OPENSEQ.org - 1499177294 - GREMLIN Submission

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cox2

ID:	1499177294	Query Sequence MATWLNMSLQDGASPIMEQLVFFHDHVLMIMLMITTTVSYMMITLIRNQTITSSTNNNHMNHCTCNHPCIHRHTIPTTSLPNSRSPQPSINAKSSWTPMMKMWMLSLHKASVEDLMYNSTTIPTTSHQPNRFRLLEVTYKLTYPINRYIRVLVSAEDVLHSSSCPTLGVNNPKTGGKNSRHTFITTKPSSWYRTVSNLRSKPQIHAHYNWKSTPLKKFENW	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	221 (221)
Sequences:	809 (274.1)
Seq/Len:	3.661
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: 3.661).

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
99_M	154_S	3.936	1.00
137_V	209_N	2.607	1.00
145_I	188_P	2.302	1.00
155_A	159_L	2.263	1.00
27_V	75_I	2.086	1.00
145_I	212_S	2.080	1.00
96_W	141_L	2.076	1.00
96_W	143_Y	2.065	1.00
171_N	181_H	1.956	1.00
106_S	118_N	1.864	1.00
214_P	217_K	1.853	1.00
52_T	57_N	1.846	1.00
16_I	86_P	1.793	0.99
13_A	191_W	1.778	0.99
26_H	81_P	1.756	0.99
164_C	167_L	1.744	0.99
109_K	141_L	1.624	0.98
185_T	212_S	1.609	0.98
57_N	69_C	1.593	0.98
134_L	205_H	1.584	0.98
112_V	219_E	1.573	0.98
13_A	166_T	1.500	0.97
4_W	52_T	1.489	0.97
134_L	202_P	1.488	0.97
26_H	40_Y	1.480	0.97
153_V	171_N	1.459	0.96
140_K	209_N	1.454	0.96
190_S	210_W	1.443	0.96
96_W	109_K	1.440	0.96
213_T	217_K	1.395	0.95
38_V	123_P	1.394	0.95
202_P	205_H	1.361	0.94
26_H	69_C	1.303	0.92
67_H	155_A	1.272	0.91
56_N	74_T	1.270	0.91
73_H	77_T	1.255	0.90
136_E	220_N	1.252	0.90
101_K	198_L	1.249	0.90
74_T	85_S	1.222	0.88
52_T	55_T	1.221	0.88
159_L	163_S	1.216	0.88
95_S	152_L	1.213	0.88
67_H	71_H	1.204	0.88
56_N	82_N	1.203	0.87
132_F	205_H	1.202	0.87
16_I	174_T	1.201	0.87
11_D	91_N	1.199	0.87
4_W	21_V	1.193	0.87
9_L	59_H	1.179	0.86
122_I	191_W	1.178	0.86
9_L	70_I	1.168	0.85
43_I	166_T	1.161	0.85
143_Y	185_T	1.150	0.84
52_T	137_V	1.149	0.84
159_L	219_E	1.135	0.83
140_K	152_L	1.134	0.83
181_H	191_W	1.126	0.82
32_L	36_T	1.124	0.82
113_E	154_S	1.124	0.82
136_E	192_Y	1.122	0.82
29_M	50_T	1.122	0.82
23_F	49_Q	1.118	0.82
8_S	28_L	1.117	0.82
93_K	112_V	1.115	0.81
140_K	190_S	1.112	0.81
42_M	75_I	1.105	0.81
75_I	139_Y	1.104	0.81
33_M	122_I	1.103	0.80
2_A	182_T	1.095	0.80
122_I	181_H	1.094	0.80
27_V	81_P	1.092	0.80
19_Q	55_T	1.091	0.79
124_T	214_P	1.091	0.79
37_T	60_M	1.089	0.79
4_W	48_N	1.087	0.79
53_S	166_T	1.086	0.79
75_I	120_T	1.085	0.79
118_N	155_A	1.080	0.79
97_T	108_H	1.074	0.78
57_N	174_T	1.071	0.78
62_H	66_N	1.070	0.78
104_M	205_H	1.066	0.77
2_A	71_H	1.065	0.77
40_Y	88_P	1.065	0.77
3_T	187_K	1.064	0.77
159_L	173_K	1.059	0.77
149_I	153_V	1.056	0.76
9_L	174_T	1.056	0.76
33_M	40_Y	1.052	0.76
55_T	113_E	1.048	0.76
13_A	215_L	1.046	0.75
26_H	88_P	1.040	0.75
31_M	42_M	1.038	0.75
96_W	217_K	1.035	0.74
30_I	67_H	1.034	0.74
23_F	198_L	1.023	0.73
86_P	181_H	1.021	0.73
66_N	71_H	1.020	0.73
12_G	86_P	1.018	0.73
46_I	137_V	1.018	0.73
29_M	80_L	1.014	0.72
9_L	171_N	1.011	0.72
32_L	89_S	1.006	0.71
2_A	75_I	1.005	0.71
164_C	210_W	1.005	0.71
98_P	210_W	1.003	0.71
151_V	164_C	1.002	0.71
142_T	166_T	1.002	0.71
5_L	82_N	1.000	0.71

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
1v54B	2	0.9955	100	0.271	Contact Map
3hb3B	1	0.9955	100	0.328	Contact Map
2gsmB	2	0.9955	100	0.342	Contact Map
2yevB	2	0.8869	100	0.453	Contact Map
1fftB	2	0.8733	100	0.476	Contact Map
4txvB	2	0.6018	100	0.52	Contact Map
3s8fB	1	0.7149	100	0.612	Contact Map
1cyxA	1	0.4932	100	0.616	Contact Map
3sbqA	2	0.9005	100	0.732	Contact Map
2cuaA	2	0.5701	99.9	0.788	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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