OPENSEQ.org - 1424268779 - GREMLIN Submission

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SYNTH235-345 ACT608-702 filtered manually no enrichment

ID:	1424268779	Query Sequence GREKHLYSIYCKMVLKEQRFHSIMDIYAFRVIVNDSDTCYRVLGQMHSLYKPRPGRVKDYIAIPKANGYQSLHTSMIGPHGVPVEVQIRTEDMDQMAEMGVAAHWAYKEHGEPEKFMAVEWDKETAQEFITEIKVEMFNHQGALANLTAAINTTTSNIQSLNTEEKDGRVYSAFIRLTARDRVHLANIMRKIRVMPDVIKVTRNRN	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	206 (205)
Sequences:	522 (358.9)
Seq/Len:	2.546
Nf(neff/√len):	25.1

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: 2.546).

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 > 50% 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
37_D	41_R	3.401	1.00
189_M	201_V	3.384	1.00
161_L	175_I	2.418	1.00
35_D	38_T	2.328	1.00
4_K	12_K	2.139	1.00
182_R	186_A	2.127	1.00
18_Q	23_I	1.784	0.98
12_K	85_E	1.722	0.98
145_A	148_T	1.659	0.97
179_A	184_H	1.648	0.97
182_R	190_R	1.577	0.96
91_E	95_Q	1.563	0.96
34_N	91_E	1.519	0.95
73_H	87_Q	1.506	0.94
2_R	8_S	1.477	0.93
4_K	85_E	1.465	0.93
133_I	189_M	1.465	0.93
151_I	156_S	1.453	0.93
156_S	184_H	1.438	0.92
2_R	12_K	1.428	0.92
43_L	47_H	1.406	0.91
63_I	76_M	1.359	0.89
73_H	89_R	1.325	0.87
186_A	190_R	1.324	0.87
4_K	25_D	1.321	0.87
40_Y	47_H	1.315	0.87
40_Y	44_G	1.315	0.87
50_Y	68_G	1.314	0.87
28_A	75_S	1.306	0.86
112_E	140_H	1.290	0.85
33_V	42_V	1.288	0.85
68_G	86_V	1.287	0.85
34_N	38_T	1.284	0.85
53_R	57_V	1.281	0.85
42_V	88_I	1.272	0.84
47_H	74_T	1.259	0.84
2_R	30_R	1.252	0.83
2_R	85_E	1.252	0.83
10_Y	52_P	1.230	0.82
184_H	188_I	1.216	0.81
65_K	73_H	1.211	0.80
40_Y	62_A	1.206	0.80
177_L	188_I	1.205	0.80
43_L	88_I	1.204	0.80
41_R	82_V	1.195	0.79
140_H	147_L	1.184	0.78
12_K	25_D	1.178	0.78
40_Y	43_L	1.178	0.78
26_I	48_S	1.175	0.77
1_G	71_S	1.172	0.77
5_H	86_V	1.164	0.76
52_P	62_A	1.163	0.76
38_T	42_V	1.160	0.76
79_P	144_L	1.154	0.75
8_S	12_K	1.150	0.75
12_K	28_A	1.145	0.75
8_S	102_A	1.143	0.74
28_A	163_T	1.137	0.74
6_L	62_A	1.134	0.74
66_A	86_V	1.129	0.73
25_D	85_E	1.127	0.73
117_M	159_Q	1.122	0.73
8_S	108_K	1.116	0.72
49_L	52_P	1.116	0.72
30_R	89_R	1.115	0.72
46_M	76_M	1.111	0.71
27_Y	82_V	1.101	0.70
142_G	157_N	1.096	0.70
4_K	9_I	1.096	0.70
65_K	69_Y	1.091	0.69
8_S	85_E	1.086	0.69
44_G	47_H	1.082	0.69
69_Y	73_H	1.077	0.68
94_D	98_E	1.075	0.68
145_A	152_N	1.072	0.68
135_V	192_I	1.072	0.68
85_E	102_A	1.070	0.67
62_A	70_Q	1.066	0.67
9_I	12_K	1.063	0.67
30_R	87_Q	1.063	0.67
44_G	74_T	1.061	0.66
85_E	104_H	1.058	0.66
27_Y	83_P	1.057	0.66
183_V	186_A	1.056	0.66
28_A	85_E	1.054	0.66
30_R	85_E	1.053	0.66
79_P	119_V	1.050	0.65
68_G	105_W	1.050	0.65
40_Y	74_T	1.049	0.65
2_R	108_K	1.047	0.65
194_V	202_T	1.047	0.65
3_E	76_M	1.042	0.64
102_A	142_G	1.041	0.64
8_S	87_Q	1.035	0.64
26_I	84_V	1.033	0.63
47_H	62_A	1.032	0.63
1_G	12_K	1.028	0.63
2_R	28_A	1.024	0.62
3_E	27_Y	1.019	0.62
151_I	158_I	1.017	0.62
4_K	87_Q	1.014	0.61
117_M	197_D	1.011	0.61
65_K	89_R	1.009	0.61
104_H	108_K	1.006	0.60
45_Q	188_I	1.004	0.60
76_M	81_G	1.004	0.60
194_V	199_I	1.001	0.60

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: (31Jan15)
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
1vj7A	2	0.5291	100	0.416	Contact Map
3l9dA	2	0.6893	100	0.489	Contact Map
2be3A	2	0.699	100	0.5	Contact Map
1y7pA	3	0.3835	98.9	0.859	Contact Map
2ko1A	2	0.3883	98.9	0.86	Contact Map
2lvwA	2	0.4078	98.7	0.869	Contact Map
2fgcA	1	0.3786	98.6	0.873	Contact Map
2pc6A	4	0.3786	98.6	0.873	Contact Map
2f1fA	2	0.3738	98.5	0.874	Contact Map
1zpvA	3	0.3835	98.2	0.886	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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