OPENSEQ.org - 1413284039 - GREMLIN Submission

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2ODV_A

ID:	1413284039	Query Sequence GSHMRANELQLRWQEYRELVLLLLQWMRHHTAAFEERRFPSSFEEIEILWSQFLKFKEMELPAKEADKNRSKGIYQSLEGAVQAGQLKVPPGYHPLDVEKEWGKLHVAILEREKQLRSEFERLEALQRIVTKLQMEAGLAEEQLNQADALLQSDVRLLAAGKVPQRAGEVERDLDKADSMIRLLFNDVQTLKDGRHPQGEQMYRRVYRLHKRLVAIRTEYNLRLKAGVAAPATQV	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	235 (220)
Sequences:	236 (151.9)
Seq/Len:	1.073
Nf(neff/√len):	10.2

HHblits Results: (2013_03)
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: 1.073).

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
92_G	97_D	2.102	0.97
119_E	122_R	1.935	0.95
102_W	105_L	1.878	0.94
20_V	71_S	1.843	0.93
34_F	57_K	1.715	0.89
64_K	67_D	1.693	0.88
133_L	136_E	1.642	0.86
30_H	60_E	1.625	0.85
37_R	63_A	1.593	0.84
72_K	92_G	1.530	0.80
172_R	176_K	1.517	0.80
113_E	126_L	1.511	0.79
16_Y	26_W	1.487	0.78
216_I	219_E	1.478	0.77
68_K	71_S	1.463	0.76
173_D	190_T	1.457	0.76
56_F	61_L	1.455	0.76
165_Q	170_V	1.446	0.75
26_W	60_E	1.431	0.74
167_A	171_E	1.406	0.72
10_Q	36_E	1.396	0.71
168_G	179_S	1.385	0.70
26_W	62_P	1.383	0.70
170_V	179_S	1.370	0.69
144_L	170_V	1.368	0.69
106_H	109_I	1.359	0.68
100_K	209_L	1.358	0.68
109_I	136_E	1.354	0.68
109_I	133_L	1.333	0.66
169_E	173_D	1.331	0.66
139_L	150_L	1.305	0.64
26_W	37_R	1.301	0.63
124_E	130_V	1.300	0.63
53_F	61_L	1.298	0.63
23_L	27_M	1.288	0.62
113_E	116_L	1.286	0.62
39_F	112_R	1.275	0.61
20_V	98_V	1.272	0.61
112_R	144_L	1.271	0.61
27_M	61_L	1.268	0.60
23_L	26_W	1.257	0.59
113_E	124_E	1.245	0.58
166_R	169_E	1.234	0.57
72_K	76_Q	1.230	0.57
132_K	214_V	1.223	0.56
61_L	109_I	1.215	0.55
130_V	196_H	1.210	0.55
47_E	56_F	1.209	0.55
45_E	68_K	1.205	0.55
169_E	180_M	1.202	0.54
76_Q	84_A	1.202	0.54
19_L	74_I	1.201	0.54
168_G	213_L	1.200	0.54
40_P	60_E	1.199	0.54
34_F	63_A	1.192	0.53
127_Q	133_L	1.186	0.53
161_G	167_A	1.183	0.52
34_F	37_R	1.182	0.52
71_S	98_V	1.172	0.51
94_H	97_D	1.170	0.51
46_I	120_F	1.170	0.51
67_D	81_A	1.167	0.51
106_H	136_E	1.166	0.51
188_V	196_H	1.161	0.50
156_R	177_A	1.161	0.50
37_R	135_M	1.158	0.50
217_R	220_Y	1.144	0.49
123_L	148_D	1.143	0.49
23_L	61_L	1.142	0.49
19_L	50_W	1.141	0.49
147_A	151_L	1.132	0.48
16_Y	23_L	1.122	0.47
41_S	58_E	1.115	0.46
147_A	150_L	1.113	0.46
22_L	205_R	1.110	0.46
40_P	49_L	1.108	0.45
41_S	45_E	1.106	0.45
196_H	213_L	1.106	0.45
68_K	77_S	1.105	0.45
10_Q	20_V	1.104	0.45
71_S	77_S	1.102	0.45
95_P	98_V	1.099	0.45
207_Y	213_L	1.097	0.44
25_Q	36_E	1.096	0.44
168_G	188_V	1.095	0.44
24_L	53_F	1.090	0.44
37_R	57_K	1.087	0.43
173_D	180_M	1.075	0.42
105_L	124_E	1.072	0.42
111_E	189_Q	1.061	0.41
67_D	72_K	1.059	0.41
196_H	207_Y	1.059	0.41
108_A	120_F	1.055	0.40
79_E	83_Q	1.054	0.40
220_Y	224_L	1.052	0.40
113_E	122_R	1.051	0.40
76_Q	140_A	1.051	0.40
206_V	210_H	1.044	0.39
175_D	181_I	1.043	0.39
39_F	60_E	1.038	0.39
10_Q	48_I	1.035	0.39
16_Y	20_V	1.034	0.39
24_L	101_E	1.034	0.39
70_R	120_F	1.033	0.39
24_L	141_E	1.033	0.39
68_K	90_P	1.032	0.38
106_H	113_E	1.028	0.38
45_E	56_F	1.024	0.38
196_H	202_M	1.024	0.38
26_W	34_F	1.023	0.38
140_A	172_R	1.022	0.38
169_E	190_T	1.021	0.37
43_F	126_L	1.020	0.37
137_A	197_P	1.019	0.37
39_F	115_Q	1.018	0.37
87_L	91_P	1.018	0.37
146_Q	174_L	1.016	0.37
215_A	221_N	1.014	0.37
110_L	113_E	1.013	0.37
108_A	119_E	1.012	0.37
85_G	88_K	1.009	0.36
111_E	131_T	1.008	0.36
37_R	62_P	1.006	0.36
61_L	92_G	1.005	0.36
70_R	75_Y	1.004	0.36
30_H	33_A	1.003	0.36

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
2odvA	1	0.9234	100	0.362	Contact Map
1g8xA	2	0.9957	100	0.535	Contact Map
1hciA	2	0.9957	100	0.537	Contact Map
2ycuA	1	0.9404	100	0.549	Contact Map
1sjjA	2	1	100	0.574	Contact Map
3r6nA	2	0.8426	99.5	0.787	Contact Map
3fb2A	2	0.8298	99.5	0.787	Contact Map
3pdyA	2	0.8468	99.5	0.787	Contact Map
2iakA	1	0.8128	99.5	0.788	Contact Map
3kbtA	2	0.8681	99.5	0.791	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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