OPENSEQ.org - 1402705394 - GREMLIN Submission

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T0818

ID:	1402705394	Query Sequence MDSLVKIMGSFLALSLIMIFSSCIVNEHVDEGNIKENAVRMMECIVNKDSEKLFDFYNKDMKDNYKDSSLDEIRQLFEYIDGAITSYNYEGKGGGQEAKNDGIICYYSCHPEFDFTTETGQEYTISFSYHYIWNEHPEYEGINMIQICKDGNWGEKLIIGRNYYKE	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	166 (153)
Sequences:	275 (264.7)
Seq/Len:	1.797
Nf(neff/√len):	21.4

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: 1.797).

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
49_D	52_K	3.636	1.00
41_M	53_L	2.915	1.00
68_S	73_I	1.744	0.96
61_M	65_Y	1.583	0.92
54_F	73_I	1.529	0.91
76_L	81_D	1.509	0.90
18_M	36_E	1.504	0.90
82_G	86_S	1.461	0.88
67_D	72_E	1.445	0.87
8_M	60_D	1.430	0.86
12_L	125_I	1.416	0.85
148_C	152_N	1.409	0.85
53_L	76_L	1.377	0.83
45_I	50_S	1.377	0.83
49_D	55_D	1.374	0.83
10_S	25_V	1.335	0.81
144_M	147_I	1.317	0.79
82_G	117_T	1.313	0.79
19_I	118_E	1.301	0.78
4_L	23_C	1.258	0.75
149_K	153_W	1.244	0.74
41_M	54_F	1.238	0.73
69_S	73_I	1.236	0.73
72_E	76_L	1.234	0.73
66_K	81_D	1.229	0.72
150_D	153_W	1.226	0.72
68_S	76_L	1.225	0.72
151_G	154_G	1.223	0.72
15_S	18_M	1.214	0.71
116_T	120_G	1.203	0.70
12_L	19_I	1.192	0.69
146_Q	149_K	1.179	0.68
12_L	16_L	1.178	0.68
12_L	59_K	1.167	0.67
50_S	53_L	1.158	0.66
100_N	103_I	1.158	0.66
17_I	62_K	1.155	0.65
148_C	151_G	1.155	0.65
57_Y	61_M	1.152	0.65
149_K	152_N	1.152	0.65
152_N	155_E	1.139	0.64
127_F	132_I	1.136	0.64
73_I	76_L	1.131	0.63
34_I	54_F	1.130	0.63
145_I	148_C	1.129	0.63
5_V	43_E	1.124	0.62
41_M	111_P	1.123	0.62
65_Y	73_I	1.121	0.62
44_C	52_K	1.118	0.62
45_I	53_L	1.113	0.61
15_S	78_E	1.112	0.61
41_M	130_H	1.110	0.61
84_I	134_N	1.106	0.61
46_V	84_I	1.104	0.60
76_L	79_Y	1.103	0.60
68_S	135_E	1.102	0.60
127_F	131_Y	1.100	0.60
54_F	57_Y	1.096	0.59
118_E	123_Y	1.095	0.59
80_I	84_I	1.087	0.59
110_H	115_F	1.086	0.58
86_S	91_G	1.084	0.58
8_M	35_K	1.083	0.58
139_Y	144_M	1.080	0.58
35_K	128_S	1.079	0.58
57_Y	73_I	1.079	0.58
153_W	156_K	1.071	0.57
149_K	155_E	1.063	0.56
71_D	102_G	1.059	0.56
117_T	120_G	1.058	0.55
46_V	113_F	1.053	0.55
139_Y	145_I	1.053	0.55
117_T	123_Y	1.051	0.55
22_S	26_N	1.049	0.54
18_M	132_I	1.045	0.54
73_I	77_F	1.043	0.54
11_F	14_L	1.043	0.54
115_F	119_T	1.040	0.53
6_K	98_A	1.039	0.53
102_G	141_G	1.037	0.53
21_S	142_I	1.032	0.53
6_K	10_S	1.031	0.53
73_I	81_D	1.031	0.53
67_D	71_D	1.028	0.52
20_F	51_E	1.026	0.52
80_I	83_A	1.014	0.51
7_I	11_F	1.013	0.51
8_M	13_A	1.008	0.50
11_F	21_S	1.007	0.50

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: (07Jun14)
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
3k7cA	4	0.5843	93.4	0.809	Contact Map
1vqqA	2	0.753	93.4	0.809	Contact Map
2mc8A	1	0.6867	76.2	0.853	Contact Map
3zbiC	14	0.1446	70.6	0.86	Contact Map
2ap3A	1	0.7289	50.4	0.876	Contact Map
3ombA	1	0.5542	49.4	0.877	Contact Map
3gzbA	8	0.7892	47.6	0.878	Contact Map
3h51A	2	0.8133	42.8	0.881	Contact Map
3bb9A	6	0.6867	40.1	0.884	Contact Map
4jg9A	2	0.6627	33	0.889	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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