OPENSEQ.org - 1461769431 - GREMLIN Submission

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Bacterial E2 350-580

ID:	1461769431	Query Sequence ETQPLPRIKKISGAHLHRCWLSVPHVTQFDAADITELEAFRKEQKAAAEAAGVKLTFMPFLLKAVAGALAQMPTLKASLSADGEGLVMKHYTHLGVAVDTPNGLVVPVLRDVDKKGVFDLARELMAISAKARDGKLLPGDMQGGVFSISSLGGIGGTAFTPIVNAPEVAILGVSRSEMKPVWNGREFSPRLMLPLSLSYDHRVVDGAEAVRFTTLLASLLGDIRRLLLTGP	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	231 (228)
Sequences:	6065 (3376.6)
Seq/Len:	26.601
Nf(neff/√len):	223.6

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: 26.601).

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
71_Q	215_L	3.671	1.00
126_A	130_K	3.535	1.00
115_K	123_E	3.134	1.00
72_M	215_L	2.977	1.00
31_A	179_K	2.823	1.00
1_E	90_H	2.818	1.00
123_E	126_A	2.656	1.00
129_A	133_D	2.592	1.00
78_S	89_K	2.574	1.00
182_W	189_P	2.538	1.00
11_I	14_A	2.494	1.00
62_L	94_L	2.435	1.00
33_D	190_R	2.393	1.00
182_W	187_F	2.340	1.00
178_M	191_L	2.325	1.00
130_K	140_D	2.251	1.00
2_T	85_G	2.146	1.00
65_V	146_F	2.028	1.00
63_K	67_G	1.994	1.00
91_Y	111_D	1.959	1.00
70_A	113_D	1.941	1.00
38_E	57_F	1.908	1.00
144_G	167_E	1.869	1.00
215_L	218_S	1.864	1.00
25_H	198_S	1.851	1.00
5_L	79_L	1.847	1.00
207_A	211_R	1.779	1.00
66_A	92_T	1.760	1.00
180_P	187_F	1.756	1.00
95_G	106_V	1.709	1.00
65_V	216_L	1.707	1.00
116_G	119_D	1.679	1.00
31_A	157_T	1.671	1.00
11_I	15_H	1.665	1.00
115_K	119_D	1.650	1.00
67_G	219_L	1.628	1.00
62_L	112_V	1.616	1.00
62_L	148_I	1.612	1.00
32_A	195_L	1.599	1.00
217_A	221_G	1.595	1.00
69_L	146_F	1.574	1.00
68_A	216_L	1.568	1.00
111_D	114_K	1.567	1.00
62_L	96_V	1.565	1.00
124_L	128_S	1.562	1.00
36_E	39_A	1.555	1.00
20_W	25_H	1.544	1.00
30_D	217_A	1.534	1.00
18_R	22_S	1.522	1.00
17_H	21_L	1.521	1.00
66_A	112_V	1.521	1.00
178_M	189_P	1.513	1.00
15_H	18_R	1.484	1.00
161_P	172_G	1.478	1.00
215_L	219_L	1.463	1.00
3_Q	88_M	1.457	1.00
29_F	158_A	1.454	1.00
80_S	85_G	1.453	1.00
61_L	173_V	1.439	1.00
128_S	132_R	1.420	1.00
14_A	18_R	1.403	0.99
93_H	110_R	1.401	0.99
102_N	134_G	1.385	0.99
91_Y	113_D	1.382	0.99
201_H	206_G	1.381	0.99
9_K	205_D	1.367	0.99
8_I	12_S	1.367	0.99
38_E	191_L	1.357	0.99
146_F	169_A	1.339	0.99
34_I	193_L	1.335	0.99
43_E	224_R	1.333	0.99
35_T	191_L	1.315	0.99
37_L	60_F	1.314	0.99
131_A	136_L	1.314	0.99
74_T	88_M	1.310	0.99
62_L	124_L	1.309	0.99
34_I	37_L	1.308	0.99
23_V	163_V	1.306	0.99
176_S	191_L	1.278	0.99
77_A	88_M	1.278	0.99
2_T	87_V	1.259	0.99
72_M	211_R	1.259	0.99
74_T	208_E	1.252	0.99
180_P	189_P	1.240	0.98
34_I	176_S	1.229	0.98
214_T	218_S	1.224	0.98
195_L	216_L	1.206	0.98
71_Q	219_L	1.199	0.98
39_A	43_E	1.199	0.98
223_I	226_L	1.198	0.98
164_N	167_E	1.177	0.98
95_G	167_E	1.171	0.98
7_R	10_K	1.163	0.97
96_V	124_L	1.158	0.97
146_F	171_L	1.152	0.97
28_Q	199_Y	1.132	0.97
27_T	198_S	1.132	0.97
32_A	217_A	1.124	0.97
9_K	12_S	1.118	0.96
75_L	169_A	1.114	0.96
181_V	192_M	1.113	0.96
77_A	203_V	1.110	0.96
23_V	165_A	1.102	0.96
62_L	120_L	1.099	0.96
92_T	113_D	1.088	0.96
2_T	80_S	1.088	0.96
35_T	190_R	1.085	0.96
27_T	160_T	1.078	0.95
183_N	186_E	1.071	0.95
179_K	192_M	1.067	0.95
31_A	177_E	1.061	0.95
59_P	120_L	1.057	0.95
65_V	212_F	1.055	0.95
197_L	209_A	1.050	0.94
49_E	54_K	1.043	0.94
151_L	159_F	1.042	0.94
75_L	204_V	1.039	0.94
119_D	122_R	1.029	0.94
80_S	87_V	1.029	0.94
62_L	109_L	1.026	0.94
93_H	111_D	1.020	0.93
178_M	185_R	1.017	0.93
26_V	199_Y	1.015	0.93
67_G	70_A	1.011	0.93
45_K	54_K	1.003	0.93

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
3dvaI	2	0	100	-0.045	Contact Map
1dpbA	1	0.987	100	-0.026	Contact Map
1sczA	1	0.987	100	-0.021	Contact Map
4n72A	3	0.987	100	-0.021	Contact Map
2ii3A	8	0.9957	100	-0.011	Contact Map
3maeA	3	0.9913	100	-0.009	Contact Map
3l60A	1	0.9784	100	-0.007	Contact Map
3b8kA	1	0.974	100	-0.004	Contact Map
3rqcA	7	0.9351	100	0.03	Contact Map
2xt6A	2	0.8312	100	0.086	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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