OPENSEQ.org - 1411606259 - GREMLIN Submission

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1CV8A

ID:	1411606259	Query Sequence NEQYVNKLENFKIRETQGNNGWCAGYTMSALLNATYNTNKYHAEAVMRFLHPNLQGQQFQFTGLTPREMIYFGQTQGRSPQLLNRMTTYNEVDNLTKNNKGIAILGSRVESRNGMHAGHAMAVVGNAKLNNGQEVIIIWNPWDNGFMTQDAKNNVIPVSNGDHYQWYSSIYGY	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	173 (163)
Sequences:	280 (214.1)
Seq/Len:	1.718
Nf(neff/√len):	16.8

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: 1.718).

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
101_G	122_A	1.843	0.97
97_K	126_N	1.791	0.96
23_C	119_H	1.749	0.96
34_A	101_G	1.731	0.95
28_M	73_G	1.700	0.95
138_I	158_V	1.639	0.93
31_L	103_A	1.630	0.93
24_A	120_A	1.568	0.91
30_A	139_W	1.424	0.85
158_V	169_S	1.420	0.85
22_W	43_A	1.385	0.83
96_T	125_G	1.367	0.82
162_D	168_S	1.345	0.80
89_Y	92_V	1.334	0.79
14_R	65_T	1.321	0.78
14_R	135_V	1.311	0.78
49_F	76_Q	1.306	0.77
66_P	105_L	1.301	0.77
19_N	24_A	1.301	0.77
125_G	156_I	1.297	0.77
64_L	69_M	1.286	0.76
165_Q	168_S	1.271	0.75
24_A	118_G	1.262	0.74
85_R	91_E	1.254	0.73
43_A	106_G	1.250	0.73
163_H	168_S	1.242	0.72
66_P	123_V	1.230	0.71
88_T	125_G	1.225	0.71
43_A	143_D	1.221	0.70
45_A	155_V	1.212	0.69
127_A	140_N	1.207	0.69
114_G	136_I	1.205	0.69
69_M	103_A	1.192	0.68
157_P	163_H	1.185	0.67
163_H	169_S	1.183	0.67
67_R	82_L	1.179	0.66
24_A	64_L	1.179	0.66
164_Y	167_Y	1.178	0.66
25_G	64_L	1.175	0.66
15_E	18_G	1.175	0.66
160_N	165_Q	1.170	0.66
162_D	167_Y	1.160	0.65
113_N	155_V	1.154	0.64
26_Y	143_D	1.152	0.64
90_N	98_N	1.149	0.63
94_N	98_N	1.148	0.63
162_D	165_Q	1.148	0.63
157_P	164_Y	1.147	0.63
65_T	135_V	1.146	0.63
95_L	100_K	1.145	0.63
102_I	156_I	1.139	0.62
17_Q	127_A	1.138	0.62
27_T	122_A	1.138	0.62
109_V	116_H	1.131	0.62
33_N	93_D	1.128	0.61
163_H	167_Y	1.124	0.61
65_T	113_N	1.111	0.60
106_G	161_G	1.107	0.59
88_T	91_E	1.102	0.59
24_A	107_S	1.098	0.58
12_K	102_I	1.094	0.58
10_N	141_P	1.093	0.58
27_T	138_I	1.090	0.57
24_A	61_F	1.090	0.57
151_A	154_N	1.090	0.57
74_Q	104_I	1.087	0.57
88_T	102_I	1.079	0.56
125_G	153_N	1.077	0.56
14_R	139_W	1.065	0.55
53_N	58_Q	1.064	0.55
90_N	136_I	1.062	0.54
45_A	102_I	1.060	0.54
85_R	98_N	1.056	0.54
87_T	100_K	1.051	0.53
84_N	136_I	1.048	0.53
108_R	113_N	1.044	0.53
85_R	88_T	1.040	0.52
46_V	147_M	1.039	0.52
21_G	47_M	1.035	0.52
27_T	145_G	1.033	0.51
88_T	94_N	1.032	0.51
162_D	170_I	1.020	0.50
26_Y	29_S	1.014	0.49
33_N	85_R	1.014	0.49
109_V	131_N	1.010	0.49
24_A	68_E	1.006	0.48
161_G	165_Q	1.006	0.48
43_A	47_M	1.005	0.48
96_T	138_I	1.003	0.48
160_N	163_H	1.003	0.48

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
1cv8A	1	1	100	0.171	Contact Map
1x9yA	4	0.9827	100	0.221	Contact Map
1pxvA	2	0.9942	100	0.225	Contact Map
3ervA	1	0.896	99.6	0.601	Contact Map
3k8uA	1	0.7572	99.4	0.651	Contact Map
2bu3A	2	0.9133	99.4	0.662	Contact Map
3bb7A	1	0.8902	99.1	0.71	Contact Map
3zuaA	1	0.7514	98.9	0.731	Contact Map
3b79A	1	0.6994	98.6	0.754	Contact Map
4d8bA	1	0.9249	98.5	0.761	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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