OPENSEQ.org - 1501018469 - GREMLIN Submission

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Fused B 2

ID:	1501018469	Query Sequence MLSVPARLAYVVTQDAAVFLDIDNDRYFRLPIGLEATFLAALSGAPRGGDDLDRLIGLGVLEPALDRDRPERRAAVPVAASAVDLDDGSARARLTTTLEVAASLLRARALLRRGFAQTLAALATRPGRAEASRAPETARSASLAFLAARRLVPIRPVCLLDSVALLDFLNRRGLDADLVFGVIPRPFSAHCWLQADGLALNDELDNLVGRAPILVV	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	216 (213)
Sequences:	222 (203.2)
Seq/Len:	1.042
Nf(neff/√len):	13.9

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: 1.042).

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
27_Y	189_A	2.439	0.99
194_Q	197_G	2.332	0.99
19_F	28_F	2.223	0.98
194_Q	212_P	2.147	0.98
180_F	191_C	2.146	0.98
162_S	201_N	2.075	0.97
194_Q	215_V	2.039	0.96
145_F	191_C	1.979	0.95
27_Y	187_F	1.861	0.93
165_L	200_L	1.758	0.90
153_P	156_P	1.751	0.90
27_Y	213_I	1.725	0.89
8_L	60_V	1.715	0.89
142_S	204_L	1.702	0.88
5_P	8_L	1.635	0.85
149_R	161_D	1.617	0.84
150_R	178_L	1.532	0.80
145_F	213_I	1.503	0.78
165_L	169_L	1.451	0.74
70_P	199_A	1.447	0.74
159_L	213_I	1.433	0.73
18_V	83_V	1.395	0.70
167_D	191_C	1.381	0.69
21_D	27_Y	1.365	0.68
202_D	206_N	1.354	0.67
21_D	187_F	1.348	0.66
104_L	111_L	1.345	0.66
145_F	165_L	1.322	0.64
7_R	23_D	1.321	0.64
202_D	207_L	1.313	0.63
20_L	27_Y	1.306	0.63
191_C	199_A	1.304	0.63
2_L	52_L	1.302	0.63
101_A	105_L	1.290	0.61
145_F	200_L	1.287	0.61
145_F	160_L	1.279	0.60
8_L	28_F	1.275	0.60
11_V	28_F	1.274	0.60
99_E	168_F	1.268	0.59
110_L	191_C	1.268	0.59
18_V	77_P	1.268	0.59
10_Y	19_F	1.268	0.59
106_R	109_A	1.262	0.59
167_D	180_F	1.261	0.59
157_V	178_L	1.254	0.58
138_A	178_L	1.252	0.58
144_A	168_F	1.214	0.55
187_F	213_I	1.213	0.54
25_D	30_L	1.213	0.54
80_A	84_D	1.207	0.54
182_V	187_F	1.203	0.53
26_R	182_V	1.196	0.53
183_I	188_S	1.194	0.53
187_F	202_D	1.181	0.51
188_S	210_R	1.177	0.51
28_F	38_F	1.173	0.51
166_L	193_L	1.163	0.50
170_N	175_D	1.158	0.49
156_P	161_D	1.157	0.49
149_R	200_L	1.155	0.49
161_D	210_R	1.154	0.49
73_R	122_L	1.148	0.48
174_L	195_A	1.141	0.48
171_R	194_Q	1.141	0.48
61_L	201_N	1.138	0.47
38_F	60_V	1.133	0.47
20_L	189_A	1.127	0.46
179_V	189_A	1.123	0.46
19_F	38_F	1.122	0.46
194_Q	210_R	1.118	0.46
152_V	194_Q	1.108	0.45
11_V	26_R	1.104	0.44
100_V	106_R	1.098	0.44
16_A	164_A	1.095	0.43
194_Q	211_A	1.088	0.43
173_G	176_A	1.088	0.43
182_V	213_I	1.076	0.42
141_A	162_S	1.075	0.42
161_D	180_F	1.075	0.42
11_V	213_I	1.071	0.41
27_Y	182_V	1.065	0.41
183_I	205_D	1.063	0.40
180_F	189_A	1.062	0.40
15_D	29_R	1.058	0.40
29_R	210_R	1.055	0.40
21_D	186_P	1.053	0.40
145_F	189_A	1.053	0.40
163_V	193_L	1.050	0.39
107_A	112_R	1.042	0.39
99_E	144_A	1.038	0.38
142_S	165_L	1.037	0.38
199_A	207_L	1.037	0.38
148_A	155_R	1.037	0.38
199_A	202_D	1.037	0.38
8_L	24_N	1.034	0.38
189_A	213_I	1.028	0.37
2_L	5_P	1.026	0.37
150_R	183_I	1.026	0.37
153_P	183_I	1.021	0.37
96_T	208_V	1.015	0.36
111_L	114_G	1.013	0.36
153_P	169_L	1.010	0.36
104_L	148_A	1.006	0.35
15_D	129_A	1.004	0.35
153_P	174_L	1.002	0.35
154_I	157_V	1.001	0.35
55_L	59_G	1.001	0.35
169_L	183_I	1.000	0.35

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
2hlyA	1	0.3981	67.8	0.914	Contact Map
4fgqA	2	0.5694	63.4	0.916	Contact Map
4u65E	2	0.5556	54.5	0.921	Contact Map
2f4mA	1	0.7963	42.8	0.926	Contact Map
2q3zA	1	0.9074	41.1	0.927	Contact Map
1g0dA	1	0.8009	39.3	0.927	Contact Map
3isrA	4	0.838	34.5	0.93	Contact Map
4ktyA	2	0.8148	29.2	0.932	Contact Map
1l9mA	2	0.8148	23.3	0.935	Contact Map
3g2bA	1	0.3796	22.8	0.936	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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