OPENSEQ.org - 1403640379 - GREMLIN Submission

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ndu3

ID:	1403640379	Query Sequence MATALALRSLYRARPSLRCPPVELPWAPRRGHRLSPADDELYQRTRISLLQREAAQAMYIDSYNSRGFMINGNRVLGPCALLPHSVVQWNVGSHQDITEDSFSLFWLLEPRIEIVVVGTGDRTERLQSQVLQAMRQRGIAVEVQDTPNACATFNFLCHEGRVTGAALIPPPGGTSLTSLGQAAQ	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	184 (173)
Sequences:	195 (140.6)
Seq/Len:	1.127
Nf(neff/√len):	10.7

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: 1.127).

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
96_D	108_L	1.798	0.93
62_S	105_F	1.714	0.90
130_V	141_V	1.599	0.85
142_E	167_L	1.588	0.85
129_Q	134_M	1.542	0.82
115_V	164_G	1.524	0.81
117_V	126_L	1.514	0.81
87_V	112_I	1.514	0.81
80_A	112_I	1.448	0.76
67_G	169_P	1.435	0.75
18_R	22_V	1.424	0.75
102_F	133_A	1.423	0.75
145_D	148_N	1.407	0.73
18_R	27_A	1.372	0.71
119_T	124_E	1.361	0.70
85_S	160_G	1.358	0.70
84_H	87_V	1.344	0.68
131_L	142_E	1.329	0.67
60_I	111_R	1.322	0.67
9_S	12_R	1.280	0.63
69_M	74_R	1.277	0.63
102_F	135_R	1.270	0.62
120_G	146_T	1.256	0.61
165_A	169_P	1.255	0.61
15_P	19_C	1.252	0.60
11_Y	15_P	1.232	0.59
40_E	78_P	1.221	0.58
126_L	132_Q	1.220	0.57
70_I	113_E	1.218	0.57
72_G	115_V	1.186	0.54
152_T	161_R	1.185	0.54
7_L	12_R	1.184	0.54
39_D	77_G	1.175	0.53
164_G	169_P	1.172	0.53
60_I	65_S	1.166	0.52
87_V	138_G	1.161	0.52
10_L	13_A	1.158	0.52
104_L	108_L	1.156	0.51
61_D	71_N	1.155	0.51
39_D	45_T	1.155	0.51
156_L	159_E	1.154	0.51
68_F	110_P	1.151	0.51
111_R	151_A	1.148	0.51
102_F	111_R	1.147	0.51
47_I	59_Y	1.146	0.50
14_R	18_R	1.142	0.50
17_L	20_P	1.142	0.50
106_W	133_A	1.142	0.50
29_R	33_R	1.134	0.49
36_P	136_Q	1.134	0.49
16_S	19_C	1.133	0.49
138_G	148_N	1.132	0.49
63_Y	168_I	1.130	0.49
89_W	154_N	1.129	0.49
20_P	23_E	1.122	0.48
21_P	24_L	1.121	0.48
22_V	26_W	1.117	0.48
15_P	24_L	1.115	0.47
85_S	158_H	1.115	0.47
9_S	13_A	1.106	0.47
75_V	79_C	1.106	0.47
11_Y	16_S	1.104	0.46
17_L	21_P	1.101	0.46
149_A	166_A	1.100	0.46
102_F	105_F	1.093	0.45
60_I	101_S	1.091	0.45
63_Y	152_T	1.084	0.45
50_L	146_T	1.078	0.44
8_R	12_R	1.077	0.44
47_I	155_F	1.072	0.43
72_G	169_P	1.070	0.43
68_F	101_S	1.067	0.43
7_L	10_L	1.064	0.43
153_F	168_I	1.064	0.43
14_R	20_P	1.064	0.43
128_S	145_D	1.064	0.43
112_I	131_L	1.060	0.42
13_A	16_S	1.052	0.41
40_E	44_R	1.048	0.41
106_W	137_R	1.048	0.41
19_C	24_L	1.048	0.41
67_G	115_V	1.047	0.41
7_L	14_R	1.045	0.41
15_P	18_R	1.043	0.41
23_E	27_A	1.042	0.41
44_R	170_P	1.042	0.41
63_Y	113_E	1.041	0.40
10_L	14_R	1.039	0.40
124_E	142_E	1.037	0.40
11_Y	14_R	1.035	0.40
160_G	164_G	1.035	0.40
26_W	168_I	1.032	0.40
9_S	15_P	1.028	0.39
19_C	25_P	1.025	0.39
40_E	45_T	1.024	0.39
90_N	94_H	1.023	0.39
145_D	165_A	1.022	0.39
13_A	18_R	1.021	0.39
44_R	78_P	1.021	0.39
14_R	17_L	1.020	0.39
87_V	137_R	1.020	0.39
8_R	14_R	1.020	0.39
22_V	25_P	1.018	0.38
17_L	22_V	1.015	0.38
74_R	144_Q	1.013	0.38
70_I	137_R	1.011	0.38
9_S	14_R	1.008	0.37
111_R	139_I	1.007	0.37
73_N	116_V	1.002	0.37

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: (21Jun14)
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
2fi9A	1	0.6413	100	0.44	Contact Map
3cpkA	1	0.6359	100	0.443	Contact Map
2fvtA	1	0.7337	100	0.444	Contact Map
2gm2A	1	0.712	100	0.46	Contact Map
2ab1A	2	0.625	100	0.527	Contact Map
2cyjA	1	0.587	100	0.562	Contact Map
1ihnA	2	0.5652	99.9	0.582	Contact Map
2r76A	2	0.3315	35.5	0.945	Contact Map
2dkhA	1	0.5435	30.6	0.947	Contact Map
3ahcA	1	0.9565	29.9	0.948	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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