OPENSEQ.org - 1398961032 - GREMLIN Submission

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T0760 -force run

ID:	1398961032	Query Sequence MYMKKLKFITLTLAIIITLPMLQSCLDDNDHQSRSLVISTINQISEDSKEFYFTLDNGKTMFPSNSQAWGGEKFENGQRAFVIFNELEQPVNGYDYNIQVRDITKVLTKEIVTMDDEENTEEKIGDDKINATYMWISKDKKYLTIEFQYYSTHSEDKKHFLNLVINNKEADSAAENEDNTDDEYINLEFRHNSERDSPDHLGEGYVSFKLDKIEEQIEGKKGLNIRVRTLYDGIKNYKVQFP	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	242 (234)
Sequences:	155 (135)
Seq/Len:	0.662
Nf(neff/√len):	8.8

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: 0.662).

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
147_F	204_G	1.953	0.89
107_L	206_V	1.779	0.82
5_K	9_I	1.766	0.82
143_L	210_L	1.592	0.71
159_H	196_D	1.574	0.70
80_A	233_G	1.528	0.67
229_T	233_G	1.518	0.66
137_S	185_I	1.491	0.64
161_L	189_F	1.482	0.63
53_F	97_N	1.481	0.63
24_S	129_I	1.475	0.63
6_L	10_T	1.470	0.63
129_I	163_L	1.444	0.60
12_T	15_I	1.431	0.59
4_K	10_T	1.419	0.58
65_N	225_I	1.405	0.57
72_E	184_Y	1.396	0.57
136_I	189_F	1.368	0.54
8_F	18_T	1.365	0.54
189_F	200_H	1.355	0.53
5_K	11_L	1.343	0.52
189_F	206_V	1.314	0.50
109_K	125_G	1.305	0.49
13_L	16_I	1.303	0.49
90_P	164_V	1.300	0.49
121_E	228_R	1.291	0.48
111_I	209_K	1.286	0.48
3_M	9_I	1.274	0.47
4_K	71_G	1.274	0.47
103_I	192_N	1.268	0.46
205_Y	229_T	1.263	0.46
193_S	199_D	1.259	0.45
127_D	193_S	1.259	0.45
13_L	18_T	1.259	0.45
9_I	12_T	1.254	0.45
222_G	238_K	1.250	0.45
49_K	189_F	1.249	0.44
192_N	208_F	1.248	0.44
24_S	225_I	1.243	0.44
83_I	221_K	1.243	0.44
56_D	135_W	1.234	0.43
130_N	146_E	1.233	0.43
132_T	146_E	1.231	0.43
106_V	137_S	1.230	0.43
186_N	226_R	1.228	0.43
8_F	11_L	1.225	0.43
41_I	155_E	1.220	0.42
55_L	135_W	1.211	0.41
72_E	75_E	1.197	0.40
219_G	233_G	1.193	0.40
147_F	241_F	1.189	0.40
27_D	107_L	1.177	0.39
160_F	192_N	1.169	0.38
54_T	213_I	1.166	0.38
145_I	239_V	1.164	0.38
101_R	146_E	1.164	0.38
125_G	141_K	1.159	0.37
107_L	223_L	1.157	0.37
135_W	142_Y	1.156	0.37
11_L	200_H	1.156	0.37
5_K	15_I	1.153	0.37
89_Q	187_L	1.139	0.36
232_D	237_Y	1.138	0.36
6_L	9_I	1.134	0.35
84_F	150_Y	1.131	0.35
39_S	145_I	1.129	0.35
93_G	157_K	1.128	0.35
145_I	233_G	1.123	0.34
56_D	79_R	1.122	0.34
4_K	12_T	1.119	0.34
7_K	133_Y	1.119	0.34
160_F	189_F	1.118	0.34
84_F	136_I	1.109	0.33
10_T	14_A	1.109	0.33
22_L	103_I	1.108	0.33
5_K	10_T	1.107	0.33
78_Q	145_I	1.104	0.33
43_Q	84_F	1.103	0.33
12_T	16_I	1.100	0.33
65_N	144_T	1.093	0.32
163_L	208_F	1.091	0.32
81_F	187_L	1.089	0.32
133_Y	144_T	1.080	0.31
59_K	229_T	1.078	0.31
28_D	206_V	1.075	0.31
40_T	166_N	1.074	0.31
22_L	165_I	1.072	0.31
13_L	46_E	1.072	0.31
49_K	61_M	1.071	0.31
4_K	9_I	1.071	0.31
79_R	144_T	1.069	0.31
108_T	149_Y	1.067	0.30
103_I	127_D	1.066	0.30
79_R	127_D	1.061	0.30
78_Q	105_K	1.059	0.30
145_I	189_F	1.057	0.30
80_A	115_D	1.051	0.29
61_M	84_F	1.049	0.29
42_N	235_K	1.049	0.29
166_N	188_E	1.045	0.29
114_M	118_E	1.039	0.28
65_N	137_S	1.037	0.28
20_P	56_D	1.031	0.28
11_L	95_D	1.030	0.28
4_K	13_L	1.029	0.28
6_L	19_L	1.026	0.28
11_L	116_D	1.026	0.28
57_N	116_D	1.025	0.28
145_I	227_V	1.023	0.27
34_R	93_G	1.017	0.27
98_I	118_E	1.017	0.27
30_D	100_V	1.017	0.27
24_S	161_L	1.016	0.27
5_K	14_A	1.016	0.27
4_K	11_L	1.014	0.27
143_L	196_D	1.013	0.27
93_G	201_L	1.013	0.27
124_I	164_V	1.013	0.27
134_M	144_T	1.008	0.26
99_Q	218_E	1.005	0.26
159_H	191_H	1.004	0.26

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
4j8qA	1	0.7893	100	0.227	Contact Map
4pqxA	4	0.8182	100	0.245	Contact Map
3k6oA	2	0.7893	100	0.255	Contact Map
3k0yA	1	0.7562	100	0.288	Contact Map
3qwnA	12	0.7975	100	0.304	Contact Map
3nqiA	4	0.7727	98.4	0.858	Contact Map
4lmhA	4	0.6281	34.9	0.951	Contact Map
3ucpA	1	0.6405	20.8	0.956	Contact Map
3pmqA	1	0.5413	15.8	0.958	Contact Map
3qugA	2	0.3926	11.5	0.961	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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