OPENSEQ.org - 1497562099 - GREMLIN Submission

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dhcb4

ID:	1497562099	Query Sequence GAMDPAPTVRITLLQGRPSPKRTPFYMMADGTGTIATYIHLPAFKSKMPVYGIDSPFLRCPSRLTKDVGIPGVAKLIVDALVTAQPTGPLMIGGFSAGSIVAYEVTRQLGALGRQVTGLVLIDMCCPRSSLLDEDAMNSEDDASFAIFENAVSKDGLWSLASTTQDHFRAYHVAMHAYHPPYMTAQERPSHTAVIWAEKGMVNRVVGNDRLMQMLADQGIPTTSYPGYMEDPRLGAFACLVPDRTAADLGPNGWEKYTAGEVLALSVAGDHLDLPMPGHVHLLQREMEKAFAYFEGESTEFELRRAAAENLYFQ	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	314 (277)
Sequences:	585 (456.3)
Seq/Len:	2.112
Nf(neff/√len):	27.4

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: 2.112).

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
82_V	114_R	4.628	1.00
27_M	93_G	2.779	1.00
85_Q	90_L	2.573	1.00
38_Y	95_F	2.572	1.00
104_E	108_Q	2.367	1.00
99_S	124_M	2.323	1.00
87_T	114_R	2.314	1.00
28_M	105_V	2.307	1.00
91_M	118_G	2.290	1.00
90_L	114_R	2.235	1.00
75_K	108_Q	2.230	1.00
30_D	38_Y	2.107	0.99
26_Y	90_L	1.957	0.99
25_F	93_G	1.936	0.99
30_D	95_F	1.927	0.99
85_Q	89_P	1.888	0.98
69_G	72_G	1.877	0.98
85_Q	114_R	1.859	0.98
78_V	105_V	1.856	0.98
30_D	37_T	1.807	0.98
97_A	101_V	1.770	0.97
25_F	50_V	1.664	0.96
74_A	105_V	1.652	0.96
91_M	117_T	1.630	0.95
29_A	77_I	1.615	0.95
234_L	237_F	1.605	0.95
24_P	49_P	1.605	0.95
82_V	90_L	1.597	0.95
74_A	104_E	1.590	0.94
28_M	81_L	1.588	0.94
86_P	90_L	1.559	0.94
32_T	95_F	1.546	0.93
107_R	111_A	1.534	0.93
24_P	48_M	1.489	0.91
93_G	120_V	1.489	0.91
78_V	81_L	1.474	0.91
38_Y	56_P	1.472	0.91
104_E	107_R	1.464	0.91
29_A	95_F	1.449	0.90
24_P	51_Y	1.437	0.89
14_L	38_Y	1.434	0.89
78_V	82_V	1.434	0.89
251_P	255_E	1.420	0.89
85_Q	88_G	1.408	0.88
198_E	268_A	1.406	0.88
74_A	108_Q	1.398	0.88
31_G	125_C	1.392	0.87
81_L	105_V	1.390	0.87
70_I	74_A	1.387	0.87
120_V	287_M	1.350	0.85
46_S	50_V	1.331	0.84
86_P	89_P	1.331	0.84
103_Y	107_R	1.314	0.83
20_P	49_P	1.308	0.83
81_L	92_I	1.304	0.82
96_S	123_D	1.298	0.82
69_G	255_E	1.297	0.82
70_I	101_V	1.295	0.82
37_T	95_F	1.285	0.81
89_P	114_R	1.283	0.81
71_P	108_Q	1.273	0.80
27_M	50_V	1.247	0.78
29_A	73_V	1.216	0.76
113_G	119_L	1.214	0.76
26_Y	85_Q	1.213	0.75
27_M	30_D	1.212	0.75
269_G	279_H	1.208	0.75
196_W	250_G	1.206	0.75
81_L	88_G	1.206	0.75
35_I	42_P	1.201	0.74
77_I	101_V	1.200	0.74
22_R	49_P	1.193	0.74
30_D	34_T	1.190	0.73
33_G	93_G	1.185	0.73
32_T	38_Y	1.181	0.73
80_A	83_T	1.180	0.73
30_D	33_G	1.174	0.72
225_Y	228_Y	1.159	0.71
94_G	98_G	1.156	0.70
26_Y	114_R	1.148	0.70
56_P	76_L	1.138	0.69
122_I	274_L	1.134	0.68
60_C	63_R	1.133	0.68
122_I	269_G	1.126	0.67
26_Y	273_D	1.117	0.67
41_L	284_Q	1.098	0.65
233_R	237_F	1.096	0.64
88_G	114_R	1.096	0.64
34_T	37_T	1.094	0.64
126_C	136_A	1.092	0.64
127_P	175_M	1.092	0.64
124_M	204_R	1.091	0.64
270_D	273_D	1.087	0.63
205_V	208_N	1.076	0.62
26_Y	81_L	1.075	0.62
29_A	38_Y	1.073	0.62
36_A	97_A	1.065	0.61
55_S	167_H	1.064	0.61
32_T	124_M	1.060	0.61
182_Y	191_H	1.057	0.60
97_A	124_M	1.054	0.60
30_D	272_L	1.049	0.59
194_V	264_A	1.047	0.59
29_A	275_P	1.036	0.58
77_I	175_M	1.032	0.58
126_C	180_P	1.032	0.58
292_A	296_G	1.031	0.57
26_Y	89_P	1.028	0.57
38_Y	55_S	1.019	0.56
85_Q	103_Y	1.018	0.56
293_Y	297_E	1.015	0.56
86_P	116_V	1.008	0.55
16_G	49_P	1.008	0.55
104_E	200_G	1.002	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: (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
2vz8A	2	0	100	0.474	Contact Map
2cb9A	1	0.672	100	0.645	Contact Map
3ilsA	1	0.8089	100	0.645	Contact Map
1jmkC	2	0.7197	100	0.65	Contact Map
3tejA	2	0.7357	99.9	0.667	Contact Map
1kezA	3	0.7325	99.9	0.669	Contact Map
3tjmA	1	0.7293	99.9	0.712	Contact Map
2px6A	2	0.7229	99.9	0.716	Contact Map
2k2qB	1	0.7484	99.9	0.718	Contact Map
2vsqA	1	0.7357	99.9	0.72	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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