OPENSEQ.org - 1447430598 - GREMLIN Submission

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repa_al1_8it

ID:	1447430598	Query Sequence MTSSSSNRQFLHRTANTFLTYPQCPEHPEIISQRIWDLVGRWNPLYIICAQEAHEDGNMHLHALIQTDKQVRTTDSRFFDIDGFHPNIQSAMSPNKVRDYILKEPLALFERGTFVPRKKTFLGNSSKGNSEKKPSKDEIMQDIISHATSKPEYLSMVRKSFPYDWATKLQYFEYSANKLFPDIQEEFINPHPTSEPDLLCNESIKDWLQPNIYQVSPQAYMLLQPNCYTVDDAISDLQWLDDLTSKQIMDQESRASTSSVQQGQENLLGPEA	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	272 (220)
Sequences:	474 (104.4)
Seq/Len:	2.155
Nf(neff/√len):	7.0

HHblits Results: (2015_06)
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: 2.155).

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
233_A	240_L	2.038	0.99
233_A	236_D	1.999	0.99
233_A	237_L	1.977	0.99
224_Q	235_S	1.954	0.99
224_Q	236_D	1.923	0.99
224_Q	237_L	1.920	0.99
220_Y	237_L	1.898	0.99
224_Q	233_A	1.875	0.98
236_D	244_T	1.801	0.98
241_D	244_T	1.797	0.98
233_A	241_D	1.797	0.98
220_Y	236_D	1.790	0.98
233_A	244_T	1.790	0.98
169_L	173_E	1.766	0.98
240_L	244_T	1.762	0.97
220_Y	233_A	1.759	0.97
220_Y	224_Q	1.739	0.97
237_L	244_T	1.727	0.97
224_Q	244_T	1.717	0.97
142_D	160_S	1.707	0.97
235_S	244_T	1.705	0.97
219_A	236_D	1.695	0.97
237_L	240_L	1.683	0.96
102_L	110_E	1.680	0.96
219_A	233_A	1.671	0.96
220_Y	235_S	1.668	0.96
236_D	241_D	1.649	0.96
236_D	240_L	1.611	0.95
161_F	167_T	1.605	0.95
235_S	241_D	1.587	0.95
48_I	108_L	1.586	0.95
220_Y	244_T	1.553	0.94
224_Q	240_L	1.553	0.94
149_S	152_E	1.527	0.93
219_A	241_D	1.502	0.92
219_A	240_L	1.481	0.91
220_Y	240_L	1.450	0.90
222_L	241_D	1.442	0.90
237_L	241_D	1.441	0.90
224_Q	241_D	1.439	0.90
233_A	242_D	1.430	0.89
48_I	110_E	1.429	0.89
140_M	161_F	1.421	0.89
23_Q	58_N	1.405	0.88
224_Q	243_L	1.399	0.88
222_L	236_D	1.386	0.87
17_T	73_T	1.369	0.87
235_S	240_L	1.364	0.86
225_P	238_Q	1.355	0.86
219_A	234_I	1.352	0.86
236_D	243_L	1.329	0.84
219_A	244_T	1.308	0.83
150_K	177_N	1.307	0.83
166_A	176_A	1.304	0.83
219_A	237_L	1.301	0.83
222_L	233_A	1.274	0.81
237_L	243_L	1.265	0.80
236_D	242_D	1.259	0.80
216_S	236_D	1.257	0.79
140_M	167_T	1.254	0.79
234_I	241_D	1.253	0.79
215_V	236_D	1.252	0.79
222_L	237_L	1.244	0.78
30_I	33_Q	1.231	0.77
219_A	242_D	1.216	0.76
240_L	243_L	1.198	0.75
224_Q	234_I	1.190	0.74
237_L	242_D	1.189	0.74
233_A	243_L	1.185	0.74
48_I	102_L	1.183	0.73
220_Y	243_L	1.180	0.73
235_S	243_L	1.173	0.73
217_P	221_M	1.172	0.72
17_T	42_W	1.171	0.72
160_S	166_A	1.161	0.71
140_M	163_Y	1.161	0.71
205_K	212_I	1.157	0.71
234_I	240_L	1.155	0.71
222_L	244_T	1.153	0.71
219_A	235_S	1.151	0.70
138_E	161_F	1.150	0.70
212_I	221_M	1.148	0.70
222_L	235_S	1.141	0.70
220_Y	241_D	1.139	0.69
211_N	214_Q	1.138	0.69
215_V	233_A	1.137	0.69
221_M	233_A	1.136	0.69
234_I	237_L	1.130	0.68
135_S	138_E	1.128	0.68
223_L	237_L	1.125	0.68
221_M	236_D	1.117	0.67
17_T	78_F	1.108	0.66
221_M	237_L	1.101	0.66
150_K	173_E	1.101	0.66
215_V	237_L	1.101	0.66
150_K	169_L	1.101	0.66
89_Q	97_V	1.100	0.65
215_V	244_T	1.098	0.65
221_M	241_D	1.095	0.65
234_I	244_T	1.094	0.65
182_D	204_I	1.092	0.65
223_L	236_D	1.090	0.64
205_K	211_N	1.073	0.63
91_A	97_V	1.067	0.62
221_M	240_L	1.063	0.62
221_M	244_T	1.059	0.61
217_P	220_Y	1.050	0.60
11_L	72_R	1.048	0.60
204_I	213_Y	1.047	0.60
55_E	68_D	1.047	0.60
49_C	108_L	1.045	0.60
189_N	212_I	1.041	0.59
102_L	108_L	1.038	0.59
55_E	63_A	1.035	0.58
222_L	240_L	1.033	0.58
218_Q	240_L	1.032	0.58
216_S	233_A	1.030	0.58
201_N	208_L	1.029	0.58
217_P	237_L	1.023	0.57
219_A	224_Q	1.021	0.57
108_L	111_R	1.015	0.56
187_F	204_I	1.004	0.55
205_K	209_Q	1.003	0.55

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
1l2mA	1	0.4118	100	0.555	Contact Map
2hwtA	1	0.3235	99.9	0.801	Contact Map
2hw0A	1	0.4118	99.8	0.821	Contact Map
4qhsA	7	0.25	57.9	0.965	Contact Map
2qbyA	1	0.3088	45.9	0.967	Contact Map
1fnnA	2	0.3272	45.9	0.967	Contact Map
1um8A	1	0.3125	44.1	0.968	Contact Map
2v1uA	1	0.3309	42.4	0.968	Contact Map
2chgA	4	0.3088	41.7	0.968	Contact Map
3nbxX	1	0.3125	37.6	0.969	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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