OPENSEQ.org - 1417633933 - GREMLIN Submission

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FHA1981-2580 370-560

ID:	1417633933	Query Sequence VRVAPPAVALPRPLFETRIKFIDQSKFYGSRYFFEQIGYKPDRAARVAGDNYFDTTLVREQVRRALGGYESRLPVRGVALVAKLMDSAGTVGKALGLKVGVAPTAQQLKQADRDFVWYVDTVIDGQKVLAPRLYLTEATRQGITDQYAGGGALIASGGDVTVNTDGHDVSSVNGLIQGRSVKVDAGKGKVV	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	191 (161)
Sequences:	384 (287.3)
Seq/Len:	2.385
Nf(neff/√len):	22.6

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: 2.385).

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 > 50% 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
120_D	127_K	2.573	1.00
64_R	72_R	2.395	1.00
119_V	132_R	2.231	1.00
20_K	119_V	2.202	1.00
29_G	51_N	2.171	1.00
122_V	127_K	2.083	1.00
29_G	81_V	2.027	0.99
157_G	160_V	1.962	0.99
91_V	95_L	1.937	0.99
56_T	60_E	1.915	0.99
168_D	171_S	1.689	0.97
51_N	81_V	1.639	0.96
47_V	54_D	1.585	0.95
91_V	115_F	1.568	0.95
56_T	80_L	1.552	0.95
58_V	86_D	1.548	0.95
51_N	55_T	1.544	0.95
121_T	132_R	1.544	0.95
62_V	133_L	1.513	0.94
59_R	82_A	1.503	0.93
47_V	53_F	1.464	0.92
111_A	115_F	1.452	0.92
32_Y	86_D	1.434	0.91
47_V	51_N	1.416	0.91
154_I	157_G	1.405	0.90
147_Y	153_L	1.354	0.88
31_R	53_F	1.334	0.87
21_F	88_A	1.320	0.86
53_F	114_D	1.314	0.86
18_R	88_A	1.297	0.85
66_L	101_V	1.292	0.84
47_V	81_V	1.282	0.84
88_A	95_L	1.282	0.84
23_D	26_K	1.271	0.83
95_L	108_L	1.262	0.82
88_A	117_W	1.261	0.82
32_Y	85_M	1.253	0.82
55_T	81_V	1.230	0.80
147_Y	150_G	1.209	0.78
174_G	178_G	1.205	0.78
36_Q	86_D	1.201	0.78
15_F	18_R	1.195	0.77
79_A	82_A	1.193	0.77
91_V	108_L	1.179	0.76
151_G	162_V	1.178	0.76
167_H	170_S	1.167	0.75
33_F	85_M	1.162	0.74
114_D	136_T	1.161	0.74
151_G	154_I	1.159	0.74
72_R	101_V	1.145	0.73
114_D	117_W	1.142	0.73
47_V	118_Y	1.141	0.72
36_Q	89_G	1.140	0.72
53_F	57_L	1.138	0.72
54_D	57_L	1.132	0.72
168_D	177_Q	1.125	0.71
65_A	71_S	1.120	0.70
108_L	119_V	1.115	0.70
29_G	52_Y	1.106	0.69
111_A	134_Y	1.105	0.69
168_D	179_R	1.101	0.69
90_T	110_Q	1.090	0.67
170_S	180_S	1.068	0.65
85_M	88_A	1.064	0.65
96_G	105_A	1.063	0.65
166_G	171_S	1.057	0.64
71_S	87_S	1.056	0.64
16_E	28_Y	1.053	0.64
16_E	30_S	1.052	0.63
48_A	58_V	1.049	0.63
33_F	117_W	1.048	0.63
25_S	93_K	1.028	0.61
21_F	52_Y	1.027	0.61
61_Q	133_L	1.025	0.60
157_G	161_T	1.023	0.60
103_P	111_A	1.022	0.60
99_V	129_L	1.020	0.60
151_G	155_A	1.016	0.59
24_Q	110_Q	1.012	0.59
64_R	68_G	1.011	0.59
71_S	79_A	1.010	0.59
31_R	47_V	1.009	0.59
18_R	61_Q	1.008	0.59
58_V	150_G	1.007	0.58
171_S	177_Q	1.006	0.58
175_L	179_R	1.002	0.58
114_D	139_T	1.000	0.58
120_D	128_V	1.000	0.58

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
1k4uS	1	0.3246	14	0.959	Contact Map
4hvuA	1	0.2984	13.9	0.96	Contact Map
1i07A	2	0.3089	12	0.961	Contact Map
2oawA	4	0.3089	11.9	0.961	Contact Map
2j05A	2	0.3298	11.9	0.961	Contact Map
4lnpA	1	0.3194	11.9	0.961	Contact Map
1utiA	1	0.2984	11.8	0.961	Contact Map
2fpeA	8	0.3246	10.8	0.961	Contact Map
1gl5A	1	0.3508	9.8	0.962	Contact Map
4cc2A	2	0.3298	9.8	0.962	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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