OPENSEQ.org - 1404140914 - GREMLIN Submission

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sub9_jack

ID:	1404140914	Query Sequence MTLKALAQSLGITLKYLFSKPVTVPYPDAPVALKPRFHGRHVLTRHPNGLEKCIGCSLCAAACPAYAIYVEPAENDPENPVSAGERYAKVYEINMLRCIFCGLCEEACPTGAIVLGYDFEMADYEYSDLVYGKEDMLVDVVGTKPQRREAKRTGKPVKVGYVVPYVRPELEGFKAPTEGGKR	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	182 (167)
Sequences:	899 (409.7)
Seq/Len:	5.383
Nf(neff/√len):	31.7

Jackhmmer Results: (2014_04_16)
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: 5.383).

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
105_E	115_L	2.485	1.00
125_E	128_D	2.196	1.00
62_A	107_A	2.030	1.00
120_E	129_L	1.962	1.00
8_Q	11_G	1.854	1.00
30_P	119_F	1.809	1.00
9_S	13_T	1.793	1.00
4_K	8_Q	1.751	1.00
33_L	119_F	1.742	1.00
67_A	99_I	1.673	1.00
54_I	110_T	1.647	0.99
73_A	89_K	1.596	0.99
95_M	131_Y	1.560	0.99
14_L	17_L	1.509	0.99
71_E	90_V	1.507	0.99
17_L	21_P	1.495	0.99
6_L	10_L	1.488	0.99
163_V	168_P	1.433	0.98
164_P	167_R	1.431	0.98
13_T	17_L	1.430	0.98
25_P	29_A	1.429	0.98
156_P	160_G	1.419	0.98
15_K	19_S	1.388	0.98
51_E	133_K	1.376	0.97
77_P	80_P	1.346	0.97
94_N	111_G	1.339	0.97
105_E	113_I	1.303	0.96
123_D	129_L	1.296	0.96
7_A	11_G	1.269	0.95
35_P	117_Y	1.266	0.95
41_H	65_A	1.250	0.95
65_A	99_I	1.244	0.95
125_E	132_G	1.239	0.94
157_V	161_Y	1.239	0.94
73_A	87_Y	1.224	0.94
70_V	92_E	1.216	0.94
25_P	28_D	1.214	0.94
75_N	85_E	1.208	0.93
30_P	120_E	1.206	0.93
107_A	112_A	1.206	0.93
54_I	57_S	1.205	0.93
150_A	154_G	1.201	0.93
75_N	83_A	1.200	0.93
146_Q	150_A	1.199	0.93
43_L	136_M	1.195	0.93
57_S	70_V	1.192	0.93
88_A	91_Y	1.183	0.92
5_A	8_Q	1.178	0.92
8_Q	15_K	1.178	0.92
40_R	118_D	1.169	0.92
99_I	105_E	1.166	0.92
19_S	125_E	1.144	0.91
52_K	112_A	1.132	0.90
160_G	164_P	1.131	0.90
51_E	67_A	1.124	0.90
55_G	72_P	1.118	0.89
104_C	108_C	1.115	0.89
159_V	162_V	1.114	0.89
17_L	20_K	1.112	0.89
152_R	155_K	1.110	0.89
98_C	104_C	1.105	0.89
71_E	89_K	1.103	0.89
43_L	133_K	1.102	0.88
58_L	133_K	1.100	0.88
85_E	88_A	1.092	0.88
163_V	167_R	1.080	0.87
93_I	115_L	1.074	0.87
11_G	15_K	1.073	0.87
76_D	80_P	1.072	0.87
33_L	117_Y	1.062	0.86
96_L	129_L	1.061	0.86
149_E	153_T	1.058	0.86
64_P	109_P	1.055	0.85
157_V	163_V	1.051	0.85
68_I	93_I	1.051	0.85
57_S	60_A	1.050	0.85
3_L	7_A	1.050	0.85
92_E	132_G	1.048	0.85
159_V	166_V	1.042	0.84
43_L	113_I	1.040	0.84
2_T	110_T	1.036	0.84
58_L	61_A	1.029	0.83
158_K	162_V	1.027	0.83
92_E	105_E	1.025	0.83
162_V	167_R	1.025	0.83
35_P	51_E	1.023	0.83
4_K	11_G	1.017	0.82
159_V	163_V	1.013	0.82
153_T	157_V	1.009	0.82
41_H	93_I	1.004	0.81
40_R	123_D	1.002	0.81
157_V	160_G	1.001	0.81

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: (21Jun14)
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
3i9v9	2	0.8462	100	0.455	Contact Map
1kf6B	2	0.7473	99.5	0.729	Contact Map
2gmhA	2	0.6319	99.4	0.732	Contact Map
1xerA	1	0.5549	99.4	0.735	Contact Map
1gteA	4	0.5879	99.4	0.737	Contact Map
2c42A	2	0.9396	99.3	0.747	Contact Map
2h88B	2	0.7088	99.3	0.753	Contact Map
1hfeL	2	0.8077	99.3	0.753	Contact Map
3gyxB	6	0.6868	99.3	0.755	Contact Map
2wdqB	3	0.7143	99.3	0.755	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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