OPENSEQ.org - 1404140073 - GREMLIN Submission

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ID:	1404140073	Query Sequence MTLKALAQSLGITLKYLFSKPVTVPYPDAPVALKPRFHGRHVLTRHPNGLEKCIGCSLCAAACPAYAIYVEPAENDPENPVSAGERYAKVYEINMLRCIFCGLCEEACPTGAIVLGYDFEMADYEYSDLVYGKEDMLVDVVGTKPQRREAKRTGKPVKVGYVVPYVRPELEGFKAPTEGGKR	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	182 (149)
Sequences:	330 (128.2)
Seq/Len:	2.215
Nf(neff/√len):	10.5

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: 2.215).

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	2.552	1.00
125_E	128_D	2.117	1.00
120_E	129_L	2.034	0.99
51_E	133_K	2.018	0.99
30_P	120_E	2.001	0.99
70_V	94_N	1.925	0.99
51_E	58_L	1.852	0.98
62_A	107_A	1.711	0.97
33_L	119_F	1.697	0.97
132_G	135_D	1.658	0.96
60_A	90_V	1.656	0.96
58_L	133_K	1.624	0.96
107_A	112_A	1.586	0.95
35_P	47_P	1.534	0.94
18_F	94_N	1.531	0.93
10_L	72_P	1.440	0.90
9_S	13_T	1.425	0.90
105_E	113_I	1.421	0.90
41_H	65_A	1.417	0.89
4_K	8_Q	1.336	0.85
72_P	86_R	1.294	0.83
55_G	83_A	1.289	0.82
45_R	91_Y	1.288	0.82
36_R	84_G	1.286	0.82
67_A	99_I	1.260	0.80
100_F	132_G	1.258	0.80
10_L	25_P	1.247	0.79
54_I	114_V	1.245	0.79
87_Y	97_R	1.234	0.78
16_Y	28_D	1.215	0.77
35_P	106_E	1.206	0.76
14_L	21_P	1.206	0.76
65_A	91_Y	1.204	0.76
77_P	80_P	1.175	0.73
10_L	119_F	1.171	0.73
81_V	84_G	1.158	0.72
100_F	121_M	1.155	0.72
88_A	91_Y	1.154	0.72
45_R	137_L	1.151	0.71
16_Y	74_E	1.150	0.71
3_L	7_A	1.149	0.71
47_P	142_G	1.148	0.71
40_R	118_D	1.144	0.71
97_R	115_L	1.139	0.70
85_E	96_L	1.132	0.69
123_D	130_V	1.131	0.69
54_I	91_Y	1.130	0.69
49_G	99_I	1.124	0.69
45_R	49_G	1.119	0.68
71_E	137_L	1.116	0.68
125_E	130_V	1.108	0.67
18_F	23_T	1.104	0.67
36_R	107_A	1.104	0.67
20_K	115_L	1.097	0.66
67_A	92_E	1.087	0.65
96_L	129_L	1.085	0.65
55_G	86_R	1.083	0.64
12_I	24_V	1.080	0.64
38_H	55_G	1.077	0.64
52_K	55_G	1.075	0.64
126_Y	136_M	1.070	0.63
84_G	110_T	1.053	0.61
5_A	8_Q	1.052	0.61
67_A	95_M	1.048	0.61
34_K	54_I	1.046	0.61
93_I	99_I	1.044	0.60
75_N	82_S	1.034	0.59
61_A	86_R	1.033	0.59
36_R	44_T	1.032	0.59
44_T	54_I	1.024	0.58
12_I	113_I	1.021	0.58
77_P	138_V	1.018	0.57
25_P	73_A	1.018	0.57
41_H	96_L	1.017	0.57
15_K	22_V	1.016	0.57
94_N	111_G	1.012	0.57
28_D	105_E	1.009	0.56
44_T	88_A	1.007	0.56
57_S	86_R	1.007	0.56
95_M	105_E	1.004	0.56
79_N	94_N	1.003	0.56
99_I	105_E	1.002	0.56

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	0.454	Contact Map
1kf6B	2	0.7527	99.4	0.805	Contact Map
1hfeL	2	0.7637	99.4	0.811	Contact Map
2gmhA	2	0.6374	99.4	0.812	Contact Map
1xerA	1	0.5549	99.3	0.818	Contact Map
1gteA	4	0.5879	99.3	0.819	Contact Map
2h88B	2	0.7088	99.3	0.819	Contact Map
2wdqB	3	0.7143	99.3	0.821	Contact Map
2c42A	2	0.9231	99.3	0.822	Contact Map
3gyxB	6	0.5769	99.2	0.826	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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