OPENSEQ.org - 1410902696 - GREMLIN Submission

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tasA_2

ID:	1410902696	Query Sequence MSIKKKLGAGVLAGALGLSLVGGGTFAYFSDTAEQTNTFASGTINLDVNPEMQVPMENIKPGDWMPRDFELLNNGSLDIAYVDLNTDYTVRDSNGHEVGDDLADEYAEQLYVQFLKNTTGDEDYKVLFEVSLKDLRDLTPEDLATKVNIEEIMTEEGYEYWEWIIWPIFGKWITVDPVFEDVPEEVTGIPAGEKAEFDVQFRFNDTGERQNNLQDLDLELDWTFEGYQ	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	228 (201)
Sequences:	224 (166.7)
Seq/Len:	1.114
Nf(neff/√len):	11.8

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: 1.114).

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
11_V	18_L	2.122	0.98
58_N	76_S	1.899	0.95
29_F	37_N	1.898	0.95
4_K	7_L	1.879	0.94
31_D	42_G	1.848	0.94
50_P	67_R	1.772	0.92
54_V	59_I	1.704	0.89
4_K	8_G	1.648	0.87
108_E	133_K	1.618	0.86
37_N	48_V	1.533	0.81
47_D	60_K	1.521	0.81
30_S	44_I	1.501	0.80
45_N	74_N	1.475	0.78
43_T	76_S	1.430	0.75
111_Y	129_E	1.398	0.72
31_D	43_T	1.398	0.72
26_F	48_V	1.396	0.72
120_G	195_A	1.393	0.72
4_K	21_V	1.388	0.72
41_S	63_D	1.379	0.71
35_Q	58_N	1.357	0.69
12_L	15_A	1.350	0.69
31_D	34_E	1.336	0.67
150_E	154_T	1.335	0.67
23_G	30_S	1.317	0.66
62_G	75_G	1.313	0.66
4_K	11_V	1.301	0.64
17_G	63_D	1.282	0.63
84_L	199_V	1.282	0.63
23_G	67_R	1.278	0.62
23_G	27_A	1.277	0.62
40_A	51_E	1.270	0.62
27_A	206_T	1.259	0.61
17_G	41_S	1.255	0.60
13_A	106_Y	1.242	0.59
179_F	184_E	1.241	0.59
41_S	44_I	1.237	0.59
28_Y	39_F	1.219	0.57
184_E	187_T	1.216	0.57
31_D	45_N	1.202	0.55
12_L	18_L	1.201	0.55
23_G	39_F	1.201	0.55
8_G	75_G	1.192	0.54
10_G	24_G	1.184	0.54
117_N	218_L	1.184	0.54
30_S	72_L	1.182	0.54
43_T	63_D	1.179	0.53
23_G	77_L	1.178	0.53
6_K	63_D	1.177	0.53
22_G	25_T	1.172	0.53
199_V	203_F	1.167	0.52
199_V	218_L	1.165	0.52
110_L	201_F	1.162	0.52
31_D	38_T	1.156	0.51
63_D	67_R	1.155	0.51
8_G	18_L	1.155	0.51
3_I	19_S	1.143	0.50
12_L	21_V	1.142	0.50
197_F	213_L	1.142	0.50
44_I	77_L	1.138	0.49
2_S	154_T	1.133	0.49
92_D	96_H	1.132	0.49
5_K	16_L	1.131	0.49
9_A	12_L	1.130	0.49
8_G	14_G	1.124	0.48
19_S	29_F	1.124	0.48
60_K	63_D	1.122	0.48
119_T	127_L	1.122	0.48
35_Q	38_T	1.122	0.48
2_S	6_K	1.122	0.48
29_F	77_L	1.117	0.47
199_V	222_W	1.113	0.47
3_I	7_L	1.102	0.46
8_G	69_F	1.095	0.45
28_Y	37_N	1.094	0.45
213_L	224_F	1.091	0.45
40_A	43_T	1.090	0.45
133_K	137_D	1.088	0.45
88_Y	224_F	1.085	0.44
31_D	39_F	1.079	0.44
23_G	82_V	1.076	0.43
3_I	49_N	1.075	0.43
38_T	43_T	1.070	0.43
36_T	226_G	1.068	0.43
22_G	63_D	1.067	0.43
10_G	33_A	1.062	0.42
20_L	79_I	1.057	0.42
58_N	65_M	1.056	0.42
103_A	106_Y	1.054	0.41
30_S	37_N	1.051	0.41
9_A	15_A	1.049	0.41
1_M	4_K	1.046	0.41
29_F	79_I	1.044	0.40
25_T	31_D	1.041	0.40
33_A	37_N	1.041	0.40
183_P	193_E	1.040	0.40
23_G	50_P	1.038	0.40
153_M	179_F	1.035	0.40
16_L	58_N	1.031	0.39
26_F	71_L	1.028	0.39
130_V	209_R	1.026	0.39
104_D	108_E	1.026	0.39
152_I	155_E	1.024	0.39
42_G	77_L	1.017	0.38
180_E	183_P	1.013	0.38
11_V	36_T	1.012	0.38
16_L	79_I	1.010	0.37
20_L	23_G	1.010	0.37
33_A	58_N	1.009	0.37
23_G	54_V	1.008	0.37
178_V	184_E	1.008	0.37
102_L	151_E	1.005	0.37
205_D	210_Q	1.005	0.37
150_E	153_M	1.001	0.37
44_I	69_F	1.000	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: (17Jul14)
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
2x3cA	1	0.5044	64.9	0.928	Contact Map
2kutA	1	0.4079	48.6	0.935	Contact Map
1yewA	3	0.6711	47.4	0.935	Contact Map
4phzA	3	0.6667	32.7	0.941	Contact Map
3isyA	1	0.4781	24.1	0.945	Contact Map
2e6jA	1	0.4298	22.6	0.945	Contact Map
2l0dA	1	0.386	15.9	0.949	Contact Map
2k6wA	1	0.2719	11.3	0.952	Contact Map
2fauA	1	0.5	11.2	0.952	Contact Map
3iduA	2	0.5175	11.1	0.952	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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