OPENSEQ.org - 1420826135 - GREMLIN Submission

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BMRR

ID:	1420826135	Query Sequence MKESYYSIGEVSKLANVSIKALRYYDKIDLFKPAYVDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDLEMEELFAFYTEQERQIREKLDFLSALEQTISLVKKRMKRQMEYPALGEVFVLDEEEIRIIQTEAEGIGPENVLNASYSKLKKFIESADGFTNNSYGATFSFQPYTSIDEMTYRHIFTPVLTNKQISSITPDMEITTIPKGRYACIAYNFSPEHYFLNLQKLIKYIADRQLTVVSDVYELIIPIHYSPKKQEEYRVEMKIRIAE	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	278 (274)
Sequences:	578 (518.4)
Seq/Len:	2.109
Nf(neff/√len):	31.3

Jackhmmer Results: (2014_04_16)
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: 2.109).

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
87_Q	90_Q	3.565	1.00
246_T	277_A	2.986	1.00
218_A	240_I	2.979	1.00
224_F	270_V	2.809	1.00
92_R	102_E	2.797	1.00
222_Y	232_N	2.753	1.00
60_K	66_L	2.672	1.00
126_V	276_I	2.602	1.00
240_I	247_V	2.447	1.00
127_L	271_E	2.440	1.00
171_G	191_F	2.181	1.00
239_Y	245_L	2.137	1.00
88_E	106_S	2.088	0.99
218_A	239_Y	1.999	0.99
19_I	23_R	1.955	0.99
264_K	267_E	1.885	0.98
8_I	23_R	1.882	0.98
28_I	66_L	1.823	0.98
128_D	214_K	1.810	0.98
220_I	232_N	1.789	0.98
131_E	211_T	1.776	0.98
15_A	50_L	1.720	0.97
37_D	40_T	1.694	0.96
131_E	214_K	1.680	0.96
6_Y	47_D	1.653	0.96
26_D	49_Q	1.622	0.95
94_K	97_F	1.621	0.95
81_F	109_K	1.577	0.94
9_G	19_I	1.570	0.94
255_I	270_V	1.560	0.94
222_Y	253_E	1.525	0.93
32_K	36_V	1.518	0.92
233_L	253_E	1.492	0.92
126_V	216_R	1.470	0.91
11_V	53_L	1.460	0.90
17_V	53_L	1.456	0.90
88_E	102_E	1.451	0.90
176_F	180_T	1.443	0.90
34_A	46_T	1.418	0.89
15_A	53_L	1.407	0.88
66_L	69_M	1.402	0.88
60_K	63_G	1.400	0.88
19_I	40_T	1.388	0.87
70_K	74_D	1.371	0.86
132_I	273_K	1.368	0.86
26_D	32_K	1.362	0.86
53_L	255_I	1.350	0.85
262_P	267_E	1.344	0.85
60_K	65_P	1.336	0.84
89_R	93_E	1.312	0.83
128_D	216_R	1.310	0.83
35_Y	44_Y	1.298	0.82
257_P	262_P	1.284	0.81
124_V	218_A	1.280	0.81
53_L	273_K	1.275	0.80
95_L	98_L	1.273	0.80
18_S	24_Y	1.270	0.80
20_K	27_K	1.266	0.80
44_Y	66_L	1.256	0.79
84_Y	105_I	1.253	0.79
11_V	49_Q	1.250	0.78
95_L	99_S	1.248	0.78
24_Y	66_L	1.248	0.78
29_D	32_K	1.240	0.78
88_E	109_K	1.239	0.78
220_I	235_K	1.223	0.76
94_K	98_L	1.216	0.76
238_K	242_D	1.205	0.75
220_I	236_L	1.201	0.74
223_N	269_R	1.198	0.74
8_I	275_R	1.177	0.72
91_I	105_I	1.173	0.72
171_G	175_S	1.169	0.72
8_I	40_T	1.167	0.71
31_F	255_I	1.164	0.71
33_P	49_Q	1.158	0.71
23_R	275_R	1.155	0.70
30_L	213_P	1.144	0.69
82_A	86_E	1.133	0.68
219_C	271_E	1.130	0.68
233_L	272_M	1.128	0.68
8_I	19_I	1.125	0.67
132_I	193_P	1.114	0.66
243_R	246_T	1.114	0.66
11_V	22_L	1.111	0.66
173_T	179_Y	1.108	0.66
175_S	187_Y	1.107	0.65
175_S	181_S	1.101	0.65
58_S	170_Y	1.095	0.64
136_Q	189_H	1.092	0.64
21_A	24_Y	1.091	0.64
245_L	276_I	1.088	0.64
53_L	57_K	1.080	0.63
98_L	102_E	1.080	0.63
252_Y	273_K	1.080	0.63
10_E	28_I	1.076	0.62
249_S	275_R	1.074	0.62
261_S	267_E	1.074	0.62
40_T	194_V	1.073	0.62
240_I	274_I	1.071	0.62
222_Y	228_H	1.064	0.61
5_Y	239_Y	1.063	0.61
71_K	93_E	1.062	0.61
130_E	214_K	1.061	0.61
226_P	270_V	1.060	0.61
72_A	83_F	1.059	0.60
40_T	135_I	1.059	0.60
148_L	152_Y	1.057	0.60
175_S	189_H	1.057	0.60
149_N	152_Y	1.056	0.60
176_F	179_Y	1.054	0.60
222_Y	270_V	1.044	0.59
218_A	276_I	1.043	0.59
3_E	145_E	1.042	0.59
23_R	212_I	1.041	0.58
44_Y	60_K	1.040	0.58
189_H	210_T	1.035	0.58
9_G	23_R	1.035	0.58
30_L	238_K	1.032	0.57
239_Y	243_R	1.032	0.57
138_E	187_Y	1.032	0.57
22_L	49_Q	1.029	0.57
41_S	127_L	1.024	0.57
26_D	60_K	1.016	0.56
108_V	258_I	1.007	0.55
233_L	251_V	1.005	0.54
132_I	252_Y	1.004	0.54
244_Q	276_I	1.002	0.54
20_K	24_Y	1.001	0.54

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: (06Sep14)
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
1r8eA	1	0.9748	100	0.322	Contact Map
1d5yA	4	0.9317	100	0.62	Contact Map
3gpvA	2	0.3993	99.9	0.649	Contact Map
3gp4A	2	0.4532	99.9	0.659	Contact Map
1q06A	2	0.4353	99.9	0.667	Contact Map
3qaoA	1	0.5	99.9	0.667	Contact Map
2zhgA	1	0.4281	99.9	0.668	Contact Map
1r8dA	2	0.3921	99.9	0.669	Contact Map
3hh0A	4	0.4712	99.9	0.67	Contact Map
2vz4A	1	0.3597	99.9	0.676	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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