OPENSEQ.org - 1494890566 - GREMLIN Submission

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dnajb6

ID:	1494890566	Query Sequence MVDYYEVLGVQRHASPEDIKKAYRKLALKWHPDKNPENKEEAERKFKQVAEAYEVLSDAKKRDIYDKYGKEGLNGGGGGGSHFDSPFEFGFTFRNPDDVFREFFGGRDPFSFDFFEDPFEDFFGNRRGPRGSRSRGTGSFFSAFSGFPSFGSGFSSFDTGFTSFGSLGHGGLTSFSSTSFGGSGMGNFKSISTSTKMVNGRKITTKRIVENGQERVEVEEDGQLKSLTINGKEQLLRLDNK	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	241 (241)
Sequences:	305 (199.7)
Seq/Len:	1.266
Nf(neff/√len):	12.9

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: 1.266).

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
8_L	19_I	2.496	1.00
5_Y	8_L	2.404	0.99
5_Y	19_I	2.380	0.99
10_V	19_I	2.349	0.99
231_G	234_Q	2.314	0.99
106_G	109_P	1.873	0.95
51_E	70_K	1.836	0.95
8_L	14_A	1.673	0.90
207_R	214_E	1.662	0.90
11_Q	18_D	1.646	0.89
4_Y	55_V	1.640	0.89
8_L	20_K	1.608	0.88
195_T	204_T	1.597	0.87
5_Y	66_D	1.593	0.87
5_Y	10_V	1.572	0.86
37_E	198_V	1.552	0.85
68_Y	72_G	1.547	0.85
23_Y	32_P	1.543	0.85
161_F	164_F	1.540	0.85
212_G	231_G	1.525	0.84
219_E	222_G	1.480	0.81
220_E	225_K	1.471	0.81
15_S	18_D	1.469	0.81
98_D	168_G	1.468	0.81
14_A	19_I	1.464	0.80
16_P	49_V	1.452	0.80
10_V	15_S	1.441	0.79
187_N	199_N	1.419	0.77
25_K	141_F	1.414	0.77
8_L	22_A	1.406	0.77
30_W	34_K	1.399	0.76
201_R	223_Q	1.395	0.76
2_V	7_V	1.371	0.74
30_W	103_F	1.370	0.74
27_A	31_H	1.367	0.74
103_F	220_E	1.352	0.72
212_G	230_N	1.350	0.72
94_R	102_E	1.317	0.70
8_L	21_K	1.293	0.68
12_R	64_I	1.287	0.67
17_E	29_K	1.282	0.67
50_A	97_D	1.275	0.66
38_N	55_V	1.275	0.66
96_P	198_V	1.270	0.66
27_A	32_P	1.261	0.65
66_D	93_F	1.253	0.64
30_W	35_N	1.249	0.64
87_F	233_E	1.247	0.64
4_Y	20_K	1.241	0.63
23_Y	31_H	1.238	0.63
26_L	29_K	1.228	0.62
45_K	48_Q	1.226	0.62
29_K	41_E	1.224	0.61
144_F	153_G	1.220	0.61
39_K	43_E	1.218	0.61
217_E	224_L	1.208	0.60
237_R	240_N	1.200	0.59
193_T	220_E	1.199	0.59
95_N	217_E	1.195	0.59
208_I	217_E	1.194	0.59
9_G	219_E	1.192	0.58
45_K	59_A	1.184	0.58
197_M	202_K	1.183	0.57
215_R	227_L	1.180	0.57
3_D	7_V	1.176	0.57
72_G	75_G	1.168	0.56
35_N	38_N	1.164	0.56
149_S	216_V	1.160	0.55
230_N	234_Q	1.159	0.55
4_Y	35_N	1.156	0.55
212_G	216_V	1.151	0.54
226_S	230_N	1.149	0.54
154_F	158_D	1.149	0.54
95_N	202_K	1.148	0.54
94_R	99_V	1.144	0.54
27_A	33_D	1.143	0.54
14_A	21_K	1.138	0.53
206_K	226_S	1.137	0.53
53_Y	56_L	1.136	0.53
218_V	226_S	1.130	0.52
69_G	73_L	1.127	0.52
19_I	22_A	1.125	0.52
70_K	73_L	1.110	0.50
207_R	223_Q	1.108	0.50
238_L	241_K	1.098	0.49
5_Y	20_K	1.096	0.49
58_D	61_K	1.096	0.49
152_S	168_G	1.091	0.48
43_E	63_D	1.087	0.48
203_I	234_Q	1.079	0.47
20_K	51_E	1.079	0.47
207_R	225_K	1.079	0.47
111_S	114_F	1.079	0.47
57_S	61_K	1.075	0.47
94_R	214_E	1.074	0.47
4_Y	8_L	1.066	0.46
50_A	228_T	1.056	0.45
95_N	191_I	1.053	0.45
5_Y	22_A	1.052	0.45
49_V	103_F	1.050	0.44
30_W	194_S	1.047	0.44
27_A	56_L	1.045	0.44
64_I	73_L	1.040	0.43
8_L	15_S	1.039	0.43
217_E	222_G	1.038	0.43
94_R	101_R	1.029	0.42
25_K	195_T	1.028	0.42
4_Y	30_W	1.028	0.42
221_D	225_K	1.027	0.42
5_Y	14_A	1.027	0.42
148_P	198_V	1.025	0.42
23_Y	27_A	1.025	0.42
175_F	195_T	1.023	0.42
20_K	211_N	1.022	0.42
39_K	221_D	1.021	0.42
23_Y	33_D	1.018	0.41
10_V	105_G	1.018	0.41
75_G	216_V	1.017	0.41
34_K	213_Q	1.016	0.41
2_V	20_K	1.016	0.41
64_I	117_D	1.012	0.41
20_K	191_I	1.012	0.41
132_S	135_R	1.010	0.41
49_V	198_V	1.010	0.41
17_E	204_T	1.009	0.40
236_L	241_K	1.009	0.40
15_S	85_S	1.009	0.40
237_R	241_K	1.007	0.40
45_K	57_S	1.001	0.40
13_H	77_G	1.000	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
4j7zA	6	0.4315	100	0.672	Contact Map
3lz8A	2	0.2905	100	0.68	Contact Map
4j80A	4	0.6929	100	0.681	Contact Map
1bq0A	1	0.3154	100	0.687	Contact Map
2lgwA	1	0.2946	100	0.693	Contact Map
2dmxA	1	0.3527	100	0.694	Contact Map
2ej7A	1	0.3112	100	0.699	Contact Map
2ctqA	1	0.39	99.9	0.709	Contact Map
3apoA	1	0.5934	99.9	0.711	Contact Map
1wjzA	1	0.3112	99.9	0.713	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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