1.082	0.32
22_W	105_L	1.079	0.32
25_L	82_G	1.076	0.32
80_A	97_L	1.073	0.32
16_N	56_R	1.072	0.32
76_D	79_L	1.068	0.31
20_R	79_L	1.062	0.31
84_F	101_Y	1.061	0.31
54_H	115_Y	1.059	0.31
133_A	136_K	1.053	0.30
48_R	56_R	1.046	0.30
37_A	45_F	1.046	0.30
108_R	116_R	1.037	0.29
26_F	51_I	1.036	0.29
70_Q	75_A	1.033	0.29
5_E	82_G	1.025	0.28
54_H	119_W	1.023	0.28
48_R	130_G	1.023	0.28
24_D	129_G	1.023	0.28
37_A	106_R	1.022	0.28
26_F	95_G	1.017	0.28
38_P	68_D	1.017	0.28
100_D	121_P	1.015	0.28
31_V	76_D	1.009	0.27
76_D	126_E	1.002	0.27
32_L	103_S	1.000	0.27
80_A	108_R	1.000	0.27
24_D	46_E	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: (05Jul14)
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
1z1sA	1	0.9149	99.9	0.527	Contact Map
1s5aA	4	0.9574	99.9	0.565	Contact Map
3jumA	2	0.9858	99.8	0.596	Contact Map
3ff0A	2	0.9858	99.8	0.607	Contact Map
3grdA	2	0.8865	99.8	0.615	Contact Map
3dm8A	1	0.9149	99.8	0.621	Contact Map
3dmcA	2	0.8582	99.8	0.629	Contact Map
3fgyA	2	0.922	99.8	0.63	Contact Map
2a15A	1	0.8652	99.8	0.635	Contact Map
3f8hA	2	0.8865	99.7	0.643	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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