OPENSEQ.org - 1488468578 - GREMLIN Submission

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4CI0_C

ID:	1488468578	Query Sequence VLGTYKEIVSARSTDREIQKLAQDGGIVTGLLAYALDEGIIEGAVVAGPGEEFWKPQPMVAMSSDELKAAAGTKYTFSPNVMMLKKAVRQYGIEKLGTVAIPCQTMGIRKMQTYPFGVRFLADKIKLLVGIYCMENFPYTSLQTFICEKLGVSMELVEKMDIGKGKFWVYTQDDVLTLPLKETHGYEQAGCKICKDYVAELADVSTGSVGSPDGWSTVITRTDAGDSIFKQAVEAGLFETKPIEEVKPGLGLLEKLAAQKKEKAEKNIAARKEMGLPTPF	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	280 (261)
Sequences:	967 (751.6)
Seq/Len:	3.705
Nf(neff/√len):	46.5

HHblits Results: (2016_02)
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: 3.705).

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
220_T	229_F	3.161	1.00
226_D	230_K	3.018	1.00
7_E	226_D	2.852	1.00
105_T	128_L	2.782	1.00
13_S	30_G	2.733	1.00
63_S	66_E	2.717	1.00
130_G	199_A	2.714	1.00
127_L	228_I	2.660	1.00
32_L	99_V	2.623	1.00
109_R	112_Q	2.365	1.00
60_V	90_Q	2.332	1.00
207_G	217_T	2.301	1.00
132_Y	207_G	2.104	1.00
32_L	97_G	2.087	1.00
204_V	225_G	2.084	1.00
41_I	44_A	2.077	1.00
98_T	105_T	2.076	1.00
12_R	19_Q	2.049	1.00
103_C	194_C	2.038	1.00
100_A	105_T	2.030	1.00
61_A	70_A	1.992	1.00
109_R	128_L	1.980	1.00
29_T	71_A	1.961	1.00
132_Y	205_S	1.923	1.00
48_G	59_M	1.907	1.00
103_C	191_C	1.901	1.00
37_D	64_S	1.881	1.00
35_A	127_L	1.881	1.00
43_G	93_I	1.832	0.99
191_C	194_C	1.810	0.99
11_A	218_V	1.800	0.99
50_G	57_Q	1.718	0.99
129_V	206_T	1.678	0.99
35_A	40_I	1.650	0.99
62_M	66_E	1.617	0.98
24_D	208_S	1.585	0.98
34_Y	37_D	1.581	0.98
18_I	29_T	1.578	0.98
33_A	67_L	1.534	0.98
62_M	94_E	1.521	0.97
35_A	97_G	1.495	0.97
46_V	61_A	1.494	0.97
29_T	67_L	1.491	0.97
27_I	206_T	1.486	0.97
135_E	187_E	1.475	0.97
47_A	56_P	1.470	0.97
132_Y	217_T	1.458	0.96
11_A	27_I	1.444	0.96
50_G	55_K	1.431	0.96
158_E	172_Q	1.425	0.96
222_T	225_G	1.401	0.95
101_I	104_Q	1.397	0.95
75_Y	208_S	1.391	0.95
46_V	70_A	1.386	0.95
218_V	229_F	1.373	0.95
61_A	66_E	1.350	0.94
32_L	41_I	1.348	0.94
59_M	69_A	1.339	0.94
33_A	37_D	1.311	0.93
29_T	33_A	1.274	0.91
48_G	70_A	1.268	0.91
196_D	221_R	1.266	0.91
223_D	227_S	1.265	0.91
24_D	75_Y	1.257	0.90
8_I	219_I	1.257	0.90
25_G	75_Y	1.245	0.90
134_M	137_F	1.241	0.90
24_D	137_F	1.237	0.89
163_G	208_S	1.233	0.89
28_V	99_V	1.220	0.89
36_L	41_I	1.214	0.88
33_A	64_S	1.188	0.87
223_D	226_D	1.188	0.87
6_K	226_D	1.186	0.87
229_F	233_V	1.183	0.86
82_M	86_K	1.176	0.86
103_C	133_C	1.171	0.86
59_M	70_A	1.161	0.85
18_I	26_G	1.154	0.85
27_I	67_L	1.149	0.84
66_E	69_A	1.145	0.84
32_L	67_L	1.140	0.84
230_K	233_V	1.131	0.83
229_F	232_A	1.118	0.82
64_S	68_K	1.118	0.82
38_E	231_Q	1.116	0.82
87_A	105_T	1.116	0.82
67_L	70_A	1.116	0.82
23_Q	72_G	1.113	0.82
220_T	226_D	1.111	0.81
144_T	147_C	1.108	0.81
156_L	172_Q	1.107	0.81
133_C	194_C	1.096	0.80
80_N	98_T	1.089	0.80
16_R	19_Q	1.082	0.79
24_D	216_S	1.080	0.79
204_V	229_F	1.072	0.78
238_F	244_E	1.069	0.78
30_G	232_A	1.066	0.78
24_D	73_T	1.060	0.77
62_M	65_D	1.048	0.76
169_V	212_P	1.043	0.75
12_R	239_E	1.042	0.75
261_K	264_A	1.036	0.75
211_S	217_T	1.033	0.74
27_I	131_I	1.024	0.73
27_I	218_V	1.023	0.73
67_L	151_G	1.021	0.73
15_D	161_D	1.019	0.73
259_Q	262_E	1.019	0.73
109_R	201_L	1.018	0.73
25_G	73_T	1.016	0.73
59_M	108_I	1.015	0.73
23_Q	134_M	1.009	0.72
35_A	228_I	1.006	0.72
229_F	238_F	1.006	0.72
26_G	29_T	1.002	0.71
254_E	258_A	1.000	0.71

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: (06Aug15)
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
4omfB	1	1	100	0.118	Contact Map
2mjgA	2	0.1571	22.7	0.957	Contact Map
1rcuA	4	0.2321	10.1	0.964	Contact Map
3wxmB	4	0.1964	5.1	0.968	Contact Map
3oj0A	1	0.4571	4.7	0.969	Contact Map
3obwA	1	0.1679	4.3	0.969	Contact Map
2oo2A	1	0.1821	4.1	0.97	Contact Map
4d9bA	4	0.4964	4	0.97	Contact Map
4iqyA	2	0.4536	2.9	0.972	Contact Map
3e59A	4	0.1964	2.9	0.972	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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