OPENSEQ.org - 1480610154 - GREMLIN Submission

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ID:	1480610154	Query Sequence MDKCWFTLDNAHYPPPSLDSMRSGHPISPASLGHLIPSLAHLDQIINAKAIEPFPATMDIHGPTIIEDFKWDHSHEYSLSLGGKVPIPLAPAGVPFVDLNVGLGGAFSRSVANYWEFDRLERYIMQPTRSYVQKCIERDEVKRWIAKNKSMMMMGRWEVYMITGIIVARGGGRKKKEKTTGKEFSVEVTVEVPLIVEAGPGGKRNTARQKTWGTSQTGDFVWAVRLAKITKSGLHSDWKMETVFGKTSSFRGQKAIF	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	257 (236)
Sequences:	306 (283)
Seq/Len:	1.297
Nf(neff/√len):	18.4

HHblits Results: (2016_02)
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: 1.297).

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
122_R	166_I	3.640	1.00
39_L	226_L	2.808	1.00
35_L	161_M	2.154	0.99
5_W	166_I	2.125	0.98
171_G	220_F	2.115	0.98
36_I	226_L	1.830	0.95
4_C	7_T	1.824	0.95
169_R	219_D	1.784	0.94
115_W	222_W	1.679	0.91
135_C	161_M	1.656	0.90
5_W	122_R	1.644	0.90
16_P	28_S	1.596	0.88
130_S	140_E	1.588	0.87
12_H	166_I	1.581	0.87
6_F	223_A	1.538	0.85
167_V	219_D	1.522	0.84
102_G	167_V	1.501	0.83
39_L	42_L	1.470	0.81
159_V	171_G	1.460	0.81
87_I	115_W	1.453	0.80
189_T	221_V	1.450	0.80
6_F	36_I	1.442	0.80
158_E	228_K	1.438	0.79
35_L	229_I	1.416	0.78
118_D	172_G	1.409	0.77
68_D	215_S	1.382	0.75
66_I	217_T	1.365	0.74
42_L	224_V	1.331	0.72
5_W	124_I	1.321	0.71
157_W	222_W	1.304	0.69
104_G	221_V	1.288	0.68
165_I	221_V	1.279	0.67
87_I	222_W	1.279	0.67
136_I	222_W	1.259	0.65
35_L	134_K	1.258	0.65
32_L	125_M	1.249	0.64
3_K	104_G	1.248	0.64
178_K	221_V	1.247	0.64
163_T	228_K	1.246	0.64
72_D	194_L	1.212	0.61
103_L	138_R	1.209	0.61
213_G	221_V	1.207	0.61
39_L	160_Y	1.202	0.60
168_A	224_V	1.198	0.60
5_W	9_D	1.194	0.59
78_S	86_P	1.189	0.59
160_Y	250_F	1.187	0.59
250_F	253_Q	1.183	0.58
8_L	34_H	1.178	0.58
117_F	170_G	1.177	0.58
146_A	160_Y	1.173	0.57
184_F	194_L	1.164	0.56
11_A	40_A	1.162	0.56
6_F	132_V	1.157	0.56
60_I	228_K	1.156	0.56
131_Y	135_C	1.156	0.56
74_S	209_Q	1.153	0.55
101_V	239_K	1.151	0.55
32_L	109_R	1.151	0.55
42_L	47_N	1.143	0.54
167_V	190_V	1.143	0.54
63_P	221_V	1.142	0.54
162_I	207_A	1.141	0.54
6_F	224_V	1.137	0.54
100_N	237_D	1.134	0.53
5_W	108_S	1.133	0.53
135_C	162_I	1.126	0.53
82_G	200_P	1.121	0.52
54_F	60_I	1.117	0.52
83_G	232_S	1.112	0.51
55_P	99_L	1.106	0.51
220_F	225_R	1.103	0.50
34_H	219_D	1.101	0.50
161_M	241_E	1.101	0.50
56_A	143_R	1.100	0.50
72_D	172_G	1.097	0.50
186_V	210_K	1.094	0.49
31_S	133_Q	1.086	0.49
188_V	200_P	1.085	0.49
123_Y	242_T	1.083	0.48
51_I	82_G	1.081	0.48
34_H	135_C	1.080	0.48
87_I	221_V	1.078	0.48
170_G	229_I	1.074	0.47
38_S	229_I	1.074	0.47
101_V	196_V	1.071	0.47
188_V	194_L	1.070	0.47
121_E	169_R	1.068	0.47
82_G	201_G	1.068	0.47
67_E	226_L	1.064	0.46
28_S	45_I	1.061	0.46
34_H	73_H	1.061	0.46
120_L	168_A	1.057	0.46
51_I	160_Y	1.054	0.45
39_L	165_I	1.053	0.45
164_G	225_R	1.052	0.45
205_N	221_V	1.047	0.45
200_P	246_K	1.044	0.44
35_L	209_Q	1.043	0.44
168_A	219_D	1.041	0.44
3_K	250_F	1.037	0.44
137_E	159_V	1.034	0.44
35_L	205_N	1.032	0.43
10_N	38_S	1.031	0.43
132_V	244_F	1.027	0.43
30_A	135_C	1.023	0.42
228_K	241_E	1.023	0.42
59_D	160_Y	1.023	0.42
124_I	187_E	1.021	0.42
133_Q	160_Y	1.021	0.42
16_P	224_V	1.020	0.42
11_A	34_H	1.019	0.42
62_G	190_V	1.019	0.42
52_E	105_G	1.019	0.42
46_I	157_W	1.017	0.42
64_T	121_E	1.010	0.41
140_E	172_G	1.010	0.41
39_L	224_V	1.009	0.41
84_K	124_I	1.007	0.41
93_G	99_L	1.006	0.41
145_I	166_I	1.004	0.41
7_T	219_D	1.004	0.41
142_K	146_A	1.003	0.41
136_I	211_T	1.002	0.40
42_L	88_P	1.001	0.40

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
1tteA	1	0.4669	3.7	0.966	Contact Map
4v06A	2	0.2957	3.2	0.967	Contact Map
2e2cA	1	0.2529	2.8	0.968	Contact Map
2f1eA	1	0.2335	2.6	0.969	Contact Map
4yiiU	1	0.2374	2.1	0.97	Contact Map
1tzaA	2	0.2412	2.1	0.97	Contact Map
1i7kA	2	0.2451	2	0.971	Contact Map
1tohA	1	0.2763	1.9	0.971	Contact Map
2awfA	1	0.1167	1.7	0.972	Contact Map
2f4zA	2	0.2529	1.6	0.972	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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