OPENSEQ.org - 1412695775 - GREMLIN Submission

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ID:	1412695775	Query Sequence MIKGSMDMNEQQFFDYVTKFGAYQKRSMFGGIGLFQHDAMYVLVSEDRIFVRGGEELDPELLALGCEKYRHVKKQTTATVNYYDITELYEQHHPELDSIIERSIQFSVNQREFQRSAASRRLRDLPNMQLTLERMVKKAGIDDVETFMSLGAPEVFNKVRQAYGSDVDVKLLWKFAGAIEGIHWKLLQEPRKRQLLESCQQR	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	202 (192)
Sequences:	206 (152.5)
Seq/Len:	1.073
Nf(neff/√len):	11.0

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: 1.073).

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
121_R	124_D	2.349	0.99
130_L	135_M	1.867	0.94
51_V	99_I	1.844	0.93
51_V	85_I	1.746	0.90
17_V	36_Q	1.673	0.88
126_P	140_G	1.603	0.84
46_E	187_L	1.529	0.80
128_M	132_L	1.515	0.79
33_G	40_M	1.515	0.79
134_R	138_K	1.477	0.77
143_D	146_T	1.475	0.77
147_F	175_F	1.470	0.77
134_R	156_F	1.462	0.76
30_G	181_G	1.455	0.76
139_A	159_V	1.444	0.75
41_Y	50_F	1.423	0.73
26_R	44_V	1.391	0.71
62_L	160_R	1.372	0.69
31_G	82_Y	1.354	0.68
73_K	183_H	1.353	0.68
28_M	129_Q	1.345	0.67
82_Y	183_H	1.315	0.65
154_E	169_V	1.301	0.63
51_V	159_V	1.297	0.63
26_R	30_G	1.284	0.62
41_Y	128_M	1.269	0.60
17_V	141_I	1.267	0.60
73_K	181_G	1.252	0.59
21_G	152_A	1.250	0.59
40_M	134_R	1.250	0.59
40_M	156_F	1.232	0.57
27_S	33_G	1.229	0.57
22_A	91_Q	1.228	0.57
57_L	192_K	1.227	0.57
75_Q	175_F	1.224	0.56
26_R	167_V	1.217	0.56
58_D	156_F	1.217	0.56
34_L	96_L	1.211	0.55
33_G	65_G	1.211	0.55
13_F	26_R	1.197	0.54
25_K	53_G	1.196	0.54
153_P	157_N	1.195	0.54
32_I	114_Q	1.192	0.53
73_K	126_P	1.190	0.53
30_G	183_H	1.189	0.53
147_F	164_G	1.188	0.53
129_Q	163_Y	1.188	0.53
20_F	26_R	1.188	0.53
49_I	85_I	1.180	0.52
87_E	91_Q	1.178	0.52
92_H	98_S	1.175	0.52
65_G	141_I	1.169	0.51
18_T	22_A	1.165	0.51
47_D	67_E	1.155	0.50
44_V	194_Q	1.143	0.49
34_L	160_R	1.136	0.48
26_R	31_G	1.128	0.47
13_F	128_M	1.127	0.47
20_F	74_K	1.119	0.46
61_L	134_R	1.119	0.46
39_A	191_R	1.117	0.46
92_H	197_E	1.116	0.46
45_S	128_M	1.112	0.46
42_V	49_I	1.112	0.46
17_V	189_E	1.108	0.45
139_A	168_D	1.099	0.45
134_R	137_K	1.092	0.44
172_L	195_L	1.091	0.44
105_Q	109_N	1.089	0.44
141_I	155_V	1.085	0.43
20_F	122_L	1.083	0.43
82_Y	121_R	1.082	0.43
90_E	96_L	1.077	0.43
152_A	176_A	1.072	0.42
28_M	66_C	1.069	0.42
37_H	108_V	1.065	0.41
61_L	176_A	1.064	0.41
158_K	161_Q	1.063	0.41
38_D	171_L	1.062	0.41
65_G	134_R	1.061	0.41
31_G	121_R	1.061	0.41
122_L	188_Q	1.061	0.41
33_G	41_Y	1.056	0.41
38_D	81_N	1.051	0.40
41_Y	85_I	1.051	0.40
34_L	129_Q	1.047	0.40
86_T	89_Y	1.047	0.40
110_Q	144_V	1.045	0.40
126_P	181_G	1.039	0.39
147_F	188_Q	1.038	0.39
160_R	197_E	1.038	0.39
170_K	185_K	1.035	0.39
152_A	188_Q	1.033	0.39
30_G	82_Y	1.031	0.38
141_I	165_S	1.029	0.38
28_M	32_I	1.021	0.37
44_V	183_H	1.016	0.37
90_E	175_F	1.012	0.37
121_R	152_A	1.007	0.36
159_V	167_V	1.006	0.36
30_G	73_K	1.006	0.36
153_P	198_S	1.004	0.36
28_M	35_F	1.001	0.36

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: (06Sep14)
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
2od0A	2	0.5099	99.9	0.676	Contact Map
3bqsA	2	0.4158	99.8	0.726	Contact Map
2fkiA	1	0.5396	95.1	0.916	Contact Map
2a1vA	1	0.6089	88.6	0.931	Contact Map
2kfpA	1	0.5	67	0.945	Contact Map
1wcnA	1	0.3366	36.9	0.954	Contact Map
1im4A	1	0.6089	31.7	0.955	Contact Map
3wcnA	2	0.4208	29.5	0.956	Contact Map
1z3eB	1	0.3317	28.7	0.956	Contact Map
2z43A	3	0.3614	27.1	0.957	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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