OPENSEQ.org - 1424275019 - GREMLIN Submission

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SYNTH235-345 ACT608-702

ID:	1424275019	Query Sequence GREKHLYSIYCKMVLKEQRFHSIMDIYAFRVIVNDSDTCYRVLGQMHSLYKPRPGRVKDYIAIPKANGYQSLHTSMIGPHGVPVEVQIRTEDMDQMAEMGVAAHWAYKEHGEPEKFMAVEWDKETAQEFITEIKVEMFNHQGALANLTAAINTTTSNIQSLNTEEKDGRVYSAFIRLTARDRVHLANIMRKIRVMPDVIKVTRNRN	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	206 (205)
Sequences:	485 (327.9)
Seq/Len:	2.366
Nf(neff/√len):	22.9

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: 2.366).

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	3.271	1.00
189_M	201_V	3.247	1.00
161_L	175_I	2.530	1.00
35_D	38_T	2.413	1.00
4_K	12_K	2.134	1.00
182_R	186_A	2.046	0.99
12_K	85_E	1.756	0.98
18_Q	23_I	1.750	0.98
179_A	184_H	1.653	0.97
91_E	95_Q	1.632	0.96
182_R	190_R	1.591	0.96
4_K	85_E	1.496	0.93
2_R	8_S	1.473	0.92
145_A	148_T	1.472	0.92
156_S	184_H	1.472	0.92
73_H	87_Q	1.471	0.92
133_I	189_M	1.458	0.92
34_N	91_E	1.441	0.91
79_P	144_L	1.400	0.90
151_I	156_S	1.394	0.89
28_A	75_S	1.368	0.88
2_R	12_K	1.365	0.88
79_P	119_V	1.349	0.87
112_E	140_H	1.320	0.86
43_L	88_I	1.295	0.84
50_Y	68_G	1.295	0.84
73_H	89_R	1.285	0.84
42_V	88_I	1.280	0.83
52_P	62_A	1.276	0.83
8_S	102_A	1.276	0.83
2_R	85_E	1.272	0.83
41_R	82_V	1.270	0.83
140_H	147_L	1.259	0.82
63_I	76_M	1.254	0.82
4_K	25_D	1.252	0.81
102_A	142_G	1.247	0.81
186_A	190_R	1.239	0.80
53_R	57_V	1.233	0.80
142_G	157_N	1.233	0.80
34_N	38_T	1.229	0.80
13_M	60_Y	1.226	0.79
94_D	98_E	1.201	0.77
43_L	47_H	1.197	0.77
10_Y	51_K	1.194	0.77
2_R	30_R	1.190	0.77
65_K	73_H	1.171	0.75
8_S	85_E	1.169	0.75
68_G	86_V	1.164	0.74
10_Y	52_P	1.164	0.74
40_Y	62_A	1.159	0.74
28_A	163_T	1.151	0.73
22_S	141_Q	1.150	0.73
40_Y	44_G	1.144	0.73
49_L	52_P	1.141	0.72
33_V	42_V	1.140	0.72
27_Y	83_P	1.139	0.72
8_S	12_K	1.135	0.72
30_R	89_R	1.131	0.71
25_D	85_E	1.127	0.71
26_I	48_S	1.126	0.71
8_S	87_Q	1.116	0.70
26_I	84_V	1.115	0.70
12_K	28_A	1.115	0.70
27_Y	82_V	1.113	0.70
68_G	105_W	1.103	0.69
2_R	108_K	1.102	0.68
30_R	87_Q	1.097	0.68
85_E	104_H	1.088	0.67
12_K	25_D	1.084	0.67
28_A	85_E	1.080	0.66
78_G	151_I	1.080	0.66
101_V	130_I	1.079	0.66
6_L	62_A	1.078	0.66
4_K	9_I	1.074	0.66
85_E	102_A	1.071	0.65
30_R	85_E	1.070	0.65
51_K	158_I	1.066	0.65
177_L	188_I	1.065	0.65
23_I	82_V	1.065	0.65
47_H	74_T	1.061	0.64
135_V	192_I	1.057	0.64
9_I	12_K	1.056	0.64
8_S	73_H	1.054	0.63
101_V	171_Y	1.053	0.63
1_G	12_K	1.052	0.63
40_Y	47_H	1.048	0.63
117_M	181_D	1.042	0.62
76_M	145_A	1.042	0.62
86_V	163_T	1.040	0.62
50_Y	83_P	1.036	0.61
4_K	87_Q	1.034	0.61
40_Y	74_T	1.034	0.61
1_G	29_F	1.033	0.61
5_H	86_V	1.025	0.60
76_M	81_G	1.024	0.60
45_Q	188_I	1.023	0.60
34_N	117_M	1.022	0.60
162_N	189_M	1.021	0.60
65_K	69_Y	1.020	0.60
152_N	156_S	1.014	0.59
56_R	166_K	1.013	0.59
2_R	28_A	1.011	0.59
40_Y	43_L	1.011	0.59
49_L	62_A	1.009	0.58
40_Y	104_H	1.008	0.58
38_T	42_V	1.006	0.58
29_F	75_S	1.004	0.58
2_R	102_A	1.004	0.58
70_Q	76_M	1.003	0.58
90_T	140_H	1.003	0.58
46_M	115_K	1.003	0.58
69_Y	73_H	1.003	0.58

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	0.428	Contact Map
3l9dA	2	0.6893	100	0.498	Contact Map
2be3A	2	0.699	100	0.508	Contact Map
1y7pA	3	0.3835	99	0.857	Contact Map
2ko1A	2	0.3883	98.9	0.859	Contact Map
2lvwA	2	0.4078	98.7	0.869	Contact Map
2fgcA	1	0.3786	98.7	0.87	Contact Map
2pc6A	4	0.3786	98.7	0.87	Contact Map
2f1fA	2	0.3738	98.7	0.871	Contact Map
1zpvA	3	0.3835	98.4	0.883	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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