OPENSEQ.org - 1513452947 - GREMLIN Submission

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bv1 30-245 20-216 -force run 1-185 -force run

ID:	1513452947	Query Sequence VQENQFGPEFVLSQNSALSTFVTYPRYVRSVPNRTRTYIKLKRLRFKGTLKIERGQGDTIMDGPISTIQGVFSMVIVVGRKPHVGQSGRLHTFGALFGARIHCHGNLSVVPALKDRYYIRHVTKRVVSLQKDTLLIDLHGTTHLSNKRYNCWASFSDLERDSCNGVYGNITKNALLVYYCWLSDA	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	185 (185)
Sequences:	152 (50.7)
Seq/Len:	0.822
Nf(neff/√len):	3.7

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: 0.822).

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
4_N	50_L	2.068	0.95
5_Q	38_Y	2.056	0.95
56_Q	108_S	1.772	0.87
53_E	119_I	1.681	0.82
3_E	15_N	1.617	0.79
108_S	114_K	1.614	0.79
65_I	149_Y	1.609	0.78
50_L	160_R	1.558	0.75
12_L	24_Y	1.539	0.74
76_I	127_V	1.538	0.74
28_V	144_L	1.519	0.73
49_T	105_G	1.465	0.69
3_E	38_Y	1.451	0.68
21_F	61_M	1.446	0.67
97_F	116_R	1.429	0.66
164_N	168_G	1.410	0.64
65_I	147_K	1.395	0.63
82_P	98_G	1.384	0.62
15_N	38_Y	1.322	0.57
11_V	23_T	1.312	0.56
148_R	177_V	1.304	0.55
92_T	149_Y	1.297	0.55
22_V	136_I	1.293	0.54
70_G	97_F	1.285	0.54
70_G	116_R	1.285	0.54
3_E	107_L	1.281	0.53
38_Y	76_I	1.279	0.53
23_T	26_R	1.275	0.53
6_F	168_G	1.260	0.52
71_V	132_D	1.236	0.49
80_R	119_I	1.233	0.49
26_R	160_R	1.227	0.49
45_R	119_I	1.226	0.49
62_D	175_L	1.225	0.48
5_Q	163_C	1.203	0.47
22_V	31_V	1.200	0.46
175_L	185_A	1.195	0.46
66_S	119_I	1.190	0.45
9_E	21_F	1.189	0.45
77_V	117_Y	1.188	0.45
156_S	171_T	1.181	0.45
18_L	28_V	1.181	0.45
19_S	102_H	1.173	0.44
1_V	153_A	1.172	0.44
178_Y	184_D	1.169	0.44
76_I	87_S	1.167	0.43
14_Q	112_A	1.158	0.43
90_L	176_L	1.155	0.42
1_V	177_V	1.153	0.42
174_A	179_Y	1.151	0.42
119_I	176_L	1.140	0.41
113_L	138_L	1.138	0.41
23_T	45_R	1.135	0.41
35_T	80_R	1.127	0.40
24_Y	85_G	1.122	0.40
145_S	172_K	1.116	0.39
152_W	155_F	1.114	0.39
152_W	157_D	1.114	0.39
98_G	116_R	1.113	0.39
20_T	29_R	1.110	0.39
79_G	97_F	1.107	0.38
79_G	116_R	1.107	0.38
26_R	159_E	1.106	0.38
8_P	106_N	1.105	0.38
41_L	90_L	1.102	0.38
82_P	97_F	1.096	0.37
82_P	116_R	1.096	0.37
79_G	98_G	1.095	0.37
181_W	184_D	1.079	0.36
79_G	82_P	1.079	0.36
155_F	165_G	1.077	0.36
155_F	167_Y	1.077	0.36
157_D	165_G	1.077	0.36
157_D	167_Y	1.077	0.36
52_I	95_A	1.075	0.36
108_S	138_L	1.068	0.35
12_L	156_S	1.059	0.34
178_Y	181_W	1.058	0.34
78_V	125_R	1.055	0.34
74_M	159_E	1.051	0.34
56_Q	62_D	1.045	0.33
165_G	173_N	1.044	0.33
167_Y	173_N	1.044	0.33
122_V	128_S	1.039	0.33
5_Q	45_R	1.037	0.33
65_I	175_L	1.035	0.33
21_F	125_R	1.030	0.32
22_V	177_V	1.030	0.32
23_T	138_L	1.029	0.32
6_F	160_R	1.027	0.32
57_G	64_P	1.024	0.32
84_V	159_E	1.020	0.31
18_L	134_L	1.020	0.31
62_D	161_D	1.020	0.31
12_L	47_K	1.011	0.31
2_Q	71_V	1.011	0.31
13_S	24_Y	1.008	0.30
173_N	183_S	1.007	0.30
67_T	106_N	1.007	0.30
73_S	76_I	1.007	0.30
53_E	108_S	1.005	0.30
6_F	50_L	1.002	0.30
76_I	96_L	1.000	0.30

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
2ixkA	2	0.627	22	0.967	Contact Map
1nxmA	2	0.6108	8	0.973	Contact Map
1ep0A	1	0.6378	7.9	0.973	Contact Map
1dzrA	2	0.5946	4.2	0.976	Contact Map
1bnxA	1	0.1189	4.1	0.976	Contact Map
4hdqC	1	0.027	3.4	0.977	Contact Map
4bz7A	4	0.3405	3.3	0.977	Contact Map
3ilcA	1	0.5027	2.7	0.978	Contact Map
3k44A	4	0.2649	2.6	0.979	Contact Map
2xk0A	1	0.3568	2.4	0.979	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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